Nikolaus Dietlein
email: n.dietlein@dkfz.de

Xi Wang

Jonas Metz

Olivier Disson

Fuwei Shang

Celine Beyersdörffer

Esther Rodríguez Correa

Daniel B Lipka

Yvonne Begus-Nahrmann

Robyn Laura Kosinsky

Steven A Johnsen

Marc Lecuit

Thomas Höfer

Hans-Reimer Rodewald
email: hr.rodewald@dkfz.de

Kurt Reifenberg

Lena Hornetz

Annalena Riedasch

Tobias Fischer

Jörg Fehling

Klaus Rajewsky

Axel Roers

H Supervised

Vs Wt Cd45

W T Cd45

Usp22 is an intracellular regulator of systemic emergency hematopoiesis

Emergency hematopoiesis is a concerted response aimed towards enhanced protection from infection, involving multiple cell types and developmental stages across the immune system. Despite its importance, the underlying molecular regulation remains poorly understood. The deubiquitinase USP22 regulates the levels of monoubiquitinated histone H2B (H2Bub1), which is associated with activation of interferon responses upon viral infection. Here we show that, in the absence of infection or inflammation, mice lacking Usp22 in all hematopoietic cells display profound systemic emergency hematopoiesis, evident by increased hematopoietic stem cell proliferation, myeloid bias, and extramedullary hematopoiesis. Functionally, loss of Usp22 results in elevated phagocytosis by neutrophilic granulocytes and enhanced innate protection against Listeria monocytogenes infection. At the molecular level, we found this state of emergency hematopoiesis associated with transcriptional signatures of myeloid priming, enhanced mitochondrial respiration, as well as innate and adaptive immunity and inflammation. Augmented expression of many inflammatory genes was linked to elevated locus-specific H2Bub1 levels.

Collectively, a tunable epigenetic state promotes systemic emergency hematopoiesis in a cellautonomous manner and enhances innate protection, paving potential ways towards immune enhancement.

One Sentence Summary: Loss of Usp22 elicits a cellular and molecular program of emergency hematopoiesis and enhances innate protection in vivo.

Main Text: INTRODUCTION

Emergency hematopoiesis is an alarm state of the immune system which may serve two purposes.

First, elevated cell production compensates for greater cell loss during inflammation and infection (1), and, second, 'pre-activation' of immunity facilitates more rapid clearance of infectious agents [START_REF] Brook | BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis[END_REF]. Consequently, enhanced hematopoietic stem cell (HSC) proliferation [START_REF] Essers | IFNα activates dormant haematopoietic stem cells in vivo[END_REF][START_REF] Baldridge | Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection[END_REF](5), myeloid-biased cell production [START_REF] Ueda | Inflammation and the reciprocal production of granulocytes and lymphocytes in bone marrow[END_REF], extramedullary hematopoiesis (7), or enhanced resistance to infections [START_REF] Brook | BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis[END_REF] constitute hallmarks of emergency hematopoiesis. While pathogen-associated molecular patterns (5,[START_REF] Nagai | Toll-like receptors on hematopoietic progenitor cells stimulate innate immune system replenishment[END_REF] and inflammatory cytokines, including interferons, [START_REF] Essers | IFNα activates dormant haematopoietic stem cells in vivo[END_REF][START_REF] Baldridge | Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection[END_REF][START_REF] Boettcher | Cutting edge: LPS-induced emergency myelopoiesis depends on TLR4-expressing nonhematopoietic cells[END_REF][START_REF] Lasseaux | Type I interferons drive inflammasome-independent emergency monocytopoiesis during endotoxemia[END_REF][START_REF] Romani | Impaired neutrophil response and CD4+ T helper cell 1 development in interleukin 6-deficient mice infected with Candida albicans[END_REF] can contribute to the state of emergency hematopoiesis, it remains unclear whether an intracellular program conserved across different cell types underlies and coordinates emergency hematopoiesis, or whether emergency hematopoiesis is primarily mediated by circulating inflammatory mediators acting through distinct signaling pathways. Nevertheless, intracellular molecular switches regulating steady state versus emergency hematopoiesis remain poorly understood. Histone H2B monoubiquitination is an activating histone modification catalyzed by the RNF20/RNF40 E3 ubiquitin ligase complex [START_REF] Zhu | Monoubiquitination of Human Histone H2B: The Factors Involved and Their Roles in HOX Gene Regulation[END_REF], and monoubiquitinated H2B (H2Bub1) is mainly found in the transcribed regions of highly expressed genes [START_REF] Minsky | Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells[END_REF]. In cell lines, H2Bub1 levels increase at interferon-stimulated gene (ISG) loci upon viral infection and interferon stimulation, and RNF20 is required for proper ISG induction [START_REF] Fonseca | Adenovirus Evasion of Interferon-Mediated Innate Immunity by Direct Antagonism of a Cellular Histone Posttranslational Modification[END_REF]. H2Bub1 can be deubiquitinated by USP22, the enzymatically active component of the SAGA deubiquitinase module [START_REF] Zhang | The Putative Cancer Stem Cell Marker USP22 Is a Subunit of the Human SAGA Complex Required for Activated Transcription and Cell-Cycle Progression[END_REF][START_REF] Zhao | A TFTC/STAGA Module Mediates Histone H2A and H2B Deubiquitination, Coactivates Nuclear Receptors, and Counteracts Heterochromatin Silencing[END_REF].

Collectively, these findings raise the intriguing possibility that Usp22 might be involved in the restriction of ISG expression in vivo, and its downstream biological consequences, including emergency hematopoiesis.

To test this hypothesis and to uncover potential cell-intrinsic and systemic functions of Usp22 in hematopoiesis and immunity in vivo, we analyzed conditional Usp22 KO mice. We applied a range of approaches, including in vivo and in vitro hematopoiesis assays, bacterial infection, bulk and single cell transcriptome analysis, and epigenome profiling using ATAC and ChIP sequencing to study the role of USP22 in hematopoiesis. In a cell-autonomous manner, Usp22 deficiency elicited typical signs of emergency hematopoiesis, including increased HSC proliferation, myeloid bias, and extramedullary hematopoiesis. Emergency hematopoiesis was accompanied by coordinated molecular changes in Usp22 KO progenitors, comprising increased expression of genes involved in mitochondrial respiration, transcriptional myeloid priming, and elevated expression of immune-related and inflammatory genes including interferon-stimulated genes (ISG). These cellular and molecular indicators of immune 'pre-activation' were functionally important as shown by heightened phagocytic activity of neutrophilic granulocytes and enhanced innate protection against Listeria monocytogenes. Mechanistically, many of the ISG that were upregulated in Usp22 KO hematopoietic stem and progenitor cells (HSPC) concomitantly showed increased locus-specific H2Bub1 levels, suggesting a physical and functional link between enhanced H2B monoubiquitination and inflammatory gene expression. Collectively, we present evidence that loss, and potentially inhibition, of USP22 orchestrates in a cell-autonomous manner a transcriptional program promoting emergency hematopoiesis and enhanced innate immunity.

RESULTS

Loss of Usp22 induces emergency hematopoiesis in the absence of infection

Usp22 is expressed throughout hematopoietic stem and progenitor cells, and across the immune system (fig. S1A). To study the effects of Usp22 deficiency on hematopoiesis and the immune system in vivo, we generated pan-hematopoietic Usp22 KO mice (termed Usp22 KO hereafter) by crossing Vav1-Cre mice [START_REF] De Boer | Transgenic mice with hematopoietic and lymphoid specific expression of Cre[END_REF] with Usp22 flox/flox mice (fig. S1B). Single cell genotyping revealed efficient deletion of the Usp22 gene (fig. S1C). Within the hematopoietic system, loss of Usp22 resulted in reduced numbers of phenotypic long-term (LT-) HSC (Fig. 1A), and increased numbers of short-term (ST-) HSC (fig. S1D) but had no effect on multipotent progenitor (MPP) numbers (fig. S1D) and bone marrow cellularity (fig. S1E). Proliferation of LT-HSC was enhanced in the absence of Usp22 (Fig. 1B,C). Since increased HSC proliferation can be associated with HSC exhaustion, we performed serial, competitive bone marrow transplantations (fig. S1F). Like their wild type counterparts, Usp22 KO bone marrow cells gave rise to multilineage repopulation in four rounds of transplantations (fig. S1G). Consequently, in serial transplantation experiments, Usp22-deficient HSC did not show signs of exhaustion.

Strikingly, Usp22 KO mice showed strongly myeloid-biased numbers of mature cells in the bone marrow, evident by an increase in CD11b + Gr-1 + myeloid cells (Fig. 1D), and a concomitant reduction of B220 + B cells (Fig. 1E). To gain global insights into the cellular composition of the bone marrow in Usp22-deficient mice, we analyzed total bone marrow by single cell RNA sequencing (scRNA-seq) (Fig. 1F,G). Cell populations were identified based on their transcriptome (Fig. 1F), and relative frequencies of populations were estimated (Fig. 1G; fig. S1H). This analysis uncovered the strongest increases in NK cells, granulocyte-monocyte progenitors (GMP), and granulocytes in Usp22 KO relative to wild type bone marrow. In contrast, frequencies of B lymphocytes, dendritic cells, T cells, and erythroid progenitors were diminished in Usp22 KO bone marrow (Fig. 1G; fig. S1H). Because of the marked enrichment of NK lineage cells, we phenotypically resolved pre-NK progenitors (NKP), NKP, and four stages of NK cell maturation (fig. S1I-L). The stage of increased numbers of NK lineage cells in the bone marrow was identified as CD27 + CD11b -which corresponds to the most immature NK cells. Pre-NKP were reduced as well as more mature NK cells (CD27 -CD11b + ). Impaired erythropoiesis in the bone marrow of Usp22 KO mice was specified by analysis of stages of red blood cell development (fig. S2A).

In the spleens of Usp22 KO mice, we found increased numbers of HSC (both LT-HSC and ST-HSC) and MPP (Fig. 1H), as well as increased GMP and megakaryocyte-erythrocyte progenitors (MEP) (Fig. 1I), suggesting mobilization of stem and progenitor cells from the bone marrow, and ongoing extramedullary hematopoiesis in the spleen. Consistent with extramedullary erythropoiesis, numbers of most erythroid differentiation stages were elevated in the spleens of Usp22-deficient mice (fig. S2B). Opposing effects on erythropoiesis in bone marrow and spleen led to normal hematocrit in Usp22 KO mice (fig. S2C).

Collectively, Usp22-deficient mice displayed key cellular hallmarks of emergency hematopoiesis, which normally occurs strictly in response to infection or inflammation. We therefore extensively surveyed Usp22 KO and wild type control mice for pathogens, which yielded no indications of infections (Table S1). Furthermore, serum levels of eleven inflammationassociated cytokines (fig. S3A), as well as IFN-a, IFN-b and IFN-g (fig. S3B) were not elevated in Usp22 KO compared to wild type mice. To look for local effects in the bone marrow, we measured 40 infection-and inflammation-associated proteins in bone marrow fluid, and again found no differences (fig. S3C). Taken together, Usp22 deficiency leads to emergency hematopoiesis in the absence of infection or inflammation. This was evident by reduced LT-HSC numbers, enhanced LT-HSC proliferation, myeloid-biased cell numbers in the bone marrow, HSC mobilization, and extramedullary hematopoiesis in the spleen.

Enhanced myelopoiesis from Usp22 KO bone marrow

Given that myelopoiesis is phenotypically and functionally central to emergency hematopoiesis [START_REF] Brook | BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis[END_REF][START_REF] Boettcher | Cutting edge: LPS-induced emergency myelopoiesis depends on TLR4-expressing nonhematopoietic cells[END_REF][START_REF] Lasseaux | Type I interferons drive inflammasome-independent emergency monocytopoiesis during endotoxemia[END_REF][START_REF] Boettcher | Endothelial cells translate pathogen signals into G-CSF-driven emergency granulopoiesis[END_REF], we dissected myeloid development in further detail. Usp22 KO mice showed a strong accumulation of immature granulocytes in the bone marrow, which expressed low levels of Gr-1/Ly6G (Fig. 2A,B; fig. S4A,B), resembling 'left-shifted' granulopoiesis typically seen under inflammatory conditions [START_REF] Ueda | Inflammation and the reciprocal production of granulocytes and lymphocytes in bone marrow[END_REF][START_REF] Boettcher | Cutting edge: LPS-induced emergency myelopoiesis depends on TLR4-expressing nonhematopoietic cells[END_REF]. In line with inflammatory myelopoiesis, numbers of macrophages and Ly6C high inflammatory monocytes, but not Ly6C low patrolling monocytes, were also increased in Usp22 KO bone marrow (Fig. 2C).

To analyze in situ hematopoietic output, including towards myeloid cells, upon loss of Usp22, we employed a strategy for endogenous fate mapping. For steady state hematopoiesis, output rates have been estimated based on label propagation emerging from Tie2 + HSC using Tie2-MeriCreMer(Tie2-MCM)-mediated induction of YFP expression (Rosa26-loxP-Stop-loxP-YFP) in response to tamoxifen [START_REF] Busch | Fundamental properties of unperturbed haematopoiesis from stem cells in vivo[END_REF] (Fig. 2D). We combined this system with conditional inactivation of Usp22 by Tie2-MCM (Fig. 2E). Fractions of YFP-labeled cells were measured 14 weeks after tamoxifen pulse. The output of monocytes (Fig. 2F), and immature (B220 + CD43 + ), but not mature (B220 + CD43 -), developing B cells (Fig. 2G) was larger in Tie2 MCM/+ Rosa26 LSL-YFP/LSL-YFP Usp22 flox/flox mice compared to Tie2 MCM/+ Rosa26 LSL-YFP/LSL-YFP Usp22 +/+ mice. Granulocyte output was also larger but the difference did not reach statistical significance (p = 0.053) (Fig. 2F). These findings provide evidence for enhanced output, including the generation of monocytes and immature B cells in vivo. Together, hematopoiesis in Usp22 KO bone marrow is characterized by an abundance of immature granulocytes, macrophages and inflammatory monocytes, and by enhanced output in situ.

Usp22 deficiency drives enhanced myelopoiesis in a cell-intrinsic manner

In response to infection, emergency myelopoiesis is driven by circulating pro-inflammatory cytokines such as G-CSF, IL-6 and type I IFN [START_REF] Boettcher | Cutting edge: LPS-induced emergency myelopoiesis depends on TLR4-expressing nonhematopoietic cells[END_REF][START_REF] Lasseaux | Type I interferons drive inflammasome-independent emergency monocytopoiesis during endotoxemia[END_REF][START_REF] Romani | Impaired neutrophil response and CD4+ T helper cell 1 development in interleukin 6-deficient mice infected with Candida albicans[END_REF]. In contrast, our cytokine profiling in serum and bone marrow fluid of Usp22 KO mice revealed no indication that these or other tested mediators of emergency myelopoiesis were elevated. This raised the intriguing possibility that emergency hematopoiesis in Usp22 KO mice resulted from a cell-autonomous mechanism in cis rather than systemically between cells in trans. We first tested this idea by competitive transplantation of Usp22-deficient and wild type bone marrow cells into lethally irradiated recipients (Fig. 3A). Donor B cells were mostly from wild type origin, while contributions of wild type and Usp22-deficient donors to myeloid cells were similar (Fig. 3B). Comparison of the ratios of B versus myeloid output revealed a myeloid bias within Usp22-deficient donor cells compared to wild type donor cells (Fig. 3C). Of note, the accumulation of immature granulocytes re-emerged specifically from Usp22 KO but not wild type competitor donor bone marrow cells (Fig. 3D).

Myeloid-biased output from Usp22-deficient cells was also evident when purified HSC were competitively transplanted (fig. S4C). Hence, the myeloid bias and 'left-shifted' emergency granulopoiesis were reproduced after adoptive transfer of Usp22 KO bone marrow cells into wild type hosts, implying that enhanced myelopoiesis is cell-intrinsic to Usp22 KO HSC or bone marrow cells and independent from systemic factors.

To probe the contribution of committed progenitors to enhanced myelopoiesis, we transplanted Usp22 KO or wild type common myeloid progenitors (CMP), each with wild type competitor bone marrow cells, into lethally irradiated recipient mice (Fig. 3E). At 7 and 10 days post-transplantation, Usp22 KO CMP contributed more strongly to myeloid compartments in peripheral blood (Fig. 3F), bone marrow and spleen (Fig. 3G), and produced larger absolute numbers of myeloid cells compared to wild type CMP (fig. S4D). Hence, Usp22-deficient CMP generated more output on a per cell basis compared to wild type CMP. Enhanced myelopoiesis by Usp22 KO CMP was cell-autonomous since it was not transferable to wild type competitor cells within the same host (fig. S4D). Usp22 KO CMP did not persist long term as their contribution to peripheral myeloid cells disappeared by 21 days after transplantation (fig. S4E).

We also observed that myeloid-biased differentiation of Usp22-deficient HSPC was apparent in vitro. When we cultured wild type and Usp22 KO HSPC under conditions actively promoting B cell development [START_REF] Nakano | Generation of lymphohematopoietic cells from embryonic stem cells in culture[END_REF][START_REF] Cho | Functional characterization of B lymphocytes generated in vitro from embryonic stem cells[END_REF], wild type progenitors gave rise, as expected, to B220 + CD11b -B lineage cells. In contrast, Usp22-deficient progenitors yielded almost exclusively B220 - CD11b + myeloid lineage cells (Fig. 3H,I). Importantly, in mixed cultures composed of wild type (CD45.1 + ) and Usp22 KO (CD45.2 + ) HSPC, Usp22-deficient progenitors again gave rise to myeloid cells while the B cell fate of wild type cells was unperturbed in the presence of Usp22deficient cells. In control cultures composed of CD45.1 + and CD45.2 + wild type HSPC, both progenitors gave rise to B cells (fig. S4F; Fig. 3J,K). Thus, Usp22 KO progenitors generate myeloid cells even under B cell promoting conditions in a cell-intrinsic manner. This phenotype was not transmittable to co-cultured wild type cells. Additionally, following transduction with a retroviral vector expressing Usp22 cDNA, cells regained B cell potential (fig. S4G,H). Hence the developmental bias from B to myeloid lineages is reversible within days upon Usp22 reexpression. In summary, loss of Usp22 enhances myeloid output from HSPC and myeloid progenitors in vivo and in vitro in a cell-autonomous manner. This bias is reversible upon restoration of Usp22 expression in Usp22-deficient progenitors.

Usp22 deficiency enhances innate protection from Listeria monocytogenes infection and phagocytosis by neutrophilic granulocytes

To address whether the observed comprehensive signs of emergency hematopoiesis were functionally relevant, we used an established infection model probing early innate defense [START_REF] Maudet | Innate immune responses to Listeria in vivo[END_REF].

We infected wild type and Usp22 KO mice intravenously with a dose of 10 4 colony-forming units (CFU) Listeria monocytogenes and determined bacterial burden three days post-infection in blood, and tissue homogenates of brain, liver and spleen. Interestingly, Usp22 KO mice were markedly more protected, with CFU reduced by one or two orders of magnitude compared to infected wild type mice (Fig. 4A). These data support the conclusion that the state of emergency hematopoiesis brought about by Usp22 deficiency is associated with increased innate defense against bloodborne bacterial infection.

To directly test a key anti-bacterial function, we measured in vitro phagocytosis of fluorescently-tagged E.coli particles (Fig. 4B,C) as well as live E.coli (Fig. 4D) by ex vivo purified neutrophilic granulocytes from non-infected wild type and Usp22 KO mice. Purification selected for granulocytes expressing high levels of Ly6G in both genotypes (fig. S5A). In line with protection against bacteria in the Listeria model in vivo, enhanced phagocytosis was detected in Usp22 KO compared to wild type granulocytes in both assays (Fig. 4B-D). Enhanced phagocytosis upon loss of Usp22 was specific to neutrophils, since it was not apparent in Usp22-deficient bone marrow-derived macrophages or peritoneal macrophages (fig. S5B,C). Usp22 KO neutrophils also showed enhanced TNF-a production in vitro upon LPS stimulation but not under steady state conditions (Fig. 4E). Thus, Usp22 deficiency promotes anti-bacterial innate immunity, at least in part by enhancing neutrophilic granulocyte effector functions.

Usp22 deletion cell-intrinsically impairs B lymphocyte development

Inflammatory stimuli, such as type I interferons or adjuvants, are known to not only enhance myelopoiesis but also to impair B lymphocyte development, leading to reduced numbers of B cell progenitors in the bone marrow [START_REF] Ueda | Inflammation and the reciprocal production of granulocytes and lymphocytes in bone marrow[END_REF][START_REF] Ueda | Inflammation controls B lymphopoiesis by regulating chemokine CXCL12 expression[END_REF][START_REF] Nagaoka | Immunization and infection change the number of recombination activating gene (RAG)-expressing B cells in the periphery by altering immature lymphocyte production[END_REF][START_REF] Lin | Impairment of T and B cell development by treatment with a type I interferon[END_REF]. Indeed, B cell numbers in the bone marrow of Usp22 KO mice were diminished (Fig. 1E-G), and dissection of B cell development [START_REF] Hardy | Resolution and characterization of pro-B and pre-pro-B cell stages in normal mouse bone marrow[END_REF] revealed a strong reduction in fraction D (B220 + CD43 -IgM -) and onwards stages (fig. S6A,B). The decrease of more mature B cells in Usp22 KO mice was also evident by the altered proportions of CD43 + (more immature) versus CD43 -(more mature) B220 + cells (fig. S6C). The partial developmental block at the transition to the pre-B cell stage (fraction D) was associated with increased apoptosis of pre-B cells and following stages (fig. S6D). The stage of the developmental impairment and the increase in apoptosis resemble effects of Myc deficiency on B cell development [START_REF] Vallespinós | B Lymphocyte Commitment Program Is Driven by the Proto-Oncogene c-myc[END_REF]. In line with this notion, RNA sequencing showed strongly decreased expression of Myc and Myc target genes in Usp22-deficient pre-B cells (fig. S6E).

To test whether impaired B cell development in Usp22 KO mice occurred cellautonomously, we competitively transplanted Usp22-deficient or wild type donor bone marrow cells together with wild type competitor bone marrow cells into lethally irradiated recipients (fig. S6F). The partial block in B cell development, reflected by the larger proportion of CD43 + B220 + cells, was recapitulated in Usp22-deficient but not in wild type cells transferred into the same hosts (fig. S6G). As a consequence of impaired B cell development, absolute numbers of splenic B220 + CD19 + B cells were reduced in Usp22-deficient mice (fig. S6H), mainly resulting from a reduction in follicular B cells (CD19 + IgM -IgD + CD93 -) (fig. S6I). Collectively, Usp22 KO mice show a cell-intrinsic incomplete block in B cell development which still permits the generation of all splenic B cell subsets.

Loss of Usp22 enhances inflammatory gene expression in HSPC

To gain insights into the molecular mechanisms underlying emergency hematopoiesis in Usp22 KO mice, we compared gene expression of wild type and Usp22 KO HSPC by RNA sequencing, which identified 380 differentially expressed genes (DEG) (212 up-and 168 downregulated in Usp22 KO HSPC) (Fig. 5A). Gene ontology (GO) term enrichment analysis showed that genes upregulated in Usp22-deficient HSPC were associated with inflammation and immune responses, including interferon-stimulated genes (ISG) (GO terms "cellular response to IFN-b" and "cellular response to IFN-g", Fig. 5B). Expression of individual DEG within relevant GO terms identified in Fig. 5B is shown in Fig. 5C. Gene set enrichment analysis (GSEA) revealed enhanced expression of both IFN-a and IFN-g target genes in Usp22 KO HSPC (fig. S7A), and intersecting DEG with a comprehensive set of ISG previously found across immune cells [START_REF] Mostafavi | Parsing the Interferon Transcriptional Network and Its Disease Associations[END_REF] identified large numbers of ISG upregulated in Usp22-deficient HSPC (fig. S7B). Hence, loss of Usp22 enhances inflammatory gene expression in HSPC in the absence of infection or elevated levels of proinflammatory cytokines.

To test whether gene expression changes in Usp22-deficient HSPC occurred in a cellintrinsic manner, we performed RNA sequencing of HSPC isolated from mixed bone marrow chimeras in which Usp22 KO and wild type bone marrow cells were co-transplanted into the same recipients (Fig. 5D). Transcriptome comparison of Usp22 KO and wild type HSPC derived from the same hosts (Fig. 5D, bottom panel) identified 153 DEG (68 up-and 85 downregulated in Usp22 KO) (Fig. 5E). Only a few of the transcriptome changes resulted from the different CD45 allotypes (i.e. donor markers for wild type and Usp22 KO cells) (fig. S7C-E). Interestingly, transcriptome changes identified in 'ex vivo' isolated Usp22 KO HSPC specifically reemerged in transplanted Usp22-deficient HSPC but not in wild type HSPC in mixed bone marrow chimeras (Fig. 5F), independent of the CD45 allotype (fig. S7F). In line with the findings from our RNA sequencing experiments, Usp22 KO HSPC showed increased cell surface expression of MHC class II (MHC II), higher expression of Stat-1 mRNA and protein, increased Ifi47 mRNA expression, and elevated MPO protein levels (fig. S8A-E). While most of these are IFN-regulated genes, serum concentrations of IFN-a, IFN-b and IFN-g were not elevated in Usp22 KO compared to wild type mice (fig. S3B), and expression of the receptors for type I or type II IFN was not increased (fig. S8F,G). Despite enhanced inflammatory gene expression, Sca-1 levels were not increased in Usp22 KO HSPC (fig. S8H). Collectively, loss of Usp22 in hematopoietic cells leads to increased expression of inflammation-associated genes, including ISG. In agreement with absence of elevated systemic interferon levels or signs of infections, gene expression changes in Usp22 KO cells were not transmittable to wild type cells. Therefore, Usp22 acts as a cell-intrinsic repressor of inflammatory gene expression.

Usp22 deficiency enhances myeloid transcriptional priming

To investigate transcriptional programs involved in HSPC differentiation in wild type and Usp22 KO mice, we generated scRNA-seq data of sorted LT-HSC, ST-HSC and MPP from two independent experiments (for details see table S2). We first focused on MPP to explore molecular determinants of the myeloid bias in Usp22 KO mice. MPP were analyzed for cells that coherently expressed lineage genes (using SingleR [START_REF] Aran | Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage[END_REF]), resembling common lymphoid progenitors (CLP), granulocyte-monocyte progenitors (GMP) and megakaryocyte-erythroid progenitors (MEP). We then identified putative differentiation trajectories of these subpopulations from the more immature MPP. We used FateID [START_REF] Herman | FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data[END_REF] for identifying an informative subset of lineage-specific genes, ordering cells via diffusion map and applying Slingshot [START_REF] Street | Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics[END_REF]). Based on trajectory structure and cell-type labels, we defined the following MPP subsets: GMP-biased (branch with MPP resembling GMP), MEP-biased (branch with MPP resembling MEP or CFU-E), lymphoid primed MPP (LMPP) (branch with MPP resembling CLP), and unbiased MPP (cells not assigned to any branch) (Fig. 6A [Exp. 1]; fig S9A [Exp. 2]). This classification was consistent with expression levels of lineage-defining transcription factors (fig. S10), and correlated well with transcriptional signatures [START_REF] Rodriguez-Fraticelli | Clonal analysis of lineage fate in native haematopoiesis[END_REF] of previously described lineage-biased MPP subsets [START_REF] Pietras | Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood Production in Normal and Regenerative Conditions[END_REF] (fig. S9B).

While the overall topology of these trajectories was similar comparing wild type and Usp22 KO mice, GMP-biased MPP were increased at least ~1.4-fold, and LMPP were reduced at least ~1.4-fold in Usp22 KO mice (Fig. 6A; fig S9A). Consistent with enhanced myelopoiesis and NK cell expansion, we observed elevated expression of key transcription factor genes, e.g. Irf8 and Cebpb (both up in GMP-biased MPP), and Id2 (up in all MPP subsets) (Fig. S10). Moreover, the expression of the GMP signature was increased across LT-HSC, ST-HSC and MPP subsets, while the lymphoid signature was decreased (fig. S11A-D). Unbiased differential expression analysis yielded 20 shared upregulated and 12 shared downregulated genes across MPP subsets. The upregulated genes included immune effector molecules, such as MHC class I and II, Cd74, Stat-1, and Gbp3 (fig. S12A-E). Assigning cells to cell-cycle phase by characteristic transcripts, we found that the proportion of cells in G1 phase was decreased in all MPP subsets in Usp22 KO mice, which suggests faster proliferation of these subsets (Fig. 6B, fig. S9C), consistent with increased EdU incorporation in MPP overall (fig. S9D). Taken together, these data suggest that the enhanced production of mature cells in Usp22 KO mice is, at least in part, driven by accelerated proliferation of MPP, and that MPP differentiation has increased myeloid bias. Flow cytometrybased enumeration of lineage-biased MPP2 (MEP-biased), MPP3 (GMP-biased) and MPP4 (lymphoid biased) subpopulations showed only marginal differences between wild type and Usp22 KO mice (fig. S9E). It is possible that under conditions of perturbation such as the emergency hematopoiesis seen in Usp22-deficient mice, existing phenotypic definitions of MPP may not accurately reflect lineage priming at MPP stages.

To look for coordinately regulated gene programs in MPP beyond lineage genes, we performed GSEA for GO terms, and grouped significantly enriched terms with overlapping gene sets. As in the bulk RNA sequencing analysis (Fig. 5), we found signatures concordant with activation of innate and adaptive immunity in Usp22 KO MPP. Further gene sets indicated activation of metabolic processes, including energy metabolism via mitochondrial respiration, and biosynthetic processes (nucleotide metabolism and RNA processing), and are in line with enhanced proliferation of MPP (DNA replication, response to DNA damage stimulus) (fig. S13 [Exp. 1]; fig S14 [Exp. 2]).

Next, we analyzed highly differentially expressed genes (fold change > 1.2 or < 0.833) within GO groups (Fig. 6C, left panel; fig. S9F). These data showed a large number of immunerelated genes, the majority of which are involved in innate immune responses. Expression of genes related to MHC I and II antigen presentation was also enhanced in Usp22 KO MPP (Fig. 6C, right panel). In the first experiment, upregulation of Mif (macrophage migration inhibitory factor) and its receptor, CD74, contributed to nearly all GO immune subclusters (Fig. 6C, right panel). This also held true for clusters related to metabolism, consistent with the broad functions of Mif as a pro-inflammatory regulator of innate immunity [START_REF] Calandra | Macrophage migration inhibitory factor: a regulator of innate immunity[END_REF][START_REF] De | Macrophage migration inhibitory factor regulates mitochondrial dynamics and cell growth of human cancer cell lines through CD74-NF-κB signaling[END_REF]. However, in the second experiment, Mif was only mildly upregulated whereas the upregulation of Cd74 was consistent (fig. S9F).

Upregulated genes driving the enrichment of GO terms related to aerobic respiration indicated increased oxidative phosphorylation (Exp.1: Cox6a1, Ndufs6; Exp. 2: Gadd45gip1) (Fig. This may underlie the increased proliferation and differentiation of HSC and MPP in Usp22 KO mice, as the switch from glycolysis to oxidative phosphorylation is a driver of HSC proliferation and differentiation [START_REF] Filippi | Mitochondria in the maintenance of hematopoietic stem cells: new perspectives and opportunities[END_REF][START_REF] Papa | Mitochondrial Role in Stemness and Differentiation of Hematopoietic Stem Cells[END_REF][START_REF] Vannini | Specification of haematopoietic stem cell fate via modulation of mitochondrial activity[END_REF]. Moreover, reactive oxygen species (ROS) produced by respiration skew lineage commitment towards myeloid differentiation [START_REF] Yalcin | ROSmediated amplification of AKT/mTOR signalling pathway leads to myeloproliferative syndrome in Foxo3(-/-) mice[END_REF][START_REF] Bigarella | Stem cells and the impact of ROS signaling[END_REF]. In sum, the scRNA-seq analysis uncovered, in addition to the activation of innate immunity, a coordinated response of metabolic processes that is consistent with both increased differentiation and myeloid bias driven by Usp22 KO.

Usp22 deficiency increases H2B monoubiquitination at ISG loci

USP22 serves as a deubiquitinase for monoubiquitinated H2B. Since H2Bub1 has been implicated in ISG transcription downstream of interferon receptor activation [START_REF] Fonseca | Adenovirus Evasion of Interferon-Mediated Innate Immunity by Direct Antagonism of a Cellular Histone Posttranslational Modification[END_REF], we reasoned that inflammatory gene expression in Usp22 KO HSPC might result from enhanced H2Bub1 levels.

Therefore, we first determined levels of monoubiquitinated H2B by western blotting. Across all tested hematopoietic cell types, H2Bub1 levels were markedly increased in the absence of Usp22 (Fig. 7A).

Next, we asked how greater H2Bub1 levels affected genome-wide DNA binding. To this end, we performed chromatin immunoprecipitation sequencing (ChIP-seq) for H2Bub1. Since H2Bub1 is mainly associated with gene bodies [START_REF] Minsky | Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells[END_REF], we focused our analysis on such regions. Our data revealed the typical pattern of gene body H2B monoubiquitination [START_REF] Shema | The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression[END_REF], with H2Bub1 levels peaking at the beginning of the transcribed region and then decreasing towards the end of the gene body (fig. S18A). Consistent with RNA polymerase II-dependent recruitment of the RNF20/RNF40 complex [START_REF] Zhang | WAC, a Functional Partner of RNF20/40, Regulates Histone H2B Ubiquitination and Gene Transcription[END_REF], H2Bub1 was absent in the gene bodies of non-expressed genes, and abundant in the transcribed regions of strongly expressed genes (fig. S18B). Both of these principle attributes of H2Bub1 were unaffected by Usp22 deficiency (fig. S18A,B). By comparing Usp22 KO and wild type HSPC, we identified 2198 genes which exhibited differential H2B monoubiquitination at their gene bodies (Fig. 7B). The vast majority of these loci showed enhanced H2Bub1 levels (2008 hyper-and 190 hypo-ubiquitinated loci in Usp22 KO vs wild type) (Fig. 7B). To functionally annotate these genes, we performed GO term enrichment analysis, which revealed that hyper-ubiquitinated genes were associated, among other processes, with cytokine responses, defense responses, leukocyte activation and immune responses (Fig. 7C).

In order to link locus-specific H2Bub1 levels with gene expression, we next integrated H2Bub1 ChIP-seq data with bulk RNA sequencing data (Fig. 5). Genome-wide, there was little correlation between change in expression and change in gene body monoubiquitination (Fig. 7D, left panel). In contrast, this correlation was much higher for differentially expressed genes (Fig. 7D, right panel). Next, we focused on loci with the most robust changes (p<0.05, FC ³ 1.5 or FC £ 1/1.5) in both mRNA expression and gene body H2Bub1 levels upon loss of Usp22 (Fig. 7E).

In total, 118 genes fulfilled both criteria, 102 of which showed increased H2Bub1 levels (Fig. 7E, right quadrants), and 93 exhibited both enhanced H2B monoubiquitination and increased mRNA expression in Usp22 KO HSPC (Fig. 7E, upper right quadrant). These 93 genes correspond to approximately 44 % of the total 212 genes with increased expression (Fig. 5A). Examples of locusspecific H2Bub1 profiles are shown for upregulated, hyperubiquitinated and downregulated, hypoubiquitinated genes (Fig. 7F and fig. S18C). Of note, upregulated, hyperubiquitinated genes included important immune cell effector molecules, such as H2-Ab1 and Mpo (Fig. 7F).

Interestingly, the set of genes differentially expressed and differentially ubiquitinated in Usp22 KO HSPC was highly enriched for ISG (Fig. 7G). Importantly, all of the ISG among the latter gene set consistently showed enhanced expression and elevated gene body H2Bub1 levels in Usp22 KO cells (Fig. 7E, red dots). Consequently, loss of Usp22 results in enhanced H2Bub1 levels and concomitantly increased expression at many ISG loci. To further visualize the effect of Usp22 deficiency on H2B monoubiquitintion at ISG loci, we assessed average H2Bub1 levels across the gene bodies of interferon target genes, and found that these were elevated for all the classes of ISG analyzed (Fig. 7H; fig. S18D).

Finally, we complemented our analysis with ATAC sequencing to assess whether altered chromatin accessibility underlies the observed gene expression changes. Interestingly, both on average (fig. S18E), and when analyzing individual loci (fig. S18F), genes up-or downregulated in Usp22 KO HSPC showed no changes in their promoter accessibility. Even the genes shown in Fig. 7E had no changes in their promoter accessibility (fig. S18G). Therefore, gene expression changes in Usp22-deficient cells occur independently of altered promoter accessibility. Taken together, our ChIP-seq experiments demonstrate that USP22 deubiquitinates H2Bub1 bound to DNA, and that levels of DNA-bound H2Bub1 are hence elevated in the absence of USP22. Genes that are both hyper-monoubiquitinated and strongly upregulated are highly enriched for ISG, and these changes in gene expression are independent of alterations in promoter accessibility.

DISCUSSION

Normally, hematopoiesis switches from steady state to emergency in response to infection and inflammation. At cellular and systemic levels, triggers mediating emergency hematopoiesis during infections include signals via pathogen-associated molecular patterns (PAMP) and increased concentrations of inflammatory cytokines. HSC and progenitors can directly sense and respond to PAMP (5,[START_REF] Nagai | Toll-like receptors on hematopoietic progenitor cells stimulate innate immune system replenishment[END_REF] and inflammatory cytokines [START_REF] Essers | IFNα activates dormant haematopoietic stem cells in vivo[END_REF][START_REF] Baldridge | Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection[END_REF][START_REF] Pietras | Chronic interleukin-1 exposure drives haematopoietic stem cells towards precocious myeloid differentiation at the expense of self-renewal[END_REF]. Enhanced HSC proliferation [START_REF] Essers | IFNα activates dormant haematopoietic stem cells in vivo[END_REF][START_REF] Baldridge | Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection[END_REF], overproduction of myeloid cells, especially granulocytes, at the expense of lymphocytes [START_REF] Ueda | Inflammation and the reciprocal production of granulocytes and lymphocytes in bone marrow[END_REF], as well as HSC mobilization and extramedullary hematopoiesis (7) constitute typical aspects of emergency hematopoieis. Intriguingly, we found all of these hallmarks in mice with panhematopoietic Usp22 inactivation. The key difference we observed in Usp22 KO mice compared to inflammation-or infection-associated emergency hematopoiesis, however, was an absence of infections and lack of elevation of analyzed inflammatory cytokines, including G-CSF, IL-6 or type I IFN [START_REF] Boettcher | Cutting edge: LPS-induced emergency myelopoiesis depends on TLR4-expressing nonhematopoietic cells[END_REF][START_REF] Lasseaux | Type I interferons drive inflammasome-independent emergency monocytopoiesis during endotoxemia[END_REF][START_REF] Romani | Impaired neutrophil response and CD4+ T helper cell 1 development in interleukin 6-deficient mice infected with Candida albicans[END_REF]. We therefore consider it unlikely that emergency hematopoiesis was induced in Usp22 KO mice by the typical route via inflammation. Rather, we provide comprehensive data from co-culture experiments and mixed bone marrow chimeras demonstrating a cell-intrinsic and systemic cytokine-independent switch. Key phenotypes, including myeloid-biased hematopoiesis, 'left-shifted' granulopoiesis, impaired B cell development, and enhanced inflammatory gene expression, were not transferred from Usp22 KO to wild type cells and not reverted in Usp22deficient cells by the presence of wild type cells. While our data clearly show that cell-autonomous, system-wide emergency hematopoiesis can be elicited by loss of Usp22, it remains to be determined how Usp22 expression and H2B monoubiquitination are regulated during inflammation-or infection-induced emergency hematopoiesis.

Enhanced myelopoiesis is currently considered the primary purpose of emergency hematopoiesis. In addition to the restoration of cellular homeostasis after infection, increased myeloid cell production may also provide innate protection against infection. However, because emergency hematopoiesis is experimentally or clinically tightly linked to infection or inflammation [START_REF] Brook | BCG vaccination-induced emergency granulopoiesis provides rapid protection from neonatal sepsis[END_REF], it is difficult to disentangle the contribution of emergency hematopoiesis to protective responses. The stronger innate protection of Usp22 KO mice from Listeria monocytogenes infection that we observed might result from both quantitative and qualitative alterations of myeloid cell compartments. While increased myeloid cell numbers in Usp22 KO mice might provide evidence for the former notion, enhanced phagocytic activity of Usp22deficient neutrophils clearly supports the latter one. Therefore, we propose that emergency hematopoiesis modulates myelopoiesis both in a quantitative and qualitative manner. This idea is also supported by our transcriptome analysis. In line with the myeloid bias, enhanced expression of GMP-associated signatures was observed in HSC and MPP from Usp22 KO mice, and in fact proportions of transcriptionally GMP-biased MPP were elevated. Among upregulated genes, we found the IFN-g-inducible transcription factor Batf2 which has been shown to promote myelopoiesis [START_REF] Matatall | Chronic Infection Depletes Hematopoietic Stem Cells through Stress-Induced Terminal Differentiation[END_REF]. Collectively, these data provide a molecular underpinning for the enhanced myeloid cell production in Usp22 KO mice. GO term enrichment analysis suggested elevated mitochondrial activity, which could accelerate differentiation of Usp22 KO HSC [START_REF] Vannini | Specification of haematopoietic stem cell fate via modulation of mitochondrial activity[END_REF]. However, direct metabolic studies of mutant and wild type HSC will be required to study mitochondrial activity.

Loss of Usp22 further lead to the activation of a pro-inflammatory gene expression program in HSPC, including upregulation of a large set of ISG, which normally occurs in response to cytokines. Among these genes were important regulators of innate and adaptive immunity, including MHC II molecules (H2-Aa, H2-Ab1, H2-Eb1), their upstream co-activator (Ciita), and myeloid effector molecules (Elane, Mpo), all of which may contribute to enhanced innate protection by Usp22 KO myeloid cells. Both stronger protection and the transcriptional 'immune activation' signature in stem and progenitors in Usp22 KO mice are reminiscent of trained immunity, and future experiments will be required to determine similarities or uniqueness of both states.

Loss of Usp22 resulted in elevated H2Bub1 levels, in agreement with the role of USP22 as a non-redundant H2Bub1 deubiquitinase in hematopoietic cells [START_REF] Melo-Cardenas | USP22 deficiency leads to myeloid leukemia upon oncogenic Kras activation through a PU.1-dependent mechanism[END_REF][START_REF] Cortez | CRISPR screen in regulatory T cells reveals modulators of Foxp3[END_REF][START_REF] Li | The H2B deubiquitinase Usp22 promotes antibody class switch recombination by facilitating non-homologous end joining[END_REF]. H2Bub1 is an activating chromatin mark, which can be mainly found in the gene body of expressed genes [START_REF] Minsky | Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells[END_REF]. Perturbed H2B monoubiquitination only affects the expression of a minor fraction of the transcriptome [START_REF] Shema | The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression[END_REF][START_REF] Xie | RNF40 regulates gene expression in an epigenetic context-dependent manner[END_REF], notably including genes induced by cell-extrinsic signals such as nutrient levels, hormones and growth factors [START_REF] Shema | The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression[END_REF][START_REF] Shukla | H2B-K123 ubiquitination stimulates RNAPII elongation independent of H3-K4 methylation[END_REF][START_REF] Prenzel | Estrogen-Dependent Gene Transcription in Human Breast Cancer Cells Relies upon Proteasome-Dependent Monoubiquitination of Histone H2B[END_REF]. These notions are in accordance with the limited number of DEG identified in Usp22-deficient hematopoietic progenitors (380 genes), many of which were genes normally induced by IFN. In cell lines, H2Bub1 levels increase at ISG loci in response to type I IFN, and Rnf20, the catalytically active component of the E3 ubiquitin ligase complex mediating H2B monoubiquitination, is required for efficient ISG induction [START_REF] Fonseca | Adenovirus Evasion of Interferon-Mediated Innate Immunity by Direct Antagonism of a Cellular Histone Posttranslational Modification[END_REF]. Our H2Bub1 ChIP sequencing data demonstrate that loss of Usp22 leads to increased H2Bub1 levels at dozens of ISG loci, which exhibited concomitant elevated expression, and therefore suggests that enhanced locusspecific H2B monoubiquitination is both required [START_REF] Fonseca | Adenovirus Evasion of Interferon-Mediated Innate Immunity by Direct Antagonism of a Cellular Histone Posttranslational Modification[END_REF] and sufficient to drive ISG expression.

Transcriptome changes in Usp22 KO cells occurred in the absence of altered chromatin accessibility, implying that enhanced ISG expression driven by Usp22 deficiency and increased H2Bub1 levels are likely caused by events occurring after transcription factor binding and RNA polymerase II recruitment. H2Bub1 has been implicated in the positive regulation of transcriptional elongation [START_REF] Pavri | Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II[END_REF], which might account for the observed transcriptome changes in Usp22-deficient cells. Our data suggest that enhanced H2Bub1 levels are required for the development of the hematopoietic phenotypes seen in Usp22 KO mice; however, the precise molecular mechanisms linking Usp22 deficiency to increased inflammatory gene expression remain to be examined. In particular, the specificity in gene regulation upon loss of Usp22 will need to be explored given that the number of differentially ubiquitinated genes (DUG) was much larger than the number of DEG. Other chromatin modifications may play a role; for example, levels of H2Bub1 correlate positively with levels of activating histone modifications such as H3K4 methylation. H2Bub1-dependent genes are characterized by broad H3K4me3 peaks at their transcription start sites, which have been implicated in transcriptional elongation [START_REF] Xie | RNF40 regulates gene expression in an epigenetic context-dependent manner[END_REF]. Finally, our data cannot rule out the involvement of alternative USP22 substrates identified by others, such as PU.1 [START_REF] Melo-Cardenas | USP22 deficiency leads to myeloid leukemia upon oncogenic Kras activation through a PU.1-dependent mechanism[END_REF] and SIRT1 [START_REF] Lin | USP22 Antagonizes p53 Transcriptional Activation by Deubiquitinating Sirt1 to Suppress Cell Apoptosis and Is Required for Mouse Embryonic Development[END_REF], in the development of emergency hematopoiesis in Usp22 KO mice.

Taken together, our results demonstrate that loss of Usp22 in hematopoietic cells induces phenotypic and functional emergency hematopoiesis in a cell-autonomous manner. These findings shed light on the molecular regulation of a broad state of immune pre-activation, including enhanced innate protection, and might hence have implications for the therapeutic manipulation of this process such as through inhibition of USP22.

MATERIALS AND METHODS

Study design

The aim of this study was to investigate system-wide functions of Usp22 in the hematopoietic system. Using conditional Usp22 KO mice, we first determined cellular phenotypes in the Usp22deficient blood and immune system. We performed in situ lineage tracing, adoptive cell transfer experiments, and in vitro hematopoiesis assays to dissect changes in differentiation of Usp22 KO stem and progenitor cells, and to distinguish cell-intrinsic from cell-extrinsic mechanisms. In vivo Listeria monocytogenes infections, and in vitro phagocytosis assays were used to probe important innate effector functions. Bulk and single cell RNA sequencing of wild type and Usp22-deficient stem and progenitor cells, combined with comprehensive computational analysis, were used to explore the molecular underpinnings of the observed phenotypes. RNA sequencing data were extended by qRT-PCR and flow cytometry for selected candidate target molecules. The effects of Usp22 deficiency on H2B monoubiquitination were analyzed using Western Blotting.

Transcriptome changes were linked with epigenetic alterations using ATAC-sequencing and ChIPsequencing for H2Bub1. Detailed descriptions of the experimental, computational and statistical methods used in this study are given below. Sample size and replicates are indicated in the figure legends.

Mice

Usp22 flox mice (B6-Usp22 tm1c(KOMP)Wtsi ) were crossed to Vav1-Cre (B6.Cg-Commd10 Tg(Vav1- icre)A2Kio /J) [START_REF] De Boer | Transgenic mice with hematopoietic and lymphoid specific expression of Cre[END_REF] to obtain Usp22 KO mice. For fate mapping of LT-HSC, Usp22 flox mice were crossed to Tie2-MeriCreMer (B6;129P2-Tek tm1.1(icre/Esr1*)Hrr ) [START_REF] Busch | Fundamental properties of unperturbed haematopoiesis from stem cells in vivo[END_REF] Rosa26-loxP-Stop-loxP-YFP mice (Gt(ROSA)26Sor tm1.1(EYFP)Cos ) [START_REF] Srinivas | Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus[END_REF]. B6.SJL-Ptprc a Ptprc b mice (CD45.1/CD45.2) were used as recipients in transplantation experiments. Mice were kept in individually ventilated cages under specific pathogen-free conditions in the animal facility of the DKFZ. Age-and sex-matched young adult mice were used for all experiments. For most experiments, Cre-positive mice carrying two Usp22 wild type alleles were used as wild type controls. Both male and female mice were used.

No randomization and no blinding were done. All animal experiments were performed according to institutional and governmental regulations, and approved by the Regierungspräsidium Karlsruhe, Germany.

Bone marrow and CMP transplantation

Recipient mice were lethally irradiated with a split dose of 2 x 5.5 Gy using a Cs137 Gammacell 40 irradiator with three to four hours between irradiation cycles. Donor cells (in PBS) were injected into the tail veins. For competitive bone marrow transplantations, 1x10 6 test bone marrow cells (derived from Usp22 KO mice or wild type littermates, both CD45.2) were transplanted together with 1x10 6 competitor bone marrow cells (CD45.1) into the same recipient (CD45.1/CD45.2). For serial competitive bone marrow transplantations, bone marrow cells isolated from recipient mice at the end of each transplantation round were re-transplanted (3x10 6 bone marrow cells per recipient (CD45.1/CD45.2)). For CMP transplantations, 1x10 4 test CMP (derived from Usp22 KO or wild type mice, both CD45.2) were transplanted together with 1x10 5 lineage-depleted competitor bone marrow cells (CD45.1) into the same recipient (CD45.1 or CD45.1/CD45.2). For HSC transplantations, 100 sorted LT-HSC (from Usp22 KO or wild type mice, both CD45.2) were transplanted together with 10 5 lineage-negative bone marrow cells (CD45.1) into the same recipient (CD45.1/CD45.2). Donor cells were isolated from age-matched male and female mice (5-13 weeks) and transplanted into cohorts of age-matched male and female recipient mice (7-18 weeks). Mice were kept on Neomycin containing drinking water (1.17 g/l) for two weeks after transplantation.

In vivo fate mapping of LT-HSC

Tie2 MCM/+ Rosa26 LSL-YFP/LSL-YFP Usp22 +/+ and Tie2 MCM/+ Rosa26 LSL-YFP/LSL-YFP Usp22 flox/flox mice were injected with tamoxifen on five consecutive days (1 mg per day) for Cre induction. After 14 weeks, mice were sacrificed, and the proportion of YFP-labeled cells within different hematopoietic cell compartments in the bone marrow was determined by flow cytometry. Labeling frequencies in myeloid and developing B cells were normalized to the labeling frequency of LT-HSC within the same mouse.

Listeria monocytogenes infection and CFU quantification

Female wild type and Usp22 KO mice were infected with 10 4 CFU Listeria monocytogenes (EGDe strain) by intravenous injection. Three days post-infection, mice were sacrificed, and blood and organs were aseptically harvested. Organs were homogenized in PBS using a tissue homogenizer.

Serial dilutions of blood and tissue homogenates were plated onto BHI to enumerate L. monocytogenes CFU.

Blood, serum and bone marrow fluid collection

Blood samples were collected by puncture of the submandibular vein, or by post mortem cardiac puncture. For flow cytometry, blood samples were collected into EDTA-coated tubes, and subjected to red blood cell lysis using RBC lysis buffer (BioLegend) before further processing as described below. For serum preparation, blood was collected into serum tubes, incubated for 30 minutes at room temperature to allow for coagulation, and centrifuged at 15,000g for 90 seconds.

Serum samples were frozen in aliquots at -80°C. For bone marrow fluid collection, femora and tibiae were flushed with PBS supplemented with protease inhibitors. Cell suspensions were centrifuged, supernatants (bone marrow fluid) transferred into fresh tubes, and stored at -20°C.

Preparation of single cell suspensions from hematopoietic organs

Bones (tibiae, femura, pelvis and spine) were crushed in FACS buffer (PBS + 5 % FBS), and filtered through 40 µm cell strainers. Spleens were mashed with FACS buffer through pre-wetted 40 µm cell strainers using syringe plungers. Cell numbers were determined using a Cellometer Auto 2000 Cell Viability Counter (Nexcelom).

Flow cytometry and fluorescence activated cell sorting

Single cell suspensions, or lysed blood samples were blocked for 15 minutes in 10 % normal rat serum (diluted in FACS buffer) and stained for 20 minutes (45 minutes for NK and NKP stainings) in titrated dilutions of fluorescent dye-labeled antibodies (in FACS buffer) at 4°C. Live/dead cells were discriminated by Sytox Blue (Thermo Fisher Scientific). For the sorting of HSPC, CMP and B cell progenitors, bone marrow cells were subjected to lineage depletion prior to further antibody staining. Cells were labeled with biotinylated antibodies directed against lineage markers (CD4, CD8, CD11b, CD19 [omitted in the enrichment of B cell progenitors], Gr-1 and Ter119), and were depleted using anti-biotin microbeads (Miltenyi) on LS MACS columns (Miltenyi). Samples were analyzed on a LSRFortessa flow cytometer (BD Biosciences), or sorted on a FACSAria III cell sorter (BD Biosciences). Antibodies and second step reagents were: MPO-FITC (clone 2D4) from Abcam, BP-1-PE (BP-1), CD4-biotin (GK1.5), CD4-FITC (H129. [START_REF] Busch | Fundamental properties of unperturbed haematopoiesis from stem cells in vivo[END_REF]), CD8a-FITC (53-6.7), Click-iT Plus EdU Alexa Fluor 488 Flow Cytometry Kit (Thermo Fisher Scientific) according to the manufacturer's instructions. Samples were labeled with FxCycle Violet stain to assess DNA content, and data were acquired on a LSRFortessa flow cytometer (BD Biosciences).

Annexin V labeling

Bone marrow cells were isolated and stained as described above. Annexin V labeling was performed using the FITC Annexin V Apoptosis Detection Kit (BD Biosciences) according to the manufacturer's instructions with minor modifications. 10 6 bone marrow cells were labeled using 3 µl of FITC Annexin V. Sytox Blue was used for live/dead cell discrimination. Data were acquired on a LSRFortessa flow cytometer (BD Biosciences).

In vitro phagocytosis assay

Neutrophilic granulocytes were purified by magnetic cell separation using anti-Ly6G antibody (clone 1A8) from bone marrow of wild type and Usp22 KO mice. Bone marrow-derived macrophages (BMDM) were differentiated from total bone marrow cells for 5 days in the presence of M-CSF (10 ng/ml). Peritoneal macrophages were obtained by pertitoneal lavage. Equal numbers of neutrophils, BMDM or peritoneal macrophages were seeded onto 24-well plates and incubated with pHrodo red-labeled E. coli particles for two hours at 37°C. Cells were harvested, washed with PBS and analyzed on a LSRFortessa flow cytometer (BD Biosciences).

In vitro bactericidal assay

DH5a E.coli were grown to an OD600 of ca. 0.5, diluted 1:125 in 1xHBSS and pre-incubated with 10% mouse serum for 10 minutes at 37°C for opsonization. 10 6 ex vivo purified bone marrow neutrophils were resuspended in 500 µl 1xHBSS, supplemented with 10% mouse serum and incubated for 10 minutes at 37°C. 550 µl of opsonized bacteria suspension were added to granulocyte samples and incubated at 37°C on a shaking heating block for 90 minutes. Bacteriagranulocyte suspensions were serially diluted in LB medium, and plated onto LB agar plates to enumerate E.coli CFU counts.

In vitro LPS stimulation

Ex vivo purified bone marrow neutrophils were incubated with 2 µg/ml LPS at 37°C for 18 hours. Supernatants were harvested and used for LEGENDplex assays to determine levels of proinflammatory cytokines.

Measurement of inflammatory cytokine serum levels

Serum levels of IL1-a, IL-1b, IL-6, IL-10, IL-12p70, IL-17A, IL-23, IL-27, GM-CSF, MCP-1 and TNF-a were determined using the LEGENDplex mouse inflammation panel (BioLegend) according to the manufacturer's instructions with minor modifications. Samples were analyzed on a LSRFortessa flow cytometer (BD Biosciences).

Measurement of interferon serum levels

Serum levels of IFN-a, IFN-b and IFN-g were determined using the LEGENDplex mouse type 1/2 interferon panel (BioLegend) according to the manufacturer's instructions. Samples were analyzed on a LSRFortessa flow cytometer (BD Biosciences).

Measurement of inflammatory cytokine levels in bone marrow fluid

Levels

RNA extraction

RNA was extracted from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer's instructions including the on-column DNase digestion step.

qRT-PCR

cDNA was synthesized from RNA using the SuperScript Vilo cDNA synthesis kit (Thermo Fisher Scientific) according to the manufacturer's instructions. Oligo-dT primers were additionally added to the reaction mix. cDNA was diluted and used for qRT-PCR using SYBR Green PCR Master Mix (Thermo Fisher Scientific) on a Viia7 Real-Time PCR System (Applied Biosystems). Fold change expression values were determined with the comparative delta Ct method using Sdha as reference gene. Primer sequences are given in Table S3.

Single-cell Usp22 genotyping

Single cells were sorted directly into PCR tubes containing 25 µl PCR lysis buffer (1x Buffer 1 from the Expand Long Template PCR System [Roche], 0.5 mg/ml Proteinase K) and lysed for 1h at 55°C. Proteinase K was heat-inactivated for 10 min at 95°C before 25 µl 2x PCR mix were added for the first amplification. 2 µl of the first PCR reaction were used as template for the second round of nested PCR amplification. Primer sequences are given in Table S4.

Western Blot

Cell pellets were resuspended in RIPA buffer supplemented with Complete Protease Inhibitor Cocktail (Roche), incubated for 30 minutes on ice and sonicated using a Bioruptor Plus sonicator.

Samples were cleared of debris by centrifugation. Cell lysates were supplemented with Laemmli Buffer, heat-denatured, and separated by SDS-PAGE. Equal cell numbers were loaded. Proteins were transferred to PVDF membranes. Membranes were blocked in 5 % milk (in TBS-Tween) and probed with primary antibodies overnight. Primary antibodies were detected using HRPconjugated secondary antibodies in combination with ECL substrate solution. Due to differences in their signal strengths, different exposure times were chosen for the detection of H2B and H2Bub1. Antibodies used were: anti-H2B (clone mAbcam 52484, Abcam, order no. 52484), anti-H2Bub1 (clone D11, Cell Signaling Technologies, order no. 5546S), HRP-conjugated goat-antimouse IgG (Thermo Fisher Scientific, order no. 32430), HRP-conjugated goat-anti-rabbit IgG (Thermo Fisher Scientific, order no. 32460). Results shown in Fig. 7A are representative of n=8 mice/genotype analyzing whole tissue lysates from various hematopoietic organs (bone marrow, spleen and thymus) or lysates of purified hematopoietic cell types.

OP9 assay

Sorted LSK (500 cells/well on 24-well plates) were plated onto irradiated OP9 feeder cells in B cell differentiation medium (MEMa + 20 % FBS + Penicillin/Streptomycin + 10 ng/ml rmFlt3L + 5 ng/ml rmIL-7) and cultured for 1.5 to 3 weeks, before cells were collected by pipetting and stained for flow cytometry.

Gamma-retroviral (GRV) transduction of LSK

The GRV backbone pMIG was a gift from William Hahn (Addgene plasmid # 9044). GRV particles were produced by transient transfection of Phoenix GP cells and concentrated using Retro-X concentrator (Takara). Sorted LSK were pre-expanded for two days, spin-infected (multiplicity of infection = 15) in the presence of polybrene and subjected to OP9 in vitro differentiation assays.

Transcriptome and epigenome profiling

RNA sequencing, single cell RNA sequencing, OMNI-ATAC sequencing and H2Bub1 ChIPmentation, and associated computational analysis are provided in Supplementary Methods.

Statistical analysis

Graphs

H2-Q7 Cd74 H2-Ab1 Mif H2-Eb1 H2-Aa H2-Q6 Serpina3g Cd52 Stat1 H2-K1 Iigp1 B2m Gbp3 Stxbp4 H2-Q4 Mpo H2-T22 Gm4951 Ffar2 Igtp Ly6a Dbi Plac8 Ifi47 Psmb10 Psmb8 Fabp5 Gbp7

Single cell RNA sequencing

FACS-purified cells (2 replicates per population and genotype isolated from age-and sex-matched mice taken from the same colony) were resuspended in PBS and processed using the Chromium System (Chromium Single Cell 3' Reagent Kits v3, 10x Genomics) according to the manufacturer's instructions (CG000183 RevA/CG000206 RevD). In brief, single cells were encapsulated into droplets and mRNA was captured with indexed beads. After reverse transcription, indexed cDNA was cleaned up and amplified with the following PCR program: 3 min at 98 °C, 13-14 x (15 s at 98 °C, 20 s at 63 °C, 1 min at 72 °C) and final extension for 3 min at 72 °C. To generate sequencing libraries, 25% of the cDNA were used as input for fragmentation, Illumina sequencing adapter ligation and indexing PCR. Indexing PCR was performed with the following program: 45s at 98 °C, 13-14 x (20 s at 98 °C, 30s s at 54 °C, 20s at 72 °C) and final extension for 1 min at 72 °C. After quality control, libraries were pooled and sequenced on Illumina HiSeq4000 and Nextseq 1000/2000 platforms using the parameters recommended by 10x Genomics.

OMNI-ATAC sequencing

OMNI-ATAC sequencing was performed as described in [START_REF] Corces | An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues[END_REF] with minor modifications. Briefly, 50,000 sorted LSK were lyzed and nuclei subjected to Tn5 mediated transposition for 30 minutes at 37°C. DNA was purified using Ampure XP beads and used for indexing PCR. Sequences of the used indexing primers are given in Table S5. The number of PCR cycles was determined by qRT-PCR as described in [START_REF] Buenrostro | ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide[END_REF]. Amplified libraries were purified by two-sided Ampure XP bead purification and validated on a Bioanalyzer (Agilent). 50 bp paired-end sequencing of pooled libraries was performed on an Illumina HiSeq2500.

ChIPmentation for H2Bub1

H2Bub1 ChIPmentation of LSK was performed according to [START_REF] Schmidl | ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors[END_REF] with minor modifications.

Sorted LSK were subjected to cross-linking in 1 % formaldehyde (in PBS) for 10 minutes at room temperature, and cross-linking was stopped by adding glycine. Pellets of cross-linked cells were resuspended in shearing buffer (10 mM Tris-HCl pH 8, 0.1% SDS, 1 mM EDTA) supplemented with Complete Protease Inhibitor Cocktail (Roche), and chromatin was sheared to an average fragment size of 200-250 bp. DNA concentrations were assessed using a Qubit fluorometer, equal amounts of sheared chromatin were diluted in ChIPmentation dilution buffer (20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 % SDS, 1 % Triton-X, 1 mM EDTA, 0.5 mM EGTA), and incubated with anti-H2Bub1 (clone D11, Cell Signaling Technologies, order no. 5546S) or rabbit isotype control (BioLegend, order no. 910801) antibody over night at 4°C. On the next day, pre-blocked magnetic Protein A beads were added, and samples incubated for two hours at 4°C. Bead-bound chromatin fragments were separated on a magnetic tube rack and washed before they were subjected to tagmentation. Chromatin fragments bound to magnetic beads were resuspended in 30 µl Tagmentation mix (14 µl H2O, 15 µl Tagment DNA Buffer [Illumina, order no. 15027866], 1 µl Tagment DNA Enzyme [Illumina, order no. 15027865]), and incubated for 10 minutes at 37°C. Bead-bound chromatin was washed and decross-linked in elution buffer containing Proteinase K for eight hours at 56°C. Decross-linked chromatin was purified using Ampure XP beads, subjected to indexing PCR as described in the section "OMNI-ATAC sequencing" and purified again with Ampure XP beads. Purified libraries were validated on a Bioanalyzer instrument. 50 bp single-end sequencing of pooled libraries was performed on an Illumina HiSeq2500.

RNA sequencing data processing and analysis

The RNA sequencing reads were first subjected to adapter trimming and low-quality read filtering using flexbar (version 2.5) (57) with the following parameters: -u 10 -m 32 -ae RIGHT -at 2 -ao 2. Reads that were mapped to the reference sequences of rRNA, tRNA, snRNA, snoRNA, and miscRNA (available from Ensembl and RepeatMasker annotation) using Bowtie 2 (version 2.2.9) [START_REF] Langmead | Fast gapped-read alignment with Bowtie 2[END_REF] with default parameters (in --end-to-end & --sensitive mode) were excluded. The remaining reads were then mapped to the mouse reference genome (mm10) using Tophat2 (version 2.1.1) [START_REF] Kim | TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[END_REF] with the parameters -N 2 --read-gap-length 2 --read-edit-dist 3 --min-anchor 6 --library-type fr-unstranded --segment-mismatches 2 --segment-length 25, or STAR (version 2.7.3a) [START_REF] Dobin | STAR: ultrafast universal RNA-seq aligner[END_REF] with key parameters --outFilterMismatchNmax 8 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated. Reads that were mapped to multiple genomic sites were discarded in the following analysis. HTSeq-count (version 0.9.1) (61) was used to count reads mapped to annotated genes, with parameters -f bam -r pos -s no -a 10.

Differentially expressed gene analysis was performed with the R package DESeq2 (version 1.16.0) [START_REF] Love | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[END_REF]. In brief, size factor estimation was first conducted to normalize the data across samples, followed by dispersion estimation to account for the negative binomial distributed count data in RNA sequencing. Finally, gene expression fold changes were calculated and the significance of the gene expression difference was estimated using the Wald test. To control the false discovery rate in multiple testing, the raw p-values were adjusted using the Benjamini-Hochberg (BH) procedure. Genes with adjusted p-values less than 0.05 and fold changes over 1.5 folds were considered as differentially expressed.

ChIP sequencing data processing and analysis

The ChIP sequencing reads were first subjected to adapter trimming and low-quality read filtering using flexbar (version 2.5) (57) with the following parameters: -u 5 -m 26 -ae RIGHT -at 2 -ao 1.

The trimmed reads were mapped to the mouse reference genome (mm10) using Bowtie 2 (version 2.2.9) (58) with default parameters. Reads that mapped to mitochondrial DNA or with low mapping quality (< 30) were excluded for downstream analysis. Duplicate reads due to PCR amplification of single DNA fragments during library preparation were identified using Picard (version 2.17.3; available at http://broadinstitute.github.io/picard) and thus removed from the downstream analysis.

To obtain the pure signal of monoubiquitinated H2B, H2Bub1 ChIP sequencing data were compared to the input data (libraries prepared from DNA of cells from replicate set 1) using the bdgcmp command of macs2 (version 2.1.1) [START_REF] Zhang | Model-based analysis of ChIP-Seq (MACS)[END_REF] for signal fold enrichment. The resulting signal was then used for drawing signal profiles and heatmaps. To identify differentially ubiquitinated genes, we counted the deduplicated reads overlapping with gene bodies (introns included) of individual genes. DESeq2 (version 1.16.0) (62) was then used for statistical comparison of the read counts obtained from wild type and Usp22-deficient LSK, with a procedure similar to the analysis of the RNA sequencing data. Genes with adjusted p-values less than 0.05 and fold changes over 1.5 folds were considered as differentially ubiquitinated.

ATAC sequencing data processing and analysis

The processing steps of ATAC sequencing data for read trimming, mapping and deduplication were the same as those for the ChIP sequencing data. Genome-wide chromatin accessibility was quantified using bamCoverage from the deeptools python toolkit suit (version 3.4.3) (64) based on the deduplicated reads. To compare data from different libraries, the accessibility signal was normalized using library scale factors. Thus, the normalized accessibility signal was used for drawing signal profiles and heatmaps. To identify genes with differential accessibility in their promoters, we counted the deduplicated reads overlapping with gene promoters (defined as a 2000bp window centered at a gene's transcription start site). DESeq2 (version 1.16.0) (62) was then used for statistical comparison of the read counts obtained from wild type and Usp22-deficient LSK, with a similar procedure as for analyzing the RNA sequencing data. Genes with adjusted pvalues less than 0.05 and fold changes over 1.5 folds were considered as the ones with differential promoter accessibility.

GO/hallmark signature enrichment analysis

The gene symbols were mapped to GO terms/hallmark gene sets using either R packages GO.db, AnnotationDbi, and org.Mm.e.g.db, or based on the MSigDB collections [START_REF] Liberzon | The Molecular Signatures Database (MSigDB) hallmark gene set collection[END_REF]. Gene sets with at least 10 genes in background (i.e. all expressed genes) were tested for enrichment in DEG using the GOseq method provided in the R package goseq [START_REF] Young | Gene ontology analysis for RNAseq: accounting for selection bias[END_REF]. The raw p-values were then adjusted using the Benjamini-Hochberg (BH) procedure. Gene set enrichment analysis (GSEA) (67) was performed using the GSEA JAVA interface (version 4.0.3) available at https://www.gseamsigdb.org/gsea/.

Computational analysis of single-cell RNA-sequencing data

FASTQ files were processed by 10x Genomics Cell Ranger version 3.1.0 using the reference transcriptome mm10-3.0.0. The resulting filtered feature-barcode matrices were used for analyses in R. The complete analysis workflow in R can be reproduced by running the scripts provided on GitHub.

A renv.lock file is provided to reproduce the R environment with all required packages in the used versions. During the analysis in R, single cell data were stored in two main object types: Seurat-and SingleCellExperiment object [START_REF] Hao | Integrated analysis of multimodal single-cell data[END_REF][START_REF] Amezquita | Orchestrating single-cell analysis with Bioconductor[END_REF]. The count matrices were processed in R using version 4.0.1 of the Seurat software. For all samples, cells with fewer than 200 detected genes were excluded and only genes that were detected in at least three cells were retained. Cells were further filtered in a sample-specific manner based on a lower and upper threshold of the number of detected genes and the percentage of counts assigned to mitochondrial transcripts. Count data of all samples were normalized using the SCTransform function [START_REF] Hafemeister | Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression[END_REF] of the Seurat package. For each gene in each cell, the function computes the Pearson residual from a generalized linear model in which sequencing depth is used as a covariate. All genes with a variance of model residuals larger than 1.3 were selected for dimensionality reduction and principal component analysis (PCA) was conducted using Seurat's RunPCA function with default parameters. The number of principal components (PC) used for downstream analysis was estimated by ranking the PC based on their standard deviation and selecting the top n PC above the strong drop in standard deviation. Cells were clustered by first computing a shared-nearest-neighbor graph based on Euclidean distance between cells in PCA space (FindNeighbors function), followed by the identification of modules of the graph (FindClusters function, using the Louvain algorithm). UMAP embeddings were generated using the RunUMAP function. In some cases, the n.neighbors and min.dist parameters were adjusted to preserve the global connectivity of the cell populations.

To annotate each cell, we identified the reference cell type that had highest correlation with the cell's raw gene counts, using SingleR [START_REF] Aran | Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage[END_REF]. Raw bulk RNA-seq read count data of reference populations were downloaded from two databases: ImmGen (GSE109125, GSE122108; (71)) and

Haemosphere

(Haemopedia-Mouse-RNASeq_raw.txt and Haemopedia-Mouse-RNASeq_samples.txt; [START_REF] Choi | Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans[END_REF]). Ensemble gene IDs in the Haemosphere data set were translated to symbols using the AnnotationHub software [START_REF] Morgan | AnnotationHub: Client to access AnnotationHub resources[END_REF]. Only untreated samples which were purified from total bone marrow were used. Additionally, data from T cells and NKT cells isolated from other tissues were extracted from GSE109125 as those cell types were not available from total bone marrow. Only genes detected in all reference and single-cell data were used for the correlation analysis. The data of the reference samples were normalized by first dividing each read count by the length of the respective gene (EDASeq; [START_REF] Risso | GC-content normalization for RNA-Seq data[END_REF]) and then multiplying it with a sample-specific factor to ensure that the normalized values of each sample sum up to 10 6 . The obtained transcript per million (TPM) values were log2-transformed to allow gene selection in SingleR. Samples of populations including multiple other cell types were removed to avoid inconclusive annotations.

The pruned labels returned by SingleR were used to annotate the cells.

To assign cells to a particular cell cycle phase, a two-dimensional UMAP embedding of the respective populations was computed based on sequencing-depth corrected log-transformed counts of S-phase and G2M-phase-specific genes. For this purpose, gene lists provided by the Seurat package were used. In the obtained UMAP embedding, cells were arranged in a circular shape and annotated by cell cycle phase using Seurat's CellCycleScoring function. As the boundary between G0/G1 and S-phase was very fuzzy, intermediate cells were classified as G1Scells. Intermediate cells were defined as those cells, with a UMAP-based neighborhood (n=200) in which the smallest category (either G1 or S) made up more than 5% of the neighborhood.

To compare cell-type frequencies between wild type and Usp22 KO, each total bone marrow sample (one WT and one KO) was initially processed individually until potential doublets were removed using the scDblFinder package [START_REF] Germain | Doublet identification in single-cell sequencing data using scDblFinder[END_REF]. Then both samples were pooled and reprocessed including normalization. Cells were annotated by SingleR and labels were adjusted by summarizing some categories or adjusting them to cluster boundaries. Adjustment to cluster boundaries was performed to improve separation between NK and T cells and between B cells and CLP (CLP in the B cell cluster were relabeled as B cells). For each condition, cells were sampled with replacement. The sample size was set equal to the original number of cells in the respective sample. The log2(fold-changes) of the observed cell-type frequencies were computed between the conditions. Sampling and computation of fold-changes were repeated 10,000 times and 95% confidence intervals were estimated.

Branching events were resolved in MPP using diffusion modelling: Until stated, data of both conditions were processed separately. Cells were annotated by SingleR to identify MPP with GMP-, CLP-or MEP-like transcriptome. Effects of cell cycle were regressed out during normalization and the Pearson residuals of genes with a residual variance larger than 1.3 were used for the next step. Additionally, few cells annotated as NK, T, preT, proB, basophil, eosinophil, dendritic cell or monocyte were excluded as it was important to include only cells forming a continuum of transcriptomic states. The fateBias function of the FateID package [START_REF] Herman | FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data[END_REF] was used to classify each retained MPP as LMPP, GMP-or MEP-biased starting from the most mature cells identified by SingleR annotation. In each iteration, the fateBias function internally trained a random forest model to classify cells based on expression values of lineage-specific genes. The training started with the annotated endpoint cells and iteratively assigned more undifferentiated cells to a branch. Genes that were most important for classification during the first 25% of all iterations were extracted from the trained models using the impGenes function. Genes important during later iterations were not used as it can be expected that classification accuracy decreases for cells that show less lineage-bias. Only genes selected as lineage markers in both conditions were selected for the next steps. Selected genes (n=45) contained many known markers of lineage specification like Mpo, Flt3, Dntt and Elane (same genes were used for the analysis of the replicated experiment). After the extraction of lineage-specific genes, data of both conditions were pooled and normalization was repeated without regressing out effects of cell cycle. Sequencingdepth corrected, log-transformed counts of lineage-specific genes were used for computing a diffusion map using the destiny package [START_REF] Angerer | destiny: diffusion maps for large-scale single-cell data in R[END_REF]. After removing few extreme cells on diffusion component (DC) 3 (annotated as Pre-CFU-E), the diffusion map was recomputed. The first three dimensions resolved all branching events of interest. Clustering was performed on the cells' first three diffusion coordinates. The MEP-biased branch, which had the smallest distance to MPP that were annotated as HSC by SingleR, was defined as root cluster whereas the branches with GMPbiased MPP and LMPP were defined as tip clusters. Trajectories were inferred from the root to the tip clusters applying the Slingshot Software (31) with default parameters. Cells which wereaccording to pseudo-time -located between the tip of the MEP branch and the center of HSC-like cells, were labeled as MEP-biased cells. The remaining cells were labeled as GMP-biased MPP or LMPP if they were only assigned to one of the two trajectories. Cells assigned to both trajectories were annotated as unbiased MPP.

To perform gene expression comparisons between MPP of both conditions while accounting for differential cell distributions along the differentiation trajectories, MPP were sampled in the following manner: Only wild type cells whose first nearest neighbor in the diffusion embedding was a KO cell were retained in the embedding. KO cells were retained if they were the first neighbor of at least one WT cell and could also be sampled multiple times if they were a direct neighbor of more than one WT cell. 81.8% of the retained KO cells were only sampled once and only 1.5% were sampled more than two times with a maximum of four. This suggests that results were unlikely to be distorted by strong overrepresentation of individual cells. To assess the effect of sampling, results were always compared to results obtained when using the original populations.

Overall, the results were comparable.

To analyze differential expression of genes indicating lineage priming, those were first identified by a Wilcoxon test: GMP-biased MPP or LMPP were compared to all other MPP subsets and only genes that were significantly differentially expressed in all pairwise comparisons were defined as LMPP or GMP-bias signature genes (adjusted p-value < 0.05). Genes were filtered by a fold change threshold of 1.25 as subtle but significant changes should also be considered. For each cell, module scores were computed for both signatures using Seurat's AddModuleScore function. The same signatures were used to analyse the replicated experiment.

Gene Set Enrichment Analysis (GSEA) was conducted using the gseGO function of the ClusterProfiler package [START_REF] Wu | clusterProfiler 4.0: A universal enrichment tool for interpreting omics data[END_REF]. Significant (adjusted p-value < 0.05) Gene Ontology (GO) terms of the category "Biological Processes" were grouped based on overlaps of the corresponding gene sets: Two GO terms were added to the same group if their corresponding gene sets had a Jaccard similarity of at least 0.3. Afterwards, only GO groups with more than 70 leading edge genes in total were retained and manually annotated. For LT-HSC a threshold of 100 leading edge genes was used. Those thresholds were adjusted in the replicated experiment to retain GO groups of comparable size. The GO group containing terms related to immunity was further subdivided using hierarchical clustering based on Jaccard similarity. For GSEA of MPP, the MPP populations which were corrected for differential cell distribution along differentiation trajectories were used. For LT-HSC, the complete wild type and KO population was used.

MPP subset-specific differential expression analyses between genotypes were done using a Wilcoxon test implemented in Seurat's FindMarkers function. To reduce shrinkage of fold changes in genes with low average expression, the default pseudo-count of 1 was lowered to 0.1.

Genes with a log2(fold change) > 0.25 or < -0.25 and an adjusted p-value < 0.05 were considered differentially expressed. 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H2-Q7 Gadd45gip1 Syce2 Dnaja1 Cd74 Hsp90aa1 Ccl5 Stxbp4 H2-Ab1 H2-K1 Stat1 Hspa8 Rbm3 B2m H2-D1 Hspa5 H2-Aa Plac8 Fabp5 Dad1 Dynll1 Atp5b Hsp90ab1 Dntt Srsf7 Ppid Pdcd4 Ighm Kit Phf14 Glul Gcnt2 Il12a Mef2c Rpl38 Lmo2 -0.4 -0.2 0
LT-HSC ST-HSC unbiased MPP LMPP GMP-biased MPP MEP-biased MPP Ctsg Mpo Prtn3 Rab44 Calr Ap3s1 Sell Pgam1 Ccl9 F630028O10Rik Ms4a6c Mcpt8 Gng12 Atp8b4 Igsf6 H2afj Rrm2 Hp Tspo Cd48 Pclaf Erp29 Lgals1 Anxa3 Sdf2l1 Zeb2 Elane Mapkapk2 Msrb1 Tyrobp Cycs F13a1 Slpi Ly6c2 Ctsz Alas1 Irf8 -0.6 -0.
LT-HSC ST-HSC unbiased MPP LMPP GMP-biased MPP MEP-biased MPP Myl10 Dntt Ighm Flt3 Arpp21 Mef2c Ddx4 Satb1 Wfdc17 Il12a Bcl11a Mtdh Egfl7 Tbxa2r Tcf4 Il7r AA467197 Notch1 Klf3 Ptp4a3 Lck Smad7 Ikzf1 Sdc4 Camk1d Hoxa9 Foxp1 Wfdc18 Cmah Cd33 Lsp1 Xrcc6 Ctr9 Jakmip1 H2-Ob Gpr171 Maml3 Pan3 Med13l Xpc Lztfl1 Cox6a2 Ifi27l2a Nav1

GMP-biased signature

LT-HSC ST-HSC unbiased MPP LMPP GMP-biased MPP MEP-biased MPP Ctsg Mpo Prtn3 Rab44 Calr Ap3s1 Sell Pgam1 Ccl9 F630028O10Rik Ms4a6c Mcpt8 Gng12 Atp8b4 Igsf6 H2afj Rrm2 Hp Tspo Cd48 Pclaf Erp29 Lgals1 Anxa3 Sdf2l1 Zeb2 Elane Mapkapk2 Msrb1 Tyrobp Cycs F13a1 Slpi Ly6c2 Ctsz Alas1 Irf8 -0.2 0 0.2 0.4 log2FC (KO/WT) LMPP signature LT-HSC ST-HSC unbiased MPP LMPP GMP-biased MPP MEP-biased MPP Myl10 Dntt Ighm Flt3 Arpp21 Mef2c Ddx4 Satb1 Wfdc17 Il12a Bcl11a Mtdh Egfl7 Tbxa2r Tcf4 Il7r AA467197 Notch1 Klf3 Ptp4a3 Lck Smad7 Ikzf1 Sdc4 Camk1d Hoxa9 Foxp1 Wfdc18 Cmah Cd33 Lsp1 Xrcc6 Ctr9 Jakmip1 H2-Ob Gpr171 Maml3 Pan3 Med13l Xpc Lztfl1 Cox6a2 Ifi27l2a Nav1
S12 B A C D E LMPP Experiment 1 Experiment 2 Hbb-bt Elane H2-Q7 F13a1 Prtn3 Mpo Hspa5 Ly6c2 Lgals1 H2-K1 Cd74 H2-Ab1 Plac8 B2m Dynll1 Dad1 H2-Aa Gbp3 H2-Q6 Stat1 Ly6e H2-D1 Srsf7 Ldha Sdf2l1 Slc25a5 Cacybp Ms4a6c Chchd10 H2-Eb1 Rpgrip1 Ctsz Dnaja1 Dbi Ly86 Manf Tmed3 Hsp90b1 Hp Srm Hspd1 Psmb10 Erp29 Nme1 Bex6 Pnp Tspo Pgam1 Atp5g3 Tomm5 Gapdh Cyba Cycs Ndufb8 Prss57 Igsf6 Igfbp4 Agpat5 Casp1 Ssr2 Igtp Slc4a8 Rangrf Pycard Gusb Rexo2 Eny2 Psma4 Psma1 Gria3 Tifab Oat Mrpl16 Cd68 Gm26782 Dhx29 Ddx4 Afp Gng11 Emcn Tspan6 Coro2a Ogt Vldlr Baz2b Syf2 Pan3 Cd27 Git2 Sesn1 Paqr5 Cd34 Calcrl Cbx3 Ubald2 Zfand5 H2afv Zyx Foxp1 Glul Angpt1 Zfp608 Dapp1 Meis1 Car2 Otos Ptpre Tspan13 Ypel3 Clec2d Rgs18 Gcnt2 Nedd4 Samsn1 Usp22 Sox4 H2afy Msi2 Phf14 Mef2c Marcks Adgrl4 Lmo2 Wfdc17 Ctla2a Hlf Malat1 Experiment 1 Experiment 2 Hbb-bt H2-Q7 H2-Ab1 Iigp1 Stat1 Dynll1 Plac8 Apoe Top2a Tubb4b H2-Q6 Cks2 Smim5 H2afz H2-K1 Hsp90aa1 Srsf7 Hmgb3 Cacybp Slc25a5 Rbm3 Ldha H2-Aa Dad1 Srm Hmgb2 Cd74 Cks1b Ffar2 Tyms Nme1 Ifi47 Rfc5 Hspd1 Psmb9 Gbp3 H2-D1 Lsm2 Atp5g3 Hnrnpab Prdx1 Rpgrip1 Ranbp1 Swi5 Gm4951 Atp5g1 Pcp4l1 Padi4 Ccl4 Paqr5 Aldh2 Marcks Serpinb1a Fam107b Basp1 Msi2 Usp22 Vldlr Zfand5 Glul Otos Gm19590 Pim1 Adgrl4 Malat1 Lmo2 Gcnt2 Sox4 Hlf Experiment 1 Experiment 2 -0.5 0 0.5 1
Hbb-bt H2-Q7 H2-Ab1 Cd74 H2-Aa Dynll1 H2-Q6 Stat1 Plac8 Srsf7 Slc25a5 H2-K1 Nme1 Cacybp Hspd1 Ldha Srm Gbp3 Rpgrip1 Dad1 Otos Paqr5 Zfand5 Marcks Msi2 Vldlr Glul Usp22 Gcnt2 Lmo2 Malat1 Hlf
RNA

regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of cell cycle phase transition regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle regulation of mitotic cell cycle

skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system morphogenesis skeletal system purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly chaperone-mediated protein complex assembly protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization protein-containing complex localization binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida binding of sperm to zona pellucida negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process edge if their corresponding gene sets have a Jaccard similarity > 0.3. The threshold of the minimum number of "leading edge" genes per GO group was adjusted to 56 to retain GO groups of sizes comparable to experiment 1. Those genes drive the enrichment scores. ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process ATP metabolic process mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly mitochondrial respiratory chain complex assembly response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor response to growth factor oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation oxidative phosphorylation cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain respiratory electron transport chain cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus cellular response to growth factor stimulus NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly NADH dehydrogenase complex assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly mitochondrial respiratory chain complex I assembly ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing ncRNA processing energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis embryonic morphogenesis purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process purine ribonucleotide biosynthetic process response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta response to transforming growth factor beta ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process

cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle meiotic cell cycle

nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle positive regulation of cell cycle meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process meiotic cell cycle process

RNA

regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint cell cycle checkpoint

protein
endocytosis

cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle mitotic cell cycle cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission organelle fission

sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation sister chromatid segregation cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process purine nucleotide metabolic process

mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division

transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway transforming growth factor beta receptor signaling pathway tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing tRNA processing mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport mitochondrial ATP synthesis coupled proton transport purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport proton transmembrane transport embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis embryonic organ morphogenesis cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly cytochrome complex assembly small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process small molecule biosynthetic process ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis ribonucleoprotein complex biogenesis cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly cellular protein-containing complex assembly

cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division cell division

protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly protein-DNA complex assembly negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process negative regulation of mRNA metabolic process chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling chromatin remodeling ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex subunit organization ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus ribonucleoprotein complex export from nucleus negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process negative regulation of mRNA catabolic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process purine nucleoside triphosphate biosynthetic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process cellular nitrogen compound catabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process amide biosynthetic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process heterocycle catabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process purine-containing compound metabolic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process ribonucleoside triphosphate biosynthetic process regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation regulation of sister chromatid segregation purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process carboxylic acid metabolic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process negative regulation of apoptotic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process RNA catabolic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process peptide biosynthetic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process oxoacid metabolic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process organophosphate biosynthetic process negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of mRNA processing negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of apoptotic signaling pathway mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization mitochondrial membrane organization negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death negative regulation of programmed cell death organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process organic acid biosynthetic process

interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between

  6C, left panel; fig. S9F); similar terms were also enriched in LT-HSC (fig. S15; fig. S16; fig. S17).

  of C5/C5a, CCL1, CCL2, CCL3, CCL4, CCL5, CCL11, CCL12, CCL17, CXCL1, CXCL2, CXCL9, CXCL10, CXCL11, CXCL12, CXCL13, G-CSF, GM-CSF, sICAM-1, IFN-g, IL1-a, IL-1b, IL-1ra, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-10, IL-12p70, IL-13, IL-16, IL-17, IL-23, IL-27, M-CSF, TIMP-1, TNF-a and TREM-1 in bone marrow fluid were determined using the ProteomeProfiler mouse cytokine array panel A (R&D Ssystems) according to the manufacturer's instructions. Protein concentration of bone marrow fluid was determined using BCA assay, and equal amounts of protein were used for cytokine detection.

  were prepared using GraphPad Prism or R. Statistical details, including definition of center and precision measures, number of replicates per genotype (n) as well as statistical tests used can be found in the figure legends. Statistical significance was tested using Student's t-test, Mann-Whitney test, one-way ANOVA with Sidak's post-hoc test or two-way ANOVA with Sidak's posthoc test. Data and materials availability: Bulk RNA sequencing, single cell RNA sequencing, ChIP sequencing as well as ATAC sequencing data have been deposited in GEO under the following accession number: GSE212758. Scripts for the analysis of single cell RNA sequencing data are available on GitHub (https://github.com/jome1994/Analysis_of_single_cell_data_for_Usp22_project/tree/v1.0.1) and Zenodo (https://zenodo.org/record/7011238#.Y1v59y1h3GK). All data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.

Figure captions:Fig. 1 .

 1 Figure captions:

Fig. 2 .

 2 Fig. 2. Enhanced myelopoiesis from Usp22 KO bone marrow. (A) Flow cytometric analysis of wild type and Usp22 KO bone marrow cells stained for CD11b and Gr-1 (pre-gated on single live cells). (B) Gr-1 median fluorescence intensity (MFI) of CD11b + Gr-1 + bone marrow cells (gated as shown in A) from wild type and Usp22 KO mice normalized to wild type (n=12 mice per genotype in 4 experiments). (C) Absolute numbers of Ly6C low and Ly6C high monocytes (both Lineage - CD45 + Ly6G -CD115 + ), and macrophages (Lineage -CD45 + Ly6G -CD115 -F4/80 + SSC low ) in the bone marrow of wild type and Usp22 KO mice (n=6 mice per genotype in 2 experiments). (D)Schematic of fate mapping of LT-HSC as described in[START_REF] Busch | Fundamental properties of unperturbed haematopoiesis from stem cells in vivo[END_REF]). Tamoxifen administration leads to the heritable induction of YFP expression in LT-HSC (orange cells, middle panel). Through

Fig. 3 .

 3 Fig. 3. Usp22 deficiency drives enhanced myelopoiesis in a cell-intrinsic manner. (A) Experimental setup for the generation of mixed bone marrow chimeras. (B) Contribution of wild type or Usp22 KO bone marrow cells to B cells (B220 + ) and myeloid cells (CD11b + Gr-1 + ) in the bone marrow of recipient mice 20-22 weeks after transplantation (n=6 mice). (C) Ratio of myeloid cell chimerism and B cell chimerism in the bone marrow of mixed bone marrow chimeras comparing wild type and Usp22 KO donors (n=28-32 mice per genotype in 5 experiments). (D) Gr-1 MFI of the indicated donor CD11b + Gr-1 + myeloid cells (gated as shown in Fig. 2A) from mixed bone marrow chimeras described in A. All values were normalized to CD45.2 + wild type myeloid cells (n=6 mice per genotype; data representative of 1 out of 4 experiments). (E) Transplantation of wild type or Usp22 KO CMP together with total bone marrow competitor cells into lethally irradiated recipients. (F+G) Relative contributions of wild type and Usp22 KO CMP to CD11b + myeloid cells in peripheral blood over time (F), and in bone marrow and spleen (10 days after transplantation) (G) (n=5 mice per genotype; representative of 1 out of 3 experiments. (H) Absence of lineage markers CD11b (myeloid) and B220 (B lineage) on sorted wild type and Usp22 KO lineage marker -Sca-1 + Kit + (LSK) cells before in vitro differentiation (top panels), and CD11b versus B220 expression 3 weeks after in vitro differentiation (bottom panels) (representative of 4 experiments). (I) Relative proportions of B220 + B cells and CD11b + myeloid cells (gated as shown in bottom row of H) 3 weeks after in vitro differentiation of wild type or Usp22 KO LSK. Each dot represents the mean of 3-5 cultures from one donor mouse. Graph represents the results from 5 mice per genotype analyzed in 4 experiments. (J) In vitro differentiation (as in H), mixing either wild type or Usp22 KO LSK (both CD45.2 + ) with wild type competitor LSK (CD45.1 + ). After 3 weeks, cells were gated for CD45.1 versus CD45.2 (see fig.

Fig. 4 .

 4 Fig. 4. Usp22 deficiency enhances anti-bacterial innate immunity. (A) Quantification of Listeria monocytogenes CFU in blood, spleen, liver and brain of wild type and Usp22 KO mice three days post-infection (n=13 mice per genotype in 2 experiments). Data points at 10 0 represent mice for which we did not detect any bacteria. (B) Flow cytometric assessment of the phagocytic activity of ex vivo purified bone marrow neutrophilic granulocytes (Ly6G + ) derived from wild type and Usp22 KO mice incubated for two hours with fluorescently labeled (pHrodo red) E. coli particles. (C) pHrodo median fluorescence intensity (MFI) of bone marrow neutrophilic granulocytes from wild type and Usp22 KO mice incubated with fluorescent E. coli particles described in B (n=2 replicates from 2 mice per genotype; data shown are from 1 out of 2 experiments). (D) E.coli CFU counts in co-cultures of DH5a E.coli cells with wild type or Usp22 KO neutrophils normalized to the input number of bacteria (dashed line). The bacteria-only control (w/o Gran) is an estimate for uninhibited bacterial growth during the culture period (n=5-7 mice per genotype in 2 experiments). (E) TNF-a concentration in the supernatant of ex vivo purified wild type or Usp22 KO bone marrow neutrophils cultured in the presence or absence of LPS. Concentrations were normalized to those of unstimulated wild type neutrophils (n=5 mice per genotype in 3 experiments). Median ± interquartile range (A), mean ± s.d. (C-E). * p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001; n.s. (not significant) by unpaired, two-tailed Mann-Whitney test (A), two-way ANOVA with Sidak's post-hoc test (C, E), or one-way ANOVA with Sidak's post-hoc test (D).

Fig. 5 .

 5 Fig. 5. Loss of Usp22 enhances inflammatory gene expression in HSPC. (A) Volcano plot showing log2 fold change (FC) in expression and the associated -log10 p-value of individual genes (dots) in Usp22-deficient LSK based on RNA sequencing. Significantly differentially expressed genes (DEG) (p<0.05, FC ³ 1.5 or FC £ 1/1.5) are highlighted in orange. (B) GO term enrichment analysis of DEG upregulated in Usp22 KO versus wild type LSK. (C) Heatmap showing the

Fig. 6 .

 6 Fig. 6. Loss of Usp22 results in myeloid transcriptional priming. (A) Diffusion maps of wild type and Usp22 KO MPP based on scRNA-seq (experiment 1 shown; experiment 2 in fig. S9A). (B) Transcriptome-based cell cycle distribution of wild type and Usp22 KO MPP subsets (n=1 mouse per genotype in 1 experiment). (C) Expression (log2 fold change) of genes driving the enrichment of the indicated GO groups 1-13 (for GO term derivation, see fig. S13) (left panel:genes contributing to any GO group; right panel: genes contributing to the GO group "Immune processes"). Only genes with a fold change > 1.2 or < 0.83 are shown. Grey fields represent genes not contributing to the enrichment of the respective GO group.

Fig. 7 .

 7 Fig. 7. Usp22 deficiency increases H2B monoubiquitination at ISG loci. (A) Western blot analysis for H2B and H2Bub1 in bone marrow LSK, and splenic B (CD19 + B220 + ), T (both CD4 + and CD8a + cells) and myeloid cells (CD11b + ) from wild type and Usp22 KO mice (n=8 mice per genotype). (B) Volcano plot showing log2 fold change (FC) in gene body H2Bub1 levels and the associated -log10 p-value of individual genes (dots) upon Usp22 deletion in LSK based on ChIP sequencing. Significantly differentially ubiquitinated genes (DUG) (p<0.05, FC ³ 1.5 or FC £ 1/1.5) are highlighted in orange (n=2 replicates per genotype). (C) GO term enrichment analysis

  Figure 1

  Figure 4

  Figure 6

  Figure 7

  Equal amounts of total RNA were converted into double-stranded cDNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing -HV kit according to the manufacturer's instructions. Sequencing libraries were prepared with the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer's instructions with the following modifications. 10 µl of adapter-ligated double-stranded cDNA were amplified using NEBNext Multiplex Oligos for Illumina (25 µM primers), NEBNext High-Fidelity 2x PCR Master Mix and 15 cycles of PCR. Libraries were validated using an Agilent 2200 TapeStation and a Qubit fluorometer. 50 bp single-read sequencing of pooled libraries was performed on an Illumina HiSeq 2000 v4.

Fig. S1 .

 S1 Fig. S1. Characterization of hematopoiesis in Usp22 KO mice. (A) Usp22 mRNA expression levels in the indicated hematopoietic cell types based on publicly available bulk RNA sequencing

  Figure S1 A B Vav1-Cre tg+ Usp22 fl/fl

Fig. S3 .

 S3 Figure S2

  Figure S3A

Fig. S4 .

 S4 Fig. S4. Cell-autonomous emergency myelopoiesis in Usp22-defcient mice. (A) Expression of Kit and Ly6G resolves stages of myelopoiesis, i.e. myeloblasts (MB), promyelocytes (PM),

  Figure S4A

Fig. S6 .

 S6 Figure S5

  Figure S6A

  populations (gated as shown in A) in the bone marrow of wild type and Usp22 KO mice (n=12 mice per genotype in 4 experiments). (C) Relative proportions of early CD43 + and late CD43 -B cell progenitors within the B220 + population of wild type and Usp22 KO mice (n=12 mice per genotype in 4 experiments). (D) Percentage of Annexin V + apoptotic cells within the indicated B cell progenitor populations of wild type and Usp22 KO mice (n=11 mice per genotype in 4 experiments). (E) Heatmap showing the expression of Myc target genes in primary pre-B cells (fraction C) from wild type and Usp22 KO mice. (F) Experimental setup for the generation of mixed bone marrow chimeras. (G) Relative proportions of early CD43 + and late CD43 -B cell progenitors within the B220 + population of CD45.2 + test and CD45.1 + competitor cells in mixed bone marrow chimeras (n=6 mice per genotype, data representative for 1 out of 2 experiments). (H) Absolute numbers of CD19 + B220 + splenic B cells in wild type and Usp22 KO mice (n=7-9 mice per genotype in 3 experiments). (I) Absolute numbers of the indicated splenic B cell subsets in wild type and Usp22 KO mice (n=7 mice per genotype in 3 experiments). Mean ± s.d. (B-D, G-I).* p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001; n.s. (not significant) by unpaired, two-tailed Student's t-test.

Fig. S7 .

 S7 Fig. S7. Usp22 deficiency drives inflammatory gene expression. (A) Gene set enrichment analysis (GSEA) plots comparing wild type and Usp22 KO LSK for IFN-a target genes (top panel) and IFN-g target genes (bottom panel). (B) Expression levels of all differentially expressed

6

  Figure S7A C B

  Fig. 5D) based on DEG shown in Fig. 5A. Enrichment of upregulated and downregulated genes shown in left and right panels, respectively.

Fig. S8 .

 S8 Fig. S8. Analysis of Usp22 KO HSPC for ISG and Sca-1 expression. (A) MHC II median fluorescence intensity (MFI) in wild type and Usp22 KO stem and progenitor cell populations (n=8 mice per genotype in 3 experiments). (B) qRT-PCR analysis for Stat-1 in wild type and Usp22 KO

E

  Fig. S10. Expression of NK cell-and myeloid lineage-specific transcriptions factors in Usp22KO MPP. Average normalized mRNA read counts of the indicated transcription factor genes in

Fig. S11 .

 S11 Fig. S11. Usp22 deficiency enhances myeloid transcriptional priming in HSPC. (A+C) Violin plots showing cell scores based on the average expression of genes specifically upregulated in GMP-biased MPP (left) or LMPP (right). Scores are compared between wild type and Usp22 KO within each MPP subset (top) and within LT-and ST-HSC (bottom). Results were obtained from two independent experiments (experiment 1 is shown in A, experiment 2 is shown in C). (B+D) Heatmaps showing the log2 fold change in expression of genes used for scores in A and C. Grey

  Figure S11B A

4 -

 4

  Fig. S12. Transcriptome changes in Usp22-deficient MPP subsets. (A-D) Heatmaps showing the log2 fold change in expression of DEG in unbiased MPP (A), LMPP (B), GMP-biased MPP

Figure

  Figure S12B A C D

  and MEP-biased MPP (D) comparing Usp22 KO and wild type mice. (E) Heatmap showing the log2 fold change in expression of consensus DEG of all MPP subsets shown in A-D. Log2 fold changes shown are based on all MPP. For gene lists, see also Supplementary data file S2.

Fig. S13 .

 S13 Fig. S13. GO enrichment analysis in Usp22 KO MPP (experiment 1). Graph of GO terms significantly enriched in Usp22 KO MPP (adjusted p-value < 0.05). Terms are connected by an edge if their corresponding gene sets have a Jaccard similarity > 0.3. Only groups of GO terms

Figure S13

  Figure S13

  antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II

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  positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response positive regulation of acute inflammatory response

  organization mitochondrion organization positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of myeloid leukocyte cytokine production 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response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development circulatory system development negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator negative regulation of 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intrinsic apoptotic signaling pathway by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport mitochondrial ATP synthesis coupled electron transport unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process unsaturated fatty acid biosynthetic process

  regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response regulation of immune response transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response cytokine production involved in immune response

  Fig. S14. GO enrichment analysis in Usp22 KO MPP (experiment 2). Graph of GO terms significantly enriched in Usp22 KO MPP (adjusted p-value < 0.05). Terms are connected by an

  mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle processmitotic cell cycle process mitotic cell replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication regulation of DNA replication

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  establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound sensory perception of sound antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen via MHC class I

  DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process RNA-dependent DNA biosynthetic process

  cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition

  positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition positive regulation of cell cycle phase transition

  positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation

  mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of cell death regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome regulation of establishment of protein localization to chromosome cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication cell cycle DNA replication establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere establishment of protein localization to telomere positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process positive regulation of cell cycle process presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen via MHC class II mitotic

  positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process positive regulation of immune effector process

  DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation DNA strand elongation regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity positive regulation of telomerase activity ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process ribose phosphate metabolic process regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle phase transition nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process nucleoside triphosphate biosynthetic process positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication positive regulation of DNA replication regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of DNA-dependent DNA replication regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of leukocyte mediated immunity nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication nuclear DNA replication protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication regulation of viral genome replication positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle positive regulation of viral life cycle of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of

  establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication positive regulation of viral genome replication regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress regulation of cellular response to stress blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development blood vessel development positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition

  DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiation DNA replication initiationpurine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process purine-containing compound biosynthetic process protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane protein insertion into membrane anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide biosynthetic process purine nucleotide localization to mitochondrion; protein import/export to/from nucleus; nuclear RNA transport immune response; response to interferon-gamma; response to cytokine Immune processes

Fig. S15 .

 S15 Fig. S15. GO enrichment analysis in Usp22 KO LT-HSC (experiment 1). Graph of GO terms significantly enriched in Usp22 KO LT-HSC (adjusted p-value < 0.05). Terms are connected by an edge if their corresponding gene sets have a Jaccard similarity > 0.3. Only groups of GO terms with more than 100 unique "leading edge" genes in total are shown. Those genes drive the enrichment scores.

  Figure S15

  establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion

  DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication DNA-dependent DNA replication of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport regulation of vesicle-mediated transport

  transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway transmembrane receptor protein serine/threonine kinase signaling pathway purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process purine ribonucleoside triphosphate biosynthetic process

  positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis positive regulation of endocytosis mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane protein insertion into mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane

  endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis receptor-mediated endocytosis regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation regulation of mitotic sister chromatid separation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister chromatid segregation mitotic sister of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus regulation of cellular response to growth factor stimulus

  metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle metaphase/anaphase transition of cell cycle mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone mitochondrial electron transport, NADH to ubiquinone chromosome separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle regulation of metaphase/anaphase transition of cell cycle break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination double-strand break repair via homologous recombination

  Fig. S16. GO enrichment analysis in Usp22 KO LT-HSC (experiment 2). Graph of GO terms significantly enriched in Usp22 KO LT-HSC (adjusted p-value < 0.05). Terms are connected by an edge if their corresponding gene sets have a Jaccard similarity > 0.3. The threshold of the

  Figure S16

  cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus

  process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process mitotic cell cycle process

  complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization protein-DNA complex subunit organization regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process positive regulation of DNA biosynthetic process

  rRNA processing energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds energy derivation by oxidation of organic compounds DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change DNA conformation change regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process regulation of DNA metabolic process cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle regulation of cell cycle

  mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition mitotic cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle phase transition cell cycle

  cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus cellular response to cytokine stimulus ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport ATP synthesis coupled electron transport electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain electron transport chain positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process positive regulation of DNA metabolic process double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair double-strand break repair establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle establishment of protein localization to organelle regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process regulation of cell cycle process ncRNA localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion establishment of protein localization to mitochondrion

  response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium response to bacterium positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle positive regulation of G2/M transition of mitotic cell cycle regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process regulation of viral process

  energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient energy coupled proton transport, down electrochemical gradient ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport ATP synthesis coupled proton transport chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription chromatin organization involved in negative regulation of transcription ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process ATP biosynthetic process regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation regulation of chromosome segregation anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure homeostasis anatomical structure cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation positive regulation of cell population proliferation innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response innate immune response chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription chromatin organization involved in regulation of transcription regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition regulation of cell cycle G2/M phase transition

  positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division positive regulation of nuclear division spindle

  posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression posttranscriptional regulation of gene expression regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of nucleocytoplasmic transport regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus regulation of response to DNA damage stimulus positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of transferase activity positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process positive regulation of viral process negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization negative regulation of organelle organization nucleosome translation translation translation translation translation translation translation regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of symbiotic process regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing regulation of mRNA processing response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus response to abiotic stimulus aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process aromatic compound catabolic process regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death regulation of programmed cell death mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization mitotic spindle organization

  regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization regulation of chromosome organization negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing negative regulation of RNA splicing mRNA

  regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation regulation of translation meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I cell cycle process meiosis I localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane establishment of protein localization to mitochondrial membrane regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation regulation of cell population proliferation DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint DNA integrity checkpoint mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitotic sister chromatid separation mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport mitochondrial transmembrane transport

  response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to external biotic stimulus response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to other organism response to process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process small molecule metabolic process negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization negative regulation of chromosome organization regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of viral life cycle regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition regulation of mitotic metaphase/anaphase transition negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of gene expression, epigenetic negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle negative regulation of cell cycle positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import positive regulation of protein import

Fig. S18 .

 S18 Fig. S18. Usp22 deficiency increases H2B monoubiquitination at ISG loci. (A+B) Average H2Bub1 ChIP sequencing signal in wild type and Usp22 KO LSK across gene bodies of all genes (A), of non-expressed genes (B, top panels), and of genes highly expressed in LSK (B, bottom panels). (C) H2Bub1 ChIP sequencing tracks of Cd200 (top panel) and Fgd5 (bottom panel) loci

leukocyte-med. cytotox. def. resp. to bacterium cell. resp. to IFN-gamma cell. resp. to IFN-beta

											Xcl1 Cd160 Klre1	1 z-score
											Ccl5
											Klrk1
											Cd74 Sh2d1a	0.5
											Txk
											Gzmm
											Ifi205 H2-Ab1	0
											Crtam
											Klrb1c
											Gbp3
											Cd226	-0.5
											Ifi211
											Klrb1b
											Ifi209
											Card9	-1
											Stxbp4
											Iigp1
											Elane
											Gm4951
											Tyrobp
											Gzmb
											Stat1
											Zbp1
											Slamf8
											F830016B08Rik
											Gm12185
											Irf8
											Trem3
											Casp1
											Nlrc5
											Anxa3
											Rab7b
											Fcgr3
											Tnfsf8
											Ifit3
											Igtp
											Gbp2
											Prf1
											Mpo
											Ctsg
											Hp
											Gbp4
											Unc93b1
											Ffar2
											Gbp5
											Plac8
											Prg2
											Treml4
											Tspan6
											Cd4
											Ccl6
											Epx
						WT 1	WT 2	WT 3	KO 1		KO 2	KO 3
						E
	D
						Transcriptome
						comparison
	F		Ex vivo Usp22 KO LSK UP			Ex vivo Usp22 KO LSK DOWN
				0.1
	0.6
				0.0
	0.5
			NES = 2.26	-0.1		NES = -2.53
	0.4		p-value = 0.0	-0.2		p-value = 0.0
	0.3
				-0.3
	0.2
				-0.4
	0.1			-0.5
	0.0			-0.6
	-0.1			-0.7
	-4 -2 0 2 4 6 8	0	Enrichment profile 2,000 4,000 Rank in Ordered Dataset Hits Ranking metric scores 6,000 8,000 10,000 Zero cross at 5570 Up in KO LSK (CD45.2) vs WT LSK (CD45.1) Down in KO LSK (CD45.2) 12,000 vs WT LSK (CD45.1)	-4 -2 0 2 8 6 4	0	Enrichment profile 2,000 4,000 Rank in Ordered Dataset Hits Ranking metric scores 6,000 8,000 10,000 Up in KO LSK (CD45.2) Down in KO LSK (CD45.2) 12,000 vs WT LSK (CD45.1) vs WT LSK (CD45.1) Zero cross at 5570		CD45.2 KO 1	CD45.2 KO 2	CD45.2 KO 3	CD45.2 KO 4

pos. reg. of inn. imm. resp. CD45.1 WT 3 (vs KO) CD45.1 WT 4 (vs KO) CD45.1 WT 1 (vs KO)

BM cellularity 0 2 10 7 4 10 7 6 10 7 8 10 7 1 10 8

									LT-HSC	pro B (Fr.B)	BM granulocytes
						X
									N=82	N=142		N=67
					Vav1-Cre tg+ Usp22 fl/fl (Usp22 KO)		delta/delta	delta/flox	flox/flox
				E	n.s.
							WT
					Nucleated cells/hind leg		KO
						3x10 6 TBM cells
	1x10 6 WT or KO					from 1° recipient
	TBM cells (CD45.2 + )
		CD45.1 x CD45.2	20-25 weeks	CD45.1 x CD45.2	CD45.1 x CD45.2	20-25 weeks	CD45.1 x CD45.2	...
	1x10 6 WT competitor
	TBM cells (CD45.1 + )		Primary transplantation			Secondary transplantation
		B cells				T cells				Myeloid
				100					100
				50					50
				0					0
	2 4 6 8 12 16 20	4 8 12 16 20 24	8 12 16 24	4 8 16 20	2 4 6 8 12 16 20	4 8 12 16 20 24	8 12 16 24	4 8 16 20	2 4 6 8 12 16 20	4 8 12 16 20 24	8 12 16 24	4 8 16 20
					Weeks after transplantation		Weeks after transplantation

LT-HSC CD34- LT-HSC CD34+ ST-HSC CLP Fr. A B cells Fr. B+C B cells B cells Sp DP tyhmocytes CD4 SP CD8 SP CD4 T CD8 T Treg NK cells Sp NK cells BM pDC Sp Ly6Chi mono Ly6Clow mono Gran BM Gran Sp 0 500 1000 Usp22 expression

  6

	data from the Immgen database (71). (B) Transgenic Vav1-Cre mice were crossed with mice
	C carrying a floxed Usp22 allele to obtain mice with pan-hematopoietic Usp22 deficiency (Usp22
	KO). (C) Usp22 genotype of individual cells within the indicated cell populations isolated from
	Usp22 KO mice determined by single-cell PCR (n=67-142 cells) (delta/delta = KO). (D) Absolute
	cell numbers of ST-HSC and MPP in the bone marrow of wild type and Usp22 KO mice (n=12
	mice per genotype in 4 experiments). (E) Absolute numbers of nucleated cells in the bone marrow
	of wild type and Usp22 KO mice (n=12 mice per genotype in 4 experiments). (F) Experimental
	setup for serial competitive bone marrow transplantation. Wild type or Usp22 KO bone marrow
	cells (both CD45.2) were transplanted together with wild type competitor bone marrow cells
	(CD45.1) into irradiated recipients (CD45.1/CD45.2). (G) Contribution of wild type or Usp22 KO
	bone marrow cells (both CD45.2) to all (CD45.1 + CD45.2 + CD45.1/CD45.2) B cells (CD19 + ),
	T cells (CD3 + ) and myeloid cells (CD11b + ) in peripheral blood in serial competitive bone marrow
	transplantation experiments described in F. (H) log2 fold change (FC) of the frequencies of the
	indicated cell types in the bone marrow of Usp22 KO compared to wild type mice determined by
	scRNA-seq (experiment 2). Shown are the observed log2 FC values in 95% confidence intervals
	determined by bootstrapping. (I) Absolute numbers of pre-NK progenitor (pre-NKP; Lin -CD45 +
	CD27 + CD244 + CD127 + Flt3 -CD122 -) and NK progenitor cells (NKP; Lin -CD45 + CD27 + CD244 +
	CD127 + Flt3 -CD122 + ) in the bone marrow of wild type and Usp22 KO mice (n=6-7 mice per
	genotype in 3 experiments). (J+K) Absolute numbers of the indicated NK cell populations (pre-
	gated as Lin -CD45 + NK1.1 + NKp46 + DX5 + ) in the bone marrow (J) (n=5-7 mice per genotype in
	3 experiments) and spleen (K) (n=6-7 mice per genotype in 3 experiments) of wild type and Usp22
	-1 0 1 2 KO mice. (L) Relative frequencies of the indicated NK cell populations within total NK cells (n=8-B cells Dendritic cells T cells Erythroblasts Granulocytes Monocytes log2FC freq. (KO vs WT) 9 mice per genotype in 4 experiments). Mean ± s.d. (D, E, G, I-L). * p<0.05; ** p<0.01; *** NK cells p<0.001; **** p<0.0001; n.s. (not significant) by unpaired, two-tailed Student's t-test.
								p<0.05	p<0.05
								for all	for all
						WT		populations	populations
	Cells/spleen	*	n.s.	***	**	KO	% of NK cells	100 50	CD27+ CD11b-CD27+ CD11b+ CD27-CD11b+ CD27-CD11b-
								0
		CD27+	CD27+	CD27-	CD27-			WT KO	WT KO
		CD11b-	CD11b+	CD11b+	CD11b-			BM	Spleen

Fig. S2. Erythropoiesis and extramedullary hematopoiesis in Usp22-deficient mice. (A+B)

	Absolute numbers of proerythroblasts (I) (CD71 high Ter119 low ), basophilic erythroblasts (II)
	(CD71 high Ter119 high ), late basophilic and chromatophilic erythroblasts (III) (CD71 int Ter119 high ),
	and orthochromatophilic erythroblasts (IV) (CD71 neg Ter119 high ) in the bone marrow (n=15 mice
	per genotype in 5 experiments) (A) and in the spleen (n=8 mice per genotype in 2 experiments)
	(B) of wild type and Usp22 KO mice. (C) Hematocrit of wild type and Usp22 KO mice (n=13-14
	mice per genotype). Mean ± s.d. (A-C). * p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001; n.s.
	(not significant) by unpaired, two-tailed Student's t-test.

Fig. S5. Ly6G expression on granulocytes and phagocytosis by macrophages.

	myelocytes (MC), metamyelocytes (MM), band cells (BC) and segmented cells (SC) in wild type
	and Usp22 KO bone marrow cells. Cells were pre-gated on lineage marker (B220, CD4, CD8 and
	Ter119) -cells, and via a non-MEP gate. (B) Absolute numbers of MB, PM, MC, MM and BC/SC
	(gated as in A) in the bone marrow of wild type and Usp22 KO mice (n=6 mice per genotype in 2
	experiments). (C) Ratio of myeloid over B cell chimerism in the bone marrow of mice transplanted
	with wild type or Usp22-deficient HSC together with wild type competitor bone marrow cells
	(n=5-6 from 1 experiment). (D) Total myeloid output per organ of the indicated progenitors 10
	days after transplantation (n=5 mice per genotype, data representative of 1 out of 3 experiments).
	n.s. (E) Contributions of wild type and Usp22 KO CMP to CD11b + myeloid cells in peripheral blood n.s. **** WT Lin-(vs. WT CMP) WT Lin-(vs. KO CMP) WT CMP (vs. WT Lin-) KO CMP (vs. WT Lin-) of recipient mice followed-up for 21 days (n=5 mice per genotype from 1 experiment). (F) Gating of CD45.1 + and CD45.2 + cells in competitive OP9 cultures (Fig. 3J,K). (G) CD11b and B220 Total myeloid cells/organ * expression in cells differentiated in vitro for 1.5 weeks from Usp22 KO LSK transduced with the
	indicated vectors. Transduced cells were identified based on GFP expression. (H) Relative
	proportions of B220 + B cells and CD11b + myeloid cells (gated as in G) within cells differentiated
	for 1.5 weeks in vitro from wild type and Usp22 KO LSK transduced with the indicated gamma-
	retroviral expression vectors (n=3 replicates from 1 experiment). The partial myeloid cell
	production in these experiments also from wild type progenitors presumably results from the (A) Flow
	cellular pre-expansion conditions required for viral transduction prior to the differentiation assay. cytometric analysis of Ly6G expression levels in ex vivo purified bone marrow neutrophilic
	Mean ± s.d. (B, C, D, E, H). * p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001; n.s. (not granulocytes from wild type and Usp22 KO mice. (B) pHrodo median fluorescence intensity (MFI)
	significant) by unpaired, two-tailed Student's t-test. of bone marrow-derived macrophages from wild type and Usp22 KO mice incubated with
	fluorescent E. coli particles in vitro for 2 hours (n=4-5 mice per genotype in 2 experiments). (C)
	pHrodo median fluorescence intensity (MFI) of peritoneal macrophages from wild type and Usp22
	KO mice incubated with fluorescent E. coli particles in vitro for 2 hours (n=3 mice per genotype
	in 2 experiments). Mean ± s.d. (B, C).* p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001; n.s. (not
	significant) by two-way ANOVA with Sidak's post-hoc test.

.2 KO vs CD45.1 WT DEG

	Sva Capn11 Gpr114 Gm53 Cox6a2 Camk2b Rasal1 Kifc3 Dntt Camsap2 St6gal1 Cd33 Ly86 Gdf3 Arhgdig Csf1r Mt1 Tnfsf8 Igf2r Rap1gap Clec2i Dtx4 Cldn7 Ccdc102a Ccl3 Pdgfa Ramp2 Phlda3 Fzd9 Fam169a Gria3 9030617O03Rik Sdc3 Klrb1f Rnpep 1700030C10Rik Ctse Fcer1a Gm5833 Ptpru Serpinb8 Usp22 Atp9a Scin St8sia6 Mmp2 Cyp11a1 Rps4l Olfr248 Rnase12 Ptn Nxnl2 Parm1 Ptprv Scoc Cdk5rap1 Xlr4c Capsl Gm5134 Bdh2 Lpcat2 Robo3 Gm15446 Gm16894 Arap3 1700067K01Rik Nradd Bbs2 Rab26 Ache Marcks Slc35g2 Xlr4a Cd46 Dand5 Akr1c12 Clec2d Crnde Cxcr4 Mxra8 Treml1 Slc18b1 Abca4 Mlkl F2rl2 Hist1h2ac Clec4e Mylk Igip Afp Rapsn Tuba8 Peg12 Gchfr Tpm2 Aldh1l1 Clec4d Myo6 Pld2 Nnt F2r Pbx1 Cdkl3 Acacb Armc3 3110009E18Rik Dpp4 Gpr56 Samd14 Mdfi Mri1 Mfsd2b Spp1 Gm4944 Snx7 Naip2 Krt18 Rnf150 Otos Syce2 Kif7 Il6st Afap1 Irf2bpl Fuk Kcnip3 Pkn1 Rfx2 Gfi1 Unc93b1 Tmem229b Cd68 Hk3 Tspan2 Smim6 Clec11a Commd10 H2afy2 Bbs1 S1pr3 Tmem51 Gbp3 Prss57 Tmem170 Cd180 Sh3tc1 Ciapin1 Gart Supt16 Ddx19a Ccdc85c Cds1 Mn1 CD451 0.5 0 0.5 1 z-score
	CD45.2 WT 1	CD45.2 WT 2	CD45.2 WT 3	CD45.2 WT 4	CD45.2 WT 5	CD45.1 WT 1 (vs WT)	CD45.1 WT 2 (vs WT)	CD45.1 WT 3 (vs WT)	CD45.1 WT 4 (vs WT)	CD45.1 WT 5 (vs WT)

CD45.2 WT vs CD45.1 WT DEG

										Capn11	z-score
										4930596I21Rik	1
										Supt16
										Slc7a8 Plod1	0.5
										Col18a1
										Gm16617	0
										Nav1
										Rnpep Carhsp1	0.5
										Gart
										Ociad2	1
										Psmb5
										Cep85
										Nnt
										Cd52
										Cdk5rap1
										Cxcr4
										Ptprv
										Rps4l
										Serpinb8
										Ctse
										Ptpru
	CD45.2 WT 1	CD45.2 WT 2	CD45.2 WT 3	CD45.2 WT 4	CD45.2 WT 5	CD45.1 WT 1 (vs WT)	CD45.1 WT 2 (vs WT)	CD45.1 WT 3 (vs WT)	CD45.1 WT 4 (vs WT)	CD45.1 WT 5 (vs WT)

CD45.2 WT vs CD45.1 WT DEG

								Capn11
								4930596I21Rik
								Supt16
								Slc7a8
								Plod1
								Col18a1
								Gm16617
								Nav1
								Rnpep
								Carhsp1
								Gart
								Ociad2
								Psmb5
								Cep85
								Nnt
								Cd52
								Cdk5rap1
								Cxcr4
								Ptprv
								Rps4l
								Serpinb8
								Ctse
								Ptpru
	CD45.2 KO 1	CD45.2 KO 2	CD45.2 KO 3	CD45.2 KO 4	CD45.1 WT 1 (vs KO)	CD45.1 WT 2 (vs KO)	CD45.1 WT 3 (vs KO)	CD45.1 WT 4 (vs KO)

  cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus cellular response to DNA damage stimulus

	carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process carbohydrate derivative metabolic process

  RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile

	DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination DNA recombination
	mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division mitotic nuclear division
	nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation nuclear chromosome segregation
	rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing rRNA processing
	rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process rRNA metabolic process
	ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis ribosome biogenesis
	RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing RNA splicing
	mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome
	RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions
	cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration cellular respiration

RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA splicing, via transesterification reactions with bulged adenosine as nucleophile mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome mRNA splicing, via spliceosome

regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome negative regulation of mRNA splicing, via spliceosome

positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region positive regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region regulation of protein localization to chromosome, telomeric region

Acknowledgments:

We thank Katrin Busch for providing Tie2-MeriCreMer mice, James Di

N.D. was supported by a Helmholtz Graduate School for Cancer Research fellowship (N.D.), D.B.L. by Deutsche Krebshilfe Grant 70112574, M.L. and O.D. by Institut Pasteur and Inserm core funding, H.-R.R. and T.H. by Sonderforschungsbereich (SFB) 873-B11, and H.-R.R. by the European Research Council Advanced Grant 742883, the Helmholtz I & I Initiative program, and the Leibniz program of the Deutsche Forschungsgemeinschaft.

CD45.1 WT 2 (vs KO) CD45.2 KO vs CD45.1 WT DEG Sva Capn11 Gpr114 Gm53 Cox6a2 Camk2b Rasal1 Kifc3 Dntt Camsap2 St6gal1 Cd33 Ly86 Gdf3 Arhgdig Csf1r Mt1 Tnfsf8 Igf2r Rap1gap Clec2i Dtx4 Cldn7 Ccdc102a Ccl3 Pdgfa Ramp2 Phlda3 Fzd9 Fam169a Gria3 9030617O03Rik Sdc3 Klrb1f Rnpep Mn1 Cds1 Ccdc85c Ddx19a Supt16 Gart Ciapin1 Sh3tc1 Cd180 Tmem170 Prss57 Gbp3 Tmem51 S1pr3 Bbs1 H2afy2 Commd10 Clec11a Smim6 Tspan2 Hk3 Cd68 Tmem229b Unc93b1 Gfi1 Rfx2 Pkn1 Kcnip3 Fuk Irf2bpl Afap1 Il6st Kif7 Syce2 Otos Rnf150 Krt18 Naip2 Snx7 Gm4944 Spp1 Mfsd2b Mri1 Mdfi Samd14 Gpr56 Dpp4 3110009E18Rik Armc3 Acacb Cdkl3 Pbx1 F2r Nnt Pld2 Myo6 Clec4d Aldh1l1 Tpm2 Gchfr Peg12 Tuba8 Rapsn Afp Igip Mylk Clec4e Hist1h2ac F2rl2 Mlkl Abca4 Slc18b1 Treml1 Mxra8 Cxcr4 Crnde Clec2d Akr1c12 Dand5 Cd46 Xlr4a Slc35g2 Marcks Ache Rab26 Bbs2 Nradd 1700067K01Rik Arap3 Gm16894 Gm15446 Robo3 Lpcat2 Bdh2 Gm5134 Capsl Xlr4c Cdk5rap1 Scoc Ptprv Parm1 Nxnl2 Ptn Rnase12 Olfr248 Rps4l Cyp11a1 Mmp2 St8sia6 Scin Atp9a Usp22 Serpinb8 Ptpru Gm5833 Fcer1a Ctse 1700030C10Rik

GMP-biased

H2afy Mef2c Samsn1 Lmo2 Hoxa9 Ighm Malat1 Hlf Wfdc17 Experiment 1 Experiment 2 Hbb-bt H2-Q7 H2-Ab1 Mpo Cd74 Stat1 H2-Eb1 H2-Aa Dynll1 Pclaf H2-Q6 Stxbp4 H2-K1 Dnaja1 H2afz Top2a Plac8 Fabp5 Srsf7 Serpina3g Slc25a5 Bex6 Iigp1 Hspa5 B2m Nasp Nme1 Tubb4b Cacybp Hspd1 Spc24 Rbm3 Tuba1b Ffar2 Ldha Gbp3 Mat2a Cks2 Cks1b Tyms Srm Rpgrip1 Igtp Igfbp4 Lig1 Rrm2 Dad1 Cycs H2-D1 Cdk6 AW112010 Atad2 Hnrnpab Birc5 Sdf2l1 Dbi Lyar Nolc1 Uhrf1 Sell Ncl Psmb9 Ifi47 Cdk1 Smc2 Prdx1 Clspn Cenpm Nop56 Timm8a1 Uchl5 Lgals1 Hmgn1 Dtymk Slbp Hells Casp1 Gm4951 Fen1 Hsph1 Rfc5 H2-Q4 Manf Rpa2 Psmb10 Gspt1 Cdca7 Ywhah Ybx3 Tmem97 Gbp7 Psip1 Ak2 Timm9 Tk1 Nudcd2 Mrto4 Exosc8 Fam111a Rad51ap1 Hirip3 Cdv3 Nudt5 H2-T22 Mphosph10 Cd244 Agpat5 Tpx2 Smim5 Abce1 Nfkbia Tfdp1 Pbk Smc6 Immt Rif1 Eif1ad Kif15 Dynll2 Rnaseh2b Rad51 Dnph1 Cenps Dhfr Esco2 Snrnp40 Ccdc34 Nt5dc2 Txnl4a Clnk Hemgn Cmc2 Aurkb Ndufb6 Tm6sf1 2700038G22Rik Dhrs4 Ms4a6b Eif4e Mrps25 Gusb Gm15657 Ppih Idh3a Gbp2 Plk4 Chek1 Cit Tex30 Smco4 Haus4 Psat1 Psmc3ip Dna2 Nop16 Gria3 Camta1 E2f8 Gm26782 H2-M3 Ncapg Rrp15 Mthfd2 Oat Cenpw Rrp1b Bub1b Wdhd1 Cyp51 Dnmt3b Ifrd2 Mdga1 Ak6 Suv39h1 Mrps11 Mcm10 Tsfm Slc25a12 Gatad2a Cxcr4 Zmynd19 Asf1b Dis3 Ccna2 Mad2l1 Arl2 Brip1 Nop9 Gna15 Cdc45 Gemin6 Sigmar1 Bag2 Prpf4 Ccdc25 Ccne2 Noc4l Cenpn Zbp1 Cdc7 Nuf2 Alad Hspa4l Cse1l Mcrip2 Skp2 Itpa Prim2 Exo1 Cep295 Banp Cd180 Rad54l Haspin Sac3d1 Nlrc5 Creld2 Slc4a8 Cdkn1a Jpt2 Dck Acat2 Deptor Itgal Naa40 Ptger3 Tubg1 Larp1b Slc7a1 Itgb7 Ncaph Paxip1 Mis18a Prkar2a Ttf2 Tnfsf13os Galnt7 Tmem251 Dhx29 Eif2b1 Nup155 Xylt1 Aurka Tfrc Mybl2 Tamm41 Ndc80 Pop1 Lsm11 Cox18 Tedc1 Suv39h2 Rad54b Macrod2 Cep85l 4930555A03Rik Scarf1 Ctss Arhgef3 Samd12 Dmwd Gabbr1 Lppos Tox Il17re Gm47754 Hoxa5 Peli2 Ctsf Sytl1 Fgd4 Gm20234 Armc3 Gm16140 Tmem71 Acot2 Ccl3 Gm5914 Rasa4 Ifi44 Gsta4 Ankrd28 Dhrs3 Cd300a Tspan6 Foxo3 9930111J21Rik2 Slc25a36 Mettl27 Rhobtb3 Plxna4os1 Acot1 Ddah2 Pcmtd2 Nav1 Ctsg Rtp4 Dtx3 Tcp11l2 Mylip 2610035D17Rik Tnfrsf13b Crebrf Ern1 Slc16a11 Serpinf1 Tst Hbp1 Cnrip1 Kdm5b Arhgap18 AL590144.2 Mbnl2 Ddx4 Hacd4 Nkx2-3 Myct1 Vav3 Mecom Zyx St8sia4 Pigp Dcun1d1 A630072M18Rik Pgr Sesn1 Ccl4 Gng11 Emcn Pcp4l1 Gstm1 Pold4 Padi4 Nrros Gclm Calcrl Nfic Gimap6 Irf2bp2 Fam107b Clec2d Tspan13 Klhl24 Rsbn1l Basp1 Hoxa9 Runx2 Phf14 Otos Zfand5 Zfp608 Paqr5 Msi2 Adgrl4 Mef2c Sox4 Marcks Ypel3 Samsn1 Usp22 Vldlr Gcnt2 Glul Malat1 Lmo2 Wfdc17 Hlf

Supplementary Materials

Table S1. Extended survey for the presence of pathogens in wild type and Usp22-deficient mice reveals no signs of infections. Table S2. Mice used for scRNA sequencing. [START_REF] Mostafavi | Parsing the Interferon Transcriptional Network and Its Disease Associations[END_REF] Table S3. Primers used for qRT-PCR. Table S4. Primers used for Usp22 single-cell genotyping. Table S5. Indexing primers used for the preparation of ChIP and ATAC sequencing libraries. Supplementary data file S1. Bulk RNA sequencing. Supplementary data file S2. scRNA sequencing. Supplementary data file S3. Raw data excel file.

Competing interests:

The German Cancer Research Center filed an international patent application (PCT/EP2022/056187) related to this work. N.D. and H.-R.R. are listed as inventors.

The authors have no additional competing interests. regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process regulation of immune effector process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process purine ribonucleotide metabolic process ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly ribonucleoprotein complex assembly symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process symbiotic process interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms interspecies interaction between organisms ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process ribonucleotide metabolic process protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion protein targeting to mitochondrion regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process regulation of apoptotic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process organic cyclic compound catabolic process mitochondrial transmembrane transport mitochondrial transmembrane transport organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process organic acid metabolic process minimum number of "leading edge" genes per GO group was adjusted to 127 to retain GO groups of sizes comparable to experiment 1. Those genes drive the enrichment scores.

MYC target genes