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Epigenetics

In biology, epigenetics is the study of heritable traits, or a stable change of cell function, that happen without changes to the DNA sequence. The Greek prefix epi- ( "over, outside of, around") in epigenetics implies features that are "on top of" or "in addition to" the traditional (DNA sequence based) genetic mechanism of inheritance. Epigenetics usually involves a change that is not erased by cell division, and affects the regulation of gene expression. Such effects on cellular and physiological phenotypic traits may result from environmental factors, or be part of normal development. They can lead to cancer.

The term also refers to the mechanism of changes: functionally relevant alterations to the genome that do not involve mutation of the nucleotide sequence. Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. Further, non-coding RNA sequences have been shown to play a key role in the regulation of gene expression. Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These epigenetic changes may last through cell divisions for the duration of the cell's life, and may also last for multiple generations, even though they do not involve changes in the underlying DNA sequence of the organism; instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently.

One example of an epigenetic change in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, as a single fertilized egg cell – the zygote – continues to divide, the resulting daughter cells change into all the different cell types in an organism, including neurons, muscle cells, epithelium, endothelium of blood vessels, etc., by activating some genes while inhibiting the expression of others.

Definitions
The term epigenesis has a generic meaning of "extra growth" that has been used in English since the 17th century. In scientific publications, the term epigenetics started to appear in the 1930s (see Fig. on the right). However, its contemporary meaning emerged only in the 1990s.

A definition of the concept of epigenetic trait as a "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence" was formulated at a Cold Spring Harbor meeting in 2008, although alternate definitions that include non-heritable traits are still being used widely.

Waddington's canalisation, 1940s
The hypothesis of epigenetic changes affecting the expression of chromosomes was put forth by the Russian biologist Nikolai Koltsov. From the generic meaning, and the associated adjective epigenetic, British embryologist C. H. Waddington coined the term epigenetics in 1942 as pertaining to epigenesis, in parallel to Valentin Haecker's 'phenogenetics' (Phänogenetik). Epigenesis in the context of the biology of that period referred to the differentiation of cells from their initial totipotent state during embryonic development.

When Waddington coined the term, the physical nature of genes and their role in heredity was not known. He used it instead as a conceptual model of how genetic components might interact with their surroundings to produce a phenotype; he used the phrase "epigenetic landscape" as a metaphor for biological development. Waddington held that cell fates were established during development in a process he called canalisation much as a marble rolls down to the point of lowest local elevation. Waddington suggested visualising increasing irreversibility of cell type differentiation as ridges rising between the valleys where the marbles (analogous to cells) are travelling.

In recent times, Waddington's notion of the epigenetic landscape has been rigorously formalized in the context of the systems dynamics state approach to the study of cell-fate. Cell-fate determination is predicted to exhibit certain dynamics, such as attractor-convergence (the attractor can be an equilibrium point, limit cycle or strange attractor) or oscillatory.

Contemporary
Robin Holliday defined in 1990 epigenetics as "the study of the mechanisms of temporal and spatial control of gene activity during the development of complex organisms."

More recent usage of the word in biology follows stricter definitions. As defined by Arthur Riggs and colleagues, it is "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence."

The term has also been used, however, to describe processes which have not been demonstrated to be heritable, such as some forms of histone modification. Consequently, there are attempts to redefine "epigenetics" in broader terms that would avoid the constraints of requiring heritability. For example, Adrian Bird defined epigenetics as "the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states." This definition would be inclusive of transient modifications associated with DNA repair or cell-cycle phases as well as stable changes maintained across multiple cell generations, but exclude others such as templating of membrane architecture and prions unless they impinge on chromosome function. Such redefinitions however are not universally accepted and are still subject to debate. The NIH "Roadmap Epigenomics Project", which ran from 2008 to 2017, uses the following definition: "For purposes of this program, epigenetics refers to both heritable changes in gene activity and expression (in the progeny of cells or of individuals) and also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable." In 2008, a consensus definition of the epigenetic trait, a "stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence," was made at a Cold Spring Harbor meeting.

The similarity of the word to "genetics" has generated many parallel usages. The "epigenome" is a parallel to the word "genome", referring to the overall epigenetic state of a cell, and epigenomics refers to global analyses of epigenetic changes across the entire genome. The phrase "genetic code" has also been adapted – the "epigenetic code" has been used to describe the set of epigenetic features that create different phenotypes in different cells from the same underlying DNA sequence. Taken to its extreme, the "epigenetic code" could represent the total state of the cell, with the position of each molecule accounted for in an epigenomic map, a diagrammatic representation of the gene expression, DNA methylation and histone modification status of a particular genomic region. More typically, the term is used in reference to systematic efforts to measure specific, relevant forms of epigenetic information such as the histone code or DNA methylation patterns.

Mechanisms
Covalent modification of either DNA (e.g. cytosine methylation and hydroxymethylation) or of histone proteins (e.g. lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation) play central roles in many types of epigenetic inheritance. Therefore, the word "epigenetics" is sometimes used as a synonym for these processes. However, this can be misleading. Chromatin remodeling is not always inherited, and not all epigenetic inheritance involves chromatin remodeling. In 2019, a further lysine modification appeared in the scientific literature linking epigenetics modification to cell metabolism, i.e. Lactylation

Because the phenotype of a cell or individual is affected by which of its genes are transcribed, heritable transcription states can give rise to epigenetic effects. There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of chromatin. Chromatin is the complex of DNA and the histone proteins with which it associates. If the way that DNA is wrapped around the histones changes, gene expression can change as well. Chromatin remodeling is accomplished through two main mechanisms:
 * 1) The first way is post translational modification of the amino acids that make up histone proteins. Histone proteins are made up of long chains of amino acids. If the amino acids that are in the chain are changed, the shape of the histone might be modified. DNA is not completely unwound during replication. It is possible, then, that the modified histones may be carried into each new copy of the DNA. Once there, these histones may act as templates, initiating the surrounding new histones to be shaped in the new manner. By altering the shape of the histones around them, these modified histones would ensure that a lineage-specific transcription program is maintained after cell division.
 * 2) The second way is the addition of methyl groups to the DNA, mostly at CpG sites, to convert cytosine to 5-methylcytosine. 5-Methylcytosine performs much like a regular cytosine, pairing with a guanine in double-stranded DNA. However, when methylated cytosines are present in CpG sites in the promoter and enhancer regions of genes, the genes are often repressed.  When methylated cytosines are present in CpG sites in the gene body (in the coding region excluding the transcription start site) expression of the gene is often enhanced. Transcription of a gene usually depends on a transcription factor binding to a (10 base or less) recognition sequence at the enhancer that interacts with the promoter region of that gene (Gene expression). About 22% of transcription factors are inhibited from binding when the recognition sequence has a methylated cytosine. In addition, presence of methylated cytosines at a promoter region can attract methyl-CpG-binding domain (MBD) proteins. All MBDs interact with nucleosome remodeling and histone deacetylase complexes, which leads to gene silencing. In addition, another covalent modification involving methylated cytosine is its demethylation by TET enzymes. Hundreds of such demethylations occur, for instance, during learning and memory forming events in neurons.

There is frequently a reciprocal relationship between DNA methylation and histone lysine methylation. For instance, the methyl binding domain protein MBD1, attracted to and associating with methylated cytosine in a DNA CpG site, can also associate with H3K9 methyltransferase activity to methylate histone 3 at lysine 9. On the other hand, DNA maintenance methylation by DNMT1 appears to partly rely on recognition of histone methylation on the nucleosome present at the DNA site to carry out cytosine methylation on newly synthesized DNA. There is further crosstalk between DNA methylation carried out by DNMT3A and DNMT3B and histone methylation so that there is a correlation between the genome-wide distribution of DNA methylation and histone methylation.

Mechanisms of heritability of histone state are not well understood; however, much is known about the mechanism of heritability of DNA methylation state during cell division and differentiation. Heritability of methylation state depends on certain enzymes (such as DNMT1) that have a higher affinity for 5-methylcytosine than for cytosine. If this enzyme reaches a "hemimethylated" portion of DNA (where 5-methylcytosine is in only one of the two DNA strands) the enzyme will methylate the other half. However, it is now known that DNMT1 physically interacts with the protein UHRF1. UHRF1 has been recently recognized as essential for DNMT1-mediated maintenance of DNA methylation. UHRF1 is the protein that specifically recognizes hemi-methylated DNA, therefore bringing DNMT1 to its substrate to maintain DNA methylation.

Although histone modifications occur throughout the entire sequence, the unstructured N-termini of histones (called histone tails) are particularly highly modified. These modifications include acetylation, methylation, ubiquitylation, phosphorylation, sumoylation, ribosylation and citrullination. Acetylation is the most highly studied of these modifications. For example, acetylation of the K14 and K9 lysines of the tail of histone H3 by histone acetyltransferase enzymes (HATs) is generally related to transcriptional competence (see Figure).

One mode of thinking is that this tendency of acetylation to be associated with "active" transcription is biophysical in nature. Because it normally has a positively charged nitrogen at its end, lysine can bind the negatively charged phosphates of the DNA backbone. The acetylation event converts the positively charged amine group on the side chain into a neutral amide linkage. This removes the positive charge, thus loosening the DNA from the histone. When this occurs, complexes like SWI/SNF and other transcriptional factors can bind to the DNA and allow transcription to occur. This is the "cis" model of the epigenetic function. In other words, changes to the histone tails have a direct effect on the DNA itself.

Another model of epigenetic function is the "trans" model. In this model, changes to the histone tails act indirectly on the DNA. For example, lysine acetylation may create a binding site for chromatin-modifying enzymes (or transcription machinery as well). This chromatin remodeler can then cause changes to the state of the chromatin. Indeed, a bromodomain – a protein domain that specifically binds acetyl-lysine – is found in many enzymes that help activate transcription, including the SWI/SNF complex. It may be that acetylation acts in this and the previous way to aid in transcriptional activation.

The idea that modifications act as docking modules for related factors is borne out by histone methylation as well. Methylation of lysine 9 of histone H3 has long been associated with constitutively transcriptionally silent chromatin (constitutive heterochromatin) (see bottom Figure). It has been determined that a chromodomain (a domain that specifically binds methyl-lysine) in the transcriptionally repressive protein HP1 recruits HP1 to K9 methylated regions. One example that seems to refute this biophysical model for methylation is that tri-methylation of histone H3 at lysine 4 is strongly associated with (and required for full) transcriptional activation (see top Figure). Tri-methylation, in this case, would introduce a fixed positive charge on the tail.

It has been shown that the histone lysine methyltransferase (KMT) is responsible for this methylation activity in the pattern of histones H3 & H4. This enzyme utilizes a catalytically active site called the SET domain (Suppressor of variegation, Enhancer of Zeste, Trithorax). The SET domain is a 130-amino acid sequence involved in modulating gene activities. This domain has been demonstrated to bind to the histone tail and causes the methylation of the histone.

Differing histone modifications are likely to function in differing ways; acetylation at one position is likely to function differently from acetylation at another position. Also, multiple modifications may occur at the same time, and these modifications may work together to change the behavior of the nucleosome. The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code, although the idea that histone state can be read linearly as a digital information carrier has been largely debunked. One of the best-understood systems that orchestrate chromatin-based silencing is the SIR protein based silencing of the yeast hidden mating-type loci HML and HMR.

DNA methylation
DNA methylation frequently occurs in repeated sequences, and helps to suppress the expression and mobility of 'transposable elements': Because 5-methylcytosine can be spontaneously deaminated (replacing nitrogen by oxygen) to thymidine, CpG sites are frequently mutated and become rare in the genome, except at CpG islands where they remain unmethylated. Epigenetic changes of this type thus have the potential to direct increased frequencies of permanent genetic mutation. DNA methylation patterns are known to be established and modified in response to environmental factors by a complex interplay of at least three independent DNA methyltransferases, DNMT1, DNMT3A, and DNMT3B, the loss of any of which is lethal in mice. DNMT1 is the most abundant methyltransferase in somatic cells, localizes to replication foci, has a 10–40-fold preference for hemimethylated DNA and interacts with the proliferating cell nuclear antigen (PCNA).

By preferentially modifying hemimethylated DNA, DNMT1 transfers patterns of methylation to a newly synthesized strand after DNA replication, and therefore is often referred to as the 'maintenance' methyltransferase. DNMT1 is essential for proper embryonic development, imprinting and X-inactivation. To emphasize the difference of this molecular mechanism of inheritance from the canonical Watson-Crick base-pairing mechanism of transmission of genetic information, the term 'Epigenetic templating' was introduced. Furthermore, in addition to the maintenance and transmission of methylated DNA states, the same principle could work in the maintenance and transmission of histone modifications and even cytoplasmic (structural) heritable states.

RNA methylation
RNA methylation of N6-methyladenosine (m6A) as the most abundant eukaryotic RNA modification has recently been recognized as an important gene regulatory mechanism.

Histone modifications
Histones H3 and H4 can also be manipulated through demethylation using histone lysine demethylase (KDM). This recently identified enzyme has a catalytically active site called the Jumonji domain (JmjC). The demethylation occurs when JmjC utilizes multiple cofactors to hydroxylate the methyl group, thereby removing it. JmjC is capable of demethylating mono-, di-, and tri-methylated substrates.

Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene expression without changes to the DNA sequence. Epigenetic control is often associated with alternative covalent modifications of histones. The stability and heritability of states of larger chromosomal regions are suggested to involve positive feedback where modified nucleosomes recruit enzymes that similarly modify nearby nucleosomes. A simplified stochastic model for this type of epigenetics is found here.

It has been suggested that chromatin-based transcriptional regulation could be mediated by the effect of small RNAs. Small interfering RNAs can modulate transcriptional gene expression via epigenetic modulation of targeted promoters.

RNA transcripts
Sometimes a gene, after being turned on, transcribes a product that (directly or indirectly) maintains the activity of that gene. For example, Hnf4 and MyoD enhance the transcription of many liver-specific and muscle-specific genes, respectively, including their own, through the transcription factor activity of the proteins they encode. RNA signalling includes differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. Other epigenetic changes are mediated by the production of different splice forms of RNA, or by formation of double-stranded RNA (RNAi). Descendants of the cell in which the gene was turned on will inherit this activity, even if the original stimulus for gene-activation is no longer present. These genes are often turned on or off by signal transduction, although in some systems where syncytia or gap junctions are important, RNA may spread directly to other cells or nuclei by diffusion. A large amount of RNA and protein is contributed to the zygote by the mother during oogenesis or via nurse cells, resulting in maternal effect phenotypes. A smaller quantity of sperm RNA is transmitted from the father, but there is recent evidence that this epigenetic information can lead to visible changes in several generations of offspring.

MicroRNAs
MicroRNAs (miRNAs) are members of non-coding RNAs that range in size from 17 to 25 nucleotides. miRNAs regulate a large variety of biological functions in plants and animals. So far, in 2013, about 2000 miRNAs have been discovered in humans and these can be found online in a miRNA database. Each miRNA expressed in a cell may target about 100 to 200 messenger RNAs(mRNAs) that it downregulates. Most of the downregulation of mRNAs occurs by causing the decay of the targeted mRNA, while some downregulation occurs at the level of translation into protein.

It appears that about 60% of human protein coding genes are regulated by miRNAs. Many miRNAs are epigenetically regulated. About 50% of miRNA genes are associated with CpG islands, that may be repressed by epigenetic methylation. Transcription from methylated CpG islands is strongly and heritably repressed. Other miRNAs are epigenetically regulated by either histone modifications or by combined DNA methylation and histone modification.

mRNA
In 2011, it was demonstrated that the methylation of mRNA plays a critical role in human energy homeostasis. The obesity-associated FTO gene is shown to be able to demethylate N6-methyladenosine in RNA.

sRNAs
sRNAs are small (50–250 nucleotides), highly structured, non-coding RNA fragments found in bacteria. They control gene expression including virulence genes in pathogens and are viewed as new targets in the fight against drug-resistant bacteria. They play an important role in many biological processes, binding to mRNA and protein targets in prokaryotes. Their phylogenetic analyses, for example through sRNA–mRNA target interactions or protein binding properties, are used to build comprehensive databases. sRNA-gene maps based on their targets in microbial genomes are also constructed.

Long non-coding RNAs
Numerous investigations have demonstrated the pivotal involvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression and chromosomal modifications, thereby exerting significant control over cellular differentiation. These long non-coding RNAs also contribute to genomic imprinting and the inactivation of the X chromosome. In invertebrates such as social insects of honey bees, long non-coding RNAs are detected as a possible epigenetic mechanism via allele-specific genes underlying aggression via reciprocal crosses.

Prions
Prions are infectious forms of proteins. In general, proteins fold into discrete units that perform distinct cellular functions, but some proteins are also capable of forming an infectious conformational state known as a prion. Although often viewed in the context of infectious disease, prions are more loosely defined by their ability to catalytically convert other native state versions of the same protein to an infectious conformational state. It is in this latter sense that they can be viewed as epigenetic agents capable of inducing a phenotypic change without a modification of the genome.

Fungal prions are considered by some to be epigenetic because the infectious phenotype caused by the prion can be inherited without modification of the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971, are the two best studied of this type of prion. Prions can have a phenotypic effect through the sequestration of protein in aggregates, thereby reducing that protein's activity. In PSI+ cells, the loss of the Sup35 protein (which is involved in termination of translation) causes ribosomes to have a higher rate of read-through of stop codons, an effect that results in suppression of nonsense mutations in other genes. The ability of Sup35 to form prions may be a conserved trait. It could confer an adaptive advantage by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon mutations.

Prion-based epigenetics has also been observed in Saccharomyces cerevisiae.

Molecular basis
Epigenetic changes modify the activation of certain genes, but not the genetic code sequence of DNA. The microstructure (not code) of DNA itself or the associated chromatin proteins may be modified, causing activation or silencing. This mechanism enables differentiated cells in a multicellular organism to express only the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism's lifetime; however, these epigenetic changes can be transmitted to the organism's offspring through a process called transgenerational epigenetic inheritance. Moreover, if gene inactivation occurs in a sperm or egg cell that results in fertilization, this epigenetic modification may also be transferred to the next generation.

Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, DNA methylation reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.

DNA damage
DNA damage can also cause epigenetic changes. DNA damage is very frequent, occurring on average about 60,000 times a day per cell of the human body (see DNA damage (naturally occurring)). These damages are largely repaired, however, epigenetic changes can still remain at the site of DNA repair. In particular, a double strand break in DNA can initiate unprogrammed epigenetic gene silencing both by causing DNA methylation as well as by promoting silencing types of histone modifications (chromatin remodeling - see next section). In addition, the enzyme Parp1 (poly(ADP)-ribose polymerase) and its product poly(ADP)-ribose (PAR) accumulate at sites of DNA damage as part of the repair process. This accumulation, in turn, directs recruitment and activation of the chromatin remodeling protein, ALC1, that can cause nucleosome remodeling. Nucleosome remodeling has been found to cause, for instance, epigenetic silencing of DNA repair gene MLH1. DNA damaging chemicals, such as benzene, hydroquinone, styrene, carbon tetrachloride and trichloroethylene, cause considerable hypomethylation of DNA, some through the activation of oxidative stress pathways.

Foods are known to alter the epigenetics of rats on different diets. Some food components epigenetically increase the levels of DNA repair enzymes such as MGMT and MLH1 and p53. Other food components can reduce DNA damage, such as soy isoflavones. In one study, markers for oxidative stress, such as modified nucleotides that can result from DNA damage, were decreased by a 3-week diet supplemented with soy. A decrease in oxidative DNA damage was also observed 2 h after consumption of anthocyanin-rich bilberry (Vaccinium myrtillius L.) pomace extract.

DNA repair
Damage to DNA is very common and is constantly being repaired. Epigenetic alterations can accompany DNA repair of oxidative damage or double-strand breaks. In human cells, oxidative DNA damage occurs about 10,000 times a day and DNA double-strand breaks occur about 10 to 50 times a cell cycle in somatic replicating cells (see DNA damage (naturally occurring)). The selective advantage of DNA repair is to allow the cell to survive in the face of DNA damage. The selective advantage of epigenetic alterations that occur with DNA repair is not clear.

Repair of oxidative DNA damage can alter epigenetic markers
In the steady state (with endogenous damages occurring and being repaired), there are about 2,400 oxidatively damaged guanines that form 8-oxo-2'-deoxyguanosine (8-OHdG) in the average mammalian cell DNA. 8-OHdG constitutes about 5% of the oxidative damages commonly present in DNA. The oxidized guanines do not occur randomly among all guanines in DNA. There is a sequence preference for the guanine at a methylated CpG site (a cytosine followed by guanine along its 5' → 3' direction and where the cytosine is methylated (5-mCpG)). A 5-mCpG site has the lowest ionization potential for guanine oxidation.

Oxidized guanine has mispairing potential and is mutagenic. Oxoguanine glycosylase (OGG1) is the primary enzyme responsible for the excision of the oxidized guanine during DNA repair. OGG1 finds and binds to an 8-OHdG within a few seconds. However, OGG1 does not immediately excise 8-OHdG. In HeLa cells half maximum removal of 8-OHdG occurs in 30 minutes, and in irradiated mice, the 8-OHdGs induced in the mouse liver are removed with a half-life of 11 minutes.

When OGG1 is present at an oxidized guanine within a methylated CpG site it recruits TET1 to the 8-OHdG lesion (see Figure). This allows TET1 to demethylate an adjacent methylated cytosine. Demethylation of cytosine is an epigenetic alteration.

As an example, when human mammary epithelial cells were treated with H2O2 for six hours, 8-OHdG increased about 3.5-fold in DNA and this caused about 80% demethylation of the 5-methylcytosines in the genome. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene into messenger RNA. In cells treated with H2O2, one particular gene was examined, BACE1. The methylation level of the BACE1 CpG island was reduced (an epigenetic alteration) and this allowed about 6.5 fold increase of expression of BACE1 messenger RNA.

While six-hour incubation with H2O2 causes considerable demethylation of 5-mCpG sites, shorter times of H2O2 incubation appear to promote other epigenetic alterations. Treatment of cells with H2O2 for 30 minutes causes the mismatch repair protein heterodimer MSH2-MSH6 to recruit DNA methyltransferase 1 (DNMT1) to sites of some kinds of oxidative DNA damage. This could cause increased methylation of cytosines (epigenetic alterations) at these locations.

Jiang et al. treated HEK 293 cells with agents causing oxidative DNA damage, (potassium bromate (KBrO3) or potassium chromate (K2CrO4)). Base excision repair (BER) of oxidative damage occurred with the DNA repair enzyme polymerase beta localizing to oxidized guanines. Polymerase beta is the main human polymerase in short-patch BER of oxidative DNA damage. Jiang et al. also found that polymerase beta recruited the DNA methyltransferase protein DNMT3b to BER repair sites. They then evaluated the methylation pattern at the single nucleotide level in a small region of DNA including the promoter region and the early transcription region of the BRCA1 gene. Oxidative DNA damage from bromate modulated the DNA methylation pattern (caused epigenetic alterations) at CpG sites within the region of DNA studied. In untreated cells, CpGs located at −189, −134, −29, −19, +16, and +19 of the BRCA1 gene had methylated cytosines (where numbering is from the messenger RNA transcription start site, and negative numbers indicate nucleotides in the upstream promoter region). Bromate treatment-induced oxidation resulted in the loss of cytosine methylation at −189, −134, +16 and +19 while also leading to the formation of new methylation at the CpGs located at −80, −55, −21 and +8 after DNA repair was allowed.

Homologous recombinational repair alters epigenetic markers
At least four articles report the recruitment of DNA methyltransferase 1 (DNMT1) to sites of DNA double-strand breaks. During homologous recombinational repair (HR) of the double-strand break, the involvement of DNMT1 causes the two repaired strands of DNA to have different levels of methylated cytosines. One strand becomes frequently methylated at about 21 CpG sites downstream of the repaired double-strand break. The other DNA strand loses methylation at about six CpG sites that were previously methylated downstream of the double-strand break, as well as losing methylation at about five CpG sites that were previously methylated upstream of the double-strand break. When the chromosome is replicated, this gives rise to one daughter chromosome that is heavily methylated downstream of the previous break site and one that is unmethylated in the region both upstream and downstream of the previous break site. With respect to the gene that was broken by the double-strand break, half of the progeny cells express that gene at a high level and in the other half of the progeny cells expression of that gene is repressed. When clones of these cells were maintained for three years, the new methylation patterns were maintained over that time period.

In mice with a CRISPR-mediated homology-directed recombination insertion in their genome there were a large number of increased methylations of CpG sites within the double-strand break-associated insertion.

Non-homologous end joining can cause some epigenetic marker alterations
Non-homologous end joining (NHEJ) repair of a double-strand break can cause a small number of demethylations of pre-existing cytosine DNA methylations downstream of the repaired double-strand break. Further work by Allen et al. showed that NHEJ of a DNA double-strand break in a cell could give rise to some progeny cells having repressed expression of the gene harboring the initial double-strand break and some progeny having high expression of that gene due to epigenetic alterations associated with NHEJ repair. The frequency of epigenetic alterations causing repression of a gene after an NHEJ repair of a DNA double-strand break in that gene may be about 0.9%.

Techniques used to study epigenetics
Epigenetic research uses a wide range of molecular biological techniques to further understanding of epigenetic phenomena. These techniques include chromatin immunoprecipitation (together with its large-scale variants ChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing. Furthermore, the use of bioinformatics methods has a role in computational epigenetics.

Chromatin Immunoprecipitation
Chromatin Immunoprecipitation (ChIP) has helped bridge the gap between DNA and epigenetic interactions. With the use of ChIP, researchers are able to make findings in regards to gene regulation, transcription mechanisms, and chromatin structure.

Fluorescent in situ hybridization
Fluorescent in situ hybridization (FISH) is very important to understand epigenetic mechanisms. FISH can be used to find the location of genes on chromosomes, as well as finding noncoding RNAs. FISH is predominantly used for detecting chromosomal abnormalities in humans.

Methylation-sensitive restriction enzymes
Methylation sensitive restriction enzymes paired with PCR is a way to evaluate methylation in DNA - specifically the CpG sites. If DNA is methylated, the restriction enzymes will not cleave the strand. Contrarily, if the DNA is not methylated, the enzymes will cleave the strand and it will be amplified by PCR.

Bisulfite sequencing
Bisulfite sequencing is another way to evaluate DNA methylation. Cytosine will be changed to uracil from being treated with sodium bisulfite, whereas methylated cytosines will not be affected.

Nanopore sequencing
Certain sequencing methods, such as nanopore sequencing, allow sequencing of native DNA. Native (=unamplified) DNA retains the epigenetic modifications which would otherwise be lost during the amplification step. Nanopore basecaller models can distinguish between the signals obtained for epigenetically modified bases and unaltered based and provide an epigenetic profile in addition to the sequencing result.

Structural inheritance
In ciliates such as Tetrahymena and Paramecium, genetically identical cells show heritable differences in the patterns of ciliary rows on their cell surface. Experimentally altered patterns can be transmitted to daughter cells. It seems existing structures act as templates for new structures. The mechanisms of such inheritance are unclear, but reasons exist to assume that multicellular organisms also use existing cell structures to assemble new ones.

Nucleosome positioning
Eukaryotic genomes have numerous nucleosomes. Nucleosome position is not random, and determine the accessibility of DNA to regulatory proteins. Promoters active in different tissues have been shown to have different nucleosome positioning features. This determines differences in gene expression and cell differentiation. It has been shown that at least some nucleosomes are retained in sperm cells (where most but not all histones are replaced by protamines). Thus nucleosome positioning is to some degree inheritable. Recent studies have uncovered connections between nucleosome positioning and other epigenetic factors, such as DNA methylation and hydroxymethylation.

Histone variants
Different histone variants are incorporated into specific regions of the genome non-randomly. Their differential biochemical characteristics can affect genome functions via their roles in gene regulation, and maintenance of chromosome structures.

Genomic architecture
The three-dimensional configuration of the genome (the 3D genome) is complex, dynamic and crucial for regulating genomic function and nuclear processes such as DNA replication, transcription and DNA-damage repair.

Memory
Memory formation and maintenance are due to epigenetic alterations that cause the required dynamic changes in gene transcription that create and renew memory in neurons.

An event can set off a chain of reactions that result in altered methylations of a large set of genes in neurons, which give a representation of the event, a memory.

Areas of the brain important in the formation of memories include the hippocampus, medial prefrontal cortex (mPFC), anterior cingulate cortex and amygdala, as shown in the diagram of the human brain in this section.

When a strong memory is created, as in a rat subjected to contextual fear conditioning (CFC), one of the earliest events to occur is that more than 100 DNA double-strand breaks are formed by topoisomerase IIB in neurons of the hippocampus and the medial prefrontal cortex (mPFC). These double-strand breaks are at specific locations that allow activation of transcription of immediate early genes (IEGs) that are important in memory formation, allowing their expression in mRNA, with peak mRNA transcription at seven to ten minutes after CFC.

Two important IEGs in memory formation are EGR1 and the alternative promoter variant of DNMT3A, DNMT3A2. EGR1 protein binds to DNA at its binding motifs, 5′-GCGTGGGCG-3′ or 5′-GCGGGGGCGG-3', and there are about 12,000 genome locations at which EGR1 protein can bind. EGR1 protein binds to DNA in gene promoter and enhancer regions. EGR1 recruits the demethylating enzyme TET1 to an association, and brings TET1 to about 600 locations on the genome where TET1 can then demethylate and activate the associated genes.

The DNA methyltransferases DNMT3A1, DNMT3A2 and DNMT3B can all methylate cytosines (see image this section) at CpG sites in or near the promoters of genes. As shown by Manzo et al., these three DNA methyltransferases differ in their genomic binding locations and DNA methylation activity at different regulatory sites. Manzo et al. located 3,970 genome regions exclusively enriched for DNMT3A1, 3,838 regions for DNMT3A2 and 3,432 regions for DNMT3B. When DNMT3A2 is newly induced as an IEG (when neurons are activated), many new cytosine methylations occur, presumably in the target regions of DNMT3A2. Oliviera et al. found that the neuronal activity-inducible IEG levels of Dnmt3a2 in the hippocampus determined the ability to form long-term memories.

Rats form long-term associative memories after contextual fear conditioning (CFC). Duke et al. found that 24 hours after CFC in rats, in hippocampus neurons, 2,097 genes (9.17% of the genes in the rat genome) had altered methylation. When newly methylated cytosines are present in CpG sites in the promoter regions of genes, the genes are often repressed, and when newly demethylated cytosines are present the genes may be activated. After CFC, there were 1,048 genes with reduced mRNA expression and 564 genes with upregulated mRNA expression. Similarly, when mice undergo CFC, one hour later in the hippocampus region of the mouse brain there are 675 demethylated genes and 613 hypermethylated genes. However, memories do not remain in the hippocampus, but after four or five weeks the memories are stored in the anterior cingulate cortex. In the studies on mice after CFC, Halder et al. showed that four weeks after CFC there were at least 1,000 differentially methylated genes and more than 1,000 differentially expressed genes in the anterior cingulate cortex, while at the same time the altered methylations in the hippocampus were reversed.

The epigenetic alteration of methylation after a new memory is established creates a different pool of nuclear mRNAs. As reviewed by Bernstein, the epigenetically determined new mix of nuclear mRNAs are often packaged into neuronal granules, or messenger RNP, consisting of mRNA, small and large ribosomal subunits, translation initiation factors and RNA-binding proteins that regulate mRNA function. These neuronal granules are transported from the neuron nucleus and are directed, according to 3′ untranslated regions of the mRNA in the granules (their "zip codes"), to neuronal dendrites. Roughly 2,500 mRNAs may be localized to the dendrites of hippocampal pyramidal neurons and perhaps 450 transcripts are in excitatory presynaptic nerve terminals (dendritic spines). The altered assortments of transcripts (dependent on epigenetic alterations in the neuron nucleus) have different sensitivities in response to signals, which is the basis of altered synaptic plasticity. Altered synaptic plasticity is often considered the neurochemical foundation of learning and memory.

Aging
Epigenetics play a major role in brain aging and age-related cognitive decline, with relevance to life extension.

Other and general
In adulthood, changes in the epigenome are important for various higher cognitive functions. Dysregulation of epigenetic mechanisms is implicated in neurodegenerative disorders and diseases. Epigenetic modifications in neurons are dynamic and reversible. Epigenetic regulation impacts neuronal action, affecting learning, memory, and other cognitive processes.

Early events, including during embryonic development, can influence development, cognition, and health outcomes through epigenetic mechanisms.

Epigenetic mechanisms have been proposed as "a potential molecular mechanism for effects of endogenous hormones on the organization of developing brain circuits".

Nutrients could interact with the epigenome to "protect or boost cognitive processes across the lifespan".

A review suggests neurobiological effects of physical exercise via epigenetics seem "central to building an 'epigenetic memory' to influence long-term brain function and behavior" and may even be heritable.

With the axo-ciliary synapse, there is communication between serotonergic axons and antenna-like primary cilia of CA1 pyramidal neurons that alters the neuron's epigenetic state in the nucleus via the signalling distinct from that at the plasma membrane (and longer-term).

Epigenetics also play a major role in the brain evolution in and to humans.

Development
Developmental epigenetics can be divided into predetermined and probabilistic epigenesis. Predetermined epigenesis is a unidirectional movement from structural development in DNA to the functional maturation of the protein. "Predetermined" here means that development is scripted and predictable. Probabilistic epigenesis on the other hand is a bidirectional structure-function development with experiences and external molding development.

Somatic epigenetic inheritance, particularly through DNA and histone covalent modifications and nucleosome repositioning, is very important in the development of multicellular eukaryotic organisms. The genome sequence is static (with some notable exceptions), but cells differentiate into many different types, which perform different functions, and respond differently to the environment and intercellular signaling. Thus, as individuals develop, morphogens activate or silence genes in an epigenetically heritable fashion, giving cells a memory. In mammals, most cells terminally differentiate, with only stem cells retaining the ability to differentiate into several cell types ("totipotency" and "multipotency"). In mammals, some stem cells continue producing newly differentiated cells throughout life, such as in neurogenesis, but mammals are not able to respond to loss of some tissues, for example, the inability to regenerate limbs, which some other animals are capable of. Epigenetic modifications regulate the transition from neural stem cells to glial progenitor cells (for example, differentiation into oligodendrocytes is regulated by the deacetylation and methylation of histones. Unlike animals, plant cells do not terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. While plants do utilize many of the same epigenetic mechanisms as animals, such as chromatin remodeling, it has been hypothesized that some kinds of plant cells do not use or require "cellular memories", resetting their gene expression patterns using positional information from the environment and surrounding cells to determine their fate.

Epigenetic changes can occur in response to environmental exposure – for example, maternal dietary supplementation with genistein (250 mg/kg) have epigenetic changes affecting expression of the agouti gene, which affects their fur color, weight, and propensity to develop cancer. Ongoing research is focused on exploring the impact of other known teratogens, such as diabetic embryopathy, on methylation signatures.

Controversial results from one study suggested that traumatic experiences might produce an epigenetic signal that is capable of being passed to future generations. Mice were trained, using foot shocks, to fear a cherry blossom odor. The investigators reported that the mouse offspring had an increased aversion to this specific odor. They suggested epigenetic changes that increase gene expression, rather than in DNA itself, in a gene, M71, that governs the functioning of an odor receptor in the nose that responds specifically to this cherry blossom smell. There were physical changes that correlated with olfactory (smell) function in the brains of the trained mice and their descendants. Several criticisms were reported, including the study's low statistical power as evidence of some irregularity such as bias in reporting results. Due to limits of sample size, there is a probability that an effect will not be demonstrated to within statistical significance even if it exists. The criticism suggested that the probability that all the experiments reported would show positive results if an identical protocol was followed, assuming the claimed effects exist, is merely 0.4%. The authors also did not indicate which mice were siblings, and treated all of the mice as statistically independent. The original researchers pointed out negative results in the paper's appendix that the criticism omitted in its calculations, and undertook to track which mice were siblings in the future.

Transgenerational
Epigenetic mechanisms were a necessary part of the evolutionary origin of cell differentiation. Although epigenetics in multicellular organisms is generally thought to be a mechanism involved in differentiation, with epigenetic patterns "reset" when organisms reproduce, there have been some observations of transgenerational epigenetic inheritance (e.g., the phenomenon of paramutation observed in maize). Although most of these multigenerational epigenetic traits are gradually lost over several generations, the possibility remains that multigenerational epigenetics could be another aspect to evolution and adaptation. As mentioned above, some define epigenetics as heritable.

A sequestered germ line or Weismann barrier is specific to animals, and epigenetic inheritance is more common in plants and microbes. Eva Jablonka, Marion J. Lamb and Étienne Danchin have argued that these effects may require enhancements to the standard conceptual framework of the modern synthesis and have called for an extended evolutionary synthesis. Other evolutionary biologists, such as John Maynard Smith, have incorporated epigenetic inheritance into population-genetics models or are openly skeptical of the extended evolutionary synthesis (Michael Lynch). Thomas Dickins and Qazi Rahman state that epigenetic mechanisms such as DNA methylation and histone modification are genetically inherited under the control of natural selection and therefore fit under the earlier "modern synthesis".

Two important ways in which epigenetic inheritance can differ from traditional genetic inheritance, with important consequences for evolution, are:
 * rates of epimutation can be much faster than rates of mutation
 * the epimutations are more easily reversible

In plants, heritable DNA methylation mutations are 100,000 times more likely to occur compared to DNA mutations. An epigenetically inherited element such as the PSI+ system can act as a "stop-gap", good enough for short-term adaptation that allows the lineage to survive for long enough for mutation and/or recombination to genetically assimilate the adaptive phenotypic change. The existence of this possibility increases the evolvability of a species.

More than 100 cases of transgenerational epigenetic inheritance phenomena have been reported in a wide range of organisms, including prokaryotes, plants, and animals. For instance, mourning-cloak butterflies will change color through hormone changes in response to experimentation of varying temperatures.

The filamentous fungus Neurospora crassa is a prominent model system for understanding the control and function of cytosine methylation. In this organism, DNA methylation is associated with relics of a genome-defense system called RIP (repeat-induced point mutation) and silences gene expression by inhibiting transcription elongation.

The yeast prion PSI is generated by a conformational change of a translation termination factor, which is then inherited by daughter cells. This can provide a survival advantage under adverse conditions, exemplifying epigenetic regulation which enables unicellular organisms to respond rapidly to environmental stress. Prions can be viewed as epigenetic agents capable of inducing a phenotypic change without modification of the genome.

Direct detection of epigenetic marks in microorganisms is possible with single molecule real time sequencing, in which polymerase sensitivity allows for measuring methylation and other modifications as a DNA molecule is being sequenced. Several projects have demonstrated the ability to collect genome-wide epigenetic data in bacteria.

Epigenetics in bacteria
While epigenetics is of fundamental importance in eukaryotes, especially metazoans, it plays a different role in bacteria. Most importantly, eukaryotes use epigenetic mechanisms primarily to regulate gene expression which bacteria rarely do. However, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation is important in bacteria virulence in organisms such as Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage, transposase activity and regulation of gene expression. There exists a genetic switch controlling Streptococcus pneumoniae (the pneumococcus) that allows the bacterium to randomly change its characteristics into six alternative states that could pave the way to improved vaccines. Each form is randomly generated by a phase variable methylation system. The ability of the pneumococcus to cause deadly infections is different in each of these six states. Similar systems exist in other bacterial genera. In Bacillota such as Clostridioides difficile, adenine methylation regulates sporulation, biofilm formation and host-adaptation.

Medicine
Epigenetics has many and varied potential medical applications.

Twins
Direct comparisons of identical twins constitute an optimal model for interrogating environmental epigenetics. In the case of humans with different environmental exposures, monozygotic (identical) twins were epigenetically indistinguishable during their early years, while older twins had remarkable differences in the overall content and genomic distribution of 5-methylcytosine DNA and histone acetylation. The twin pairs who had spent less of their lifetime together and/or had greater differences in their medical histories were those who showed the largest differences in their levels of 5-methylcytosine DNA and acetylation of histones H3 and H4.

Dizygotic (fraternal) and monozygotic (identical) twins show evidence of epigenetic influence in humans. DNA sequence differences that would be abundant in a singleton-based study do not interfere with the analysis. Environmental differences can produce long-term epigenetic effects, and different developmental monozygotic twin subtypes may be different with respect to their susceptibility to be discordant from an epigenetic point of view.

A high-throughput study, which denotes technology that looks at extensive genetic markers, focused on epigenetic differences between monozygotic twins to compare global and locus-specific changes in DNA methylation and histone modifications in a sample of 40 monozygotic twin pairs. In this case, only healthy twin pairs were studied, but a wide range of ages was represented, between 3 and 74 years. One of the major conclusions from this study was that there is an age-dependent accumulation of epigenetic differences between the two siblings of twin pairs. This accumulation suggests the existence of epigenetic "drift". Epigenetic drift is the term given to epigenetic modifications as they occur as a direct function with age. While age is a known risk factor for many diseases, age-related methylation has been found to occur differentially at specific sites along the genome. Over time, this can result in measurable differences between biological and chronological age. Epigenetic changes have been found to be reflective of lifestyle and may act as functional biomarkers of disease before clinical threshold is reached.

A more recent study, where 114 monozygotic twins and 80 dizygotic twins were analyzed for the DNA methylation status of around 6000 unique genomic regions, concluded that epigenetic similarity at the time of blastocyst splitting may also contribute to phenotypic similarities in monozygotic co-twins. This supports the notion that microenvironment at early stages of embryonic development can be quite important for the establishment of epigenetic marks. Congenital genetic disease is well understood and it is clear that epigenetics can play a role, for example, in the case of Angelman syndrome and Prader–Willi syndrome. These are normal genetic diseases caused by gene deletions or inactivation of the genes but are unusually common because individuals are essentially hemizygous because of genomic imprinting, and therefore a single gene knock out is sufficient to cause the disease, where most cases would require both copies to be knocked out.

Genomic imprinting
Some human disorders are associated with genomic imprinting, a phenomenon in mammals where the father and mother contribute different epigenetic patterns for specific genomic loci in their germ cells. The best-known case of imprinting in human disorders is that of Angelman syndrome and Prader–Willi syndrome – both can be produced by the same genetic mutation, chromosome 15q partial deletion, and the particular syndrome that will develop depends on whether the mutation is inherited from the child's mother or from their father.

In the Överkalix study, paternal (but not maternal) grandsons of Swedish men who were exposed during preadolescence to famine in the 19th century were less likely to die of cardiovascular disease. If food was plentiful, then diabetes mortality in the grandchildren increased, suggesting that this was a transgenerational epigenetic inheritance. The opposite effect was observed for females – the paternal (but not maternal) granddaughters of women who experienced famine while in the womb (and therefore while their eggs were being formed) lived shorter lives on average.

Examples of drugs altering gene expression from epigenetic events
The use of beta-lactam antibiotics can alter glutamate receptor activity and the action of cyclosporine on multiple transcription factors. Additionally, lithium can impact autophagy of aberrant proteins, and opioid drugs via chronic use can increase the expression of genes associated with addictive phenotypes.

Parental nutrition, in utero exposure to stress or endocrine disrupting chemicals, male-induced maternal effects such as the attraction of differential mate quality, and maternal as well as paternal age, and offspring gender could all possibly influence whether a germline epimutation is ultimately expressed in offspring and the degree to which intergenerational inheritance remains stable throughout posterity. However, whether and to what extent epigenetic effects can be transmitted across generations remains unclear, particularly in humans.

Addiction
Addiction is a disorder of the brain's reward system which arises through transcriptional and neuroepigenetic mechanisms and occurs over time from chronically high levels of exposure to an addictive stimulus (e.g., morphine, cocaine, sexual intercourse, gambling). Transgenerational epigenetic inheritance of addictive phenotypes has been noted to occur in preclinical studies. However, robust evidence in support of the persistence of epigenetic effects across multiple generations has yet to be established in humans; for example, an epigenetic effect of prenatal exposure to smoking that is observed in great-grandchildren who had not been exposed.

Research
The two forms of heritable information, namely genetic and epigenetic, are collectively called dual inheritance. Members of the APOBEC/AID family of cytosine deaminases may concurrently influence genetic and epigenetic inheritance using similar molecular mechanisms, and may be a point of crosstalk between these conceptually compartmentalized processes.

Fluoroquinolone antibiotics induce epigenetic changes in mammalian cells through iron chelation. This leads to epigenetic effects through inhibition of α-ketoglutarate-dependent dioxygenases that require iron as a co-factor.

Various pharmacological agents are applied for the production of induced pluripotent stem cells (iPSC) or maintain the embryonic stem cell (ESC) phenotypic via epigenetic approach. Adult stem cells like bone marrow stem cells have also shown a potential to differentiate into cardiac competent cells when treated with G9a histone methyltransferase inhibitor BIX01294.

Cell plasticity, which is the adaptation of cells to stimuli without changes in their genetic code, requires epigenetic changes. These have been observed in cell plasticity in cancer cells during epithelial-to-mesenchymal transition and also in immune cells, such as macrophages. Interestingly, metabolic changes underly these adaptations, since various metabolites play crucial roles in the chemistry of epigenetic marks. This includes for instance alpha-ketoglutarate, which is required for histone demethylation, and acetyl-Coenzyme A, which is required for histone acetylation.

Epigenome editing
Epigenetic regulation of gene expression that could be altered or used in epigenome editing are or include mRNA/lncRNA modification, DNA methylation modification and histone modification.

CpG sites, SNPs and biological traits
Methylation is a widely characterized mechanism of genetic regulation that can determine biological traits. However, strong experimental evidences correlate methylation patterns in SNPs as an important additional feature for the classical activation/inhibition epigenetic dogma. Molecular interaction data, supported by colocalization analyses, identify multiple nuclear regulatory pathways, linking sequence variation to disturbances in DNA methylation and molecular and phenotypic variation.

UBASH3B locus
UBASH3B encodes a protein with tyrosine phosphatase activity, which has been previously linked to advanced neoplasia. SNP rs7115089 was identified as influencing DNA methylation and expression of this locus, as well as and Body Mass Index (BMI). In fact, SNP rs7115089 is strongly associated with BMI and with genetic variants linked to other cardiovascular and metabolic traits in GWASs. New studies suggesting UBASH3B as a potential mediator of adiposity and cardiometabolic disease. In addition, animal models demonstrated that UBASH3B expression is an indicator of caloric restriction that may drive programmed susceptibility to obesity and it is associated with other measures of adiposity in human peripherical blood.

NFKBIE locus
SNP rs730775 is located in the first intron of NFKBIE and is a cis eQTL for NFKBIE in whole blood. Nuclear factor (NF)-κB inhibitor ε (NFKBIE) directly inhibits NF-κB1 activity and is significantly co-expressed with NF-κB1, also, it is associated with rheumatoid arthritis. Colocalization analysis supports that variants for the majority of the CpG sites in SNP rs730775 cause genetic variation at the NFKBIE locus which is suggestible linked to rheumatoid arthritis through trans acting regulation of DNA methylation by NF-κB.

FADS1 locus
Fatty acid desaturase 1 (FADS1) is a key enzyme in the metabolism of fatty acids. Moreover, rs174548 in the FADS1 gene shows increased correlation with DNA methylation in people with high abundance of CD8+ T cells. SNP rs174548 is strongly associated with concentrations of arachidonic acid and other metabolites in fatty acid metabolism, blood eosinophil counts. and inflammatory diseases such as asthma. Interaction results indicated a correlation between rs174548 and asthma, providing new insights about fatty acid metabolism in CD8+ T cells with immune phenotypes.

Pseudoscience
As epigenetics is in the early stages of development as a science and is surrounded by sensationalism in the public media, David Gorski and geneticist Adam Rutherford have advised caution against the proliferation of false and pseudoscientific conclusions by new age authors making unfounded suggestions that a person's genes and health can be manipulated by mind control. Misuse of the scientific term by quack authors has produced misinformation among the general public.

title: Epigenetics


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Hereford

Hereford is a cathedral city, civil parish and the county town of Herefordshire, England. It lies on the River Wye, approximately 16 mi east of the border with Wales, 23 mi north-west of Gloucester and 24 mi south-west of Worcester. With a population of 53,112 in 2021, it is the largest settlement in Herefordshire.

An early town charter from 1189, granted by Richard I of England, describes it as "Hereford in Wales". Hereford has been recognised as a city since time immemorial, with the status being reconfirmed in October of 2000. Hereford has been a civil parish since 2000.

It is now known chiefly as a trading centre for a wider agricultural and rural area. Products from Hereford include cider, beer, leather goods, nickel alloys, poultry, chemicals and sausage rolls, as well as the famous Hereford breed of cattle.

Toponymy
The Herefordshire edition of Cambridge County Geographies states "a Welsh derivation of Hereford is more probable than a Saxon one" but the name "Hereford" is also said to come from the Anglo-Saxon "here", an army or formation of soldiers, and the "ford", a place for crossing a river (cf. Herford, Westphalia, with the same Saxon etymology). If this is the origin it suggests that Hereford was a place where a body of armed men forded or crossed the Wye. The Welsh name for Hereford is Henffordd, meaning "old road", and probably refers to the Roman road and Roman settlement at nearby Stretton Sugwas. Some historical documents refer to "Hereford in Wales".

History
Hereford became the seat of Putta, Bishop of Hereford, some time between 676 and 688 AD, after which the settlement continued to grow due to its proximity to the border between Mercia and Wales, becoming the Saxon capital of West Mercia by the beginning of the 8th century.

Hostilities between the Anglo-Saxons and the Welsh came to a head with the Battle of Hereford in 760, in which the Britons freed themselves from the influence of the English. Hereford was again targeted by the Welsh during their conflict with the Anglo-Saxon King Edward the Confessor in 1056 when, supported by Viking allies, Gruffydd ap Llywelyn, King of Gwynedd and Powys, marched on the town and put it to the torch before returning home in triumph. Hereford had the only mint west of the Severn in the reign of Athelstan (924–939), and it was to Hereford, then a border town, that Athelstan summoned the leading Welsh princes.

The present Hereford Cathedral dates from the early 12th century, as does the first bridge across the Wye. Former Bishops of Hereford include Saint Thomas de Cantilupe and Lord High Treasurer of England Thomas Charlton.

Hereford was home to a small but relatively important Jewish community until 1290, when Jews were expelled from England by Edward I. Jews from Worcester and Gloucester moved to Hereford after their expulsion in January 1275 by the Queen mother, Eleanor of Provence. The Bishops of Hereford campaigned against the presence of the community, including Cantilupe, and Richard Swinefield, who tried to stop social contact between Christians and Jews.

The city gave its name (translated to French) to two suburbs of Paris, France: Maisons-Alfort (population 54,600) and Alfortville (population 36,232), due to a manor built there by Peter of Aigueblanche, Bishop of Hereford, in the middle of the 13th century.

Hereford, a base for successive holders of the title Earl of Hereford, was once the site of a castle, Hereford Castle, which rivalled that of Windsor in size and scale. This was a base for repelling Welsh attacks and a secure stronghold for English kings such as King Henry IV when on campaign in the Welsh Marches against Owain Glyndŵr. The castle was dismantled in the 18th century and landscaped into Castle Green.

After the Battle of Mortimer's Cross in 1461, during the Wars of the Roses, the defeated Lancastrian leader Owen Tudor (grandfather of the future Henry VII of England) was taken to Hereford by Sir Roger Vaughan and executed in High Town. A plaque now marks the spot of the execution. Vaughan was later himself executed, under a flag of truce, by Owen's son Jasper.

During the English Civil War, the city changed hands several times. On 30 September 1642 Parliamentarians led by Sir Robert Harley and Henry Grey, 1st Earl of Stamford occupied the city without opposition. In December they withdrew to Gloucester because of the presence in the area of a Royalist army under Lord Herbert. The city was again occupied briefly from 23 April to 18 May 1643 by Parliamentarians commanded by Sir William Waller but it was in 1645 that the city saw most action. On 31 July 1645 a Scottish army of 14,000 under Alexander Leslie, 1st Earl of Leven besieged the city but met stiff resistance from its garrison and inhabitants. They withdrew on 1 September when they received news that a force led by King Charles was approaching. The city was finally taken for Parliament on 18 December 1645 by Colonel Birch and Colonel Morgan. King Charles showed his gratitude to the city of Hereford on 16 September 1645 by augmenting the city's coat of arms with the three lions of Richard I of England, ten Scottish Saltires signifying the ten defeated Scottish regiments, a very rare lion crest on top of the coat of arms signifying "defender of the faith" and the even rarer gold-barred peer's helm, found only on the arms of one other municipal authority: those of the City of London.

Nell Gwynne, actress and mistress of King Charles II, is said to have been born in Hereford in 1650 (although other towns and cities, notably Oxford, claim her as their own); Gwynn Street is named after her. Another famous actor born in Hereford is David Garrick (1717–1779).

The Bishop's Palace next to the cathedral was built in 1204 and is continually used to the present day. Hereford Cathedral School is one of the oldest schools in England. The Harold Street Barracks were completed in 1856.

During World War I, in 1916, a fire at the Garrick Theatre killed eight young girls who had been performing at a charity concert.

Governance
The main local government body covering Hereford is Herefordshire Council. Hereford has a "City Council" but this is actually a parish council with city status, and has only limited powers.

Historically Hereford has been the county town of Herefordshire. In 1974 Herefordshire was merged with Worcestershire to become part of the county of Hereford and Worcester, and Hereford became a district of the new county. Hereford had formed a historic borough and was reformed by the Municipal Corporations Act 1835. On 1 April 1998 the County of Hereford and Worcester was abolished, and Herefordshire and Worcestershire were re-established as separate counties.

However the new Herefordshire was a unitary authority without any districts, and so Hereford lost its district status (although, confusingly, the authority's full legal name is the County of Herefordshire District Council). Charter Trustees were appointed to preserve mayoral traditions until a civil parish council could be set up, which happened in 2000. Hereford is one of only eight civil parishes in England which have city status. It is based at Hereford Town Hall.

Hereford was the name of a parliamentary constituency that was centered in the city, from 1295 to 2010, when it was renamed as Hereford and South Herefordshire. The current Member of Parliament (MP) in the House of Commons for Hereford and South Herefordshire is Jesse Norman of the Conservative Party.

Climate
As with all of the UK, Hereford experiences a maritime climate, with limited seasonal temperature ranges, and generally moderate rainfall throughout the year. The nearest Met Office weather station for which 30-year averages are available is Credenhill weather station, about 4 mi north west of the city centre. Before 2001, the weather station at Preston Wynne (7 miles, 11 km to the north-east) provided the data.

Since 2001, extremes at Hereford Credenhill have ranged from 33.6 °C during July 2006, to as low as -15.8 °C during December 2010.

In February 2020 many houses in Hereford were evacuated due to floods.

Road
Hereford, as an ancient crossing over the River Wye, has long been important within the regional and national transport network. Today, the town is served by several major routes, including:

 * | Southbound: Ross-on-Wye. | Northbound: Leominster and Shrewsbury.
 * | Westbound: Hay-on-Wye and Brecon. | Eastbound: Ledbury and Tewkesbury.
 * | South-west: Abergavenny and Merthyr Tydfil. | North-east: Bromyard.
 * | North-east: Worcester.

The nearest motorway is the, which passes to the south of Ledbury.

Along the northern rim of the city, the A4103 is named Roman Road, running in a straight line from east to west.

Only one of these major routes crosses the River Wye, the A49/Victoria Street, which is carried by Greyfriars Bridge.

In 2017, Hereford was named Britain's second slowest city, with an average traffic speed of 14.09 mph. Cambridge topped the list, whilst London came third with vehicles travelling at an average 14.59 mph.

Future
There have been plans for many years for a north–south bypass and currently the plan is for a nine-mile (14 km) dual carriageway; however, HM Government as yet has refused to grant permission or supply funds. However, the Hereford Link Road was completed in December 2017, costing around £34,000,000 to build. There are plans to add new homes, a university building and a transport hub to this area.

Plans for the north–south bypass were scrapped in February 2021.

Railway
Hereford railway station is situated to the north of the city centre. The station is the western terminus of the Cotswold Line; it is a through station on the Welsh Marches Line between Abergavenny and Leominster.

The station is managed by Transport for Wales, which operates services to destinations such as Newport, Cardiff and Swansea to the south. Transport for Wales also operates services northbound towards Leominster, Shrewsbury, Chester, Manchester and Holyhead.

On the Cotswold Line, services are operated by West Midlands Railway towards Birmingham, via destinations such as Great Malvern, Worcester and Bromsgrove. Great Western Railway operates regular services to London Paddington via Worcester, Oxford and Reading, amongst other destinations.

A second station served Hereford, Hereford Barton, which closed in 1893.

Cycling
Cycling infrastructure in Hereford is maintained by Herefordshire Council and Sustrans.

An unbroken shared-use path for cyclists and pedestrians runs along the western rim of the city, from Newton Farm to Holmer. The Great Western Way route crosses the River Wye using Hunderton Bridge.

National Cycle Route 46 runs southbound from Hereford to Swansea. The route is signposted and unbroken, and the next destination from Hereford en route is Kilpeck Castle. The route passes through Abergavenny and the Heads of the Valleys as it enters Wales. As of Summer 2020, Sustrans proposes an extension to Route 46 running eastbound from Hereford to Worcester.

National Cycle Route 44 leaves Hereford to the southeast and runs as far as Rotherwas. The route is incomplete; once completed, Route 44 will run to Ludlow Castle to the north and Cinderford, Forest of Dean to the south. The nearest bike park is the Black Mountain Bike Park.

Buses
Since the decision of First Midland Red to pull out of the city in 2015, the majority of bus routes have been operated by Hereford bus and coach operator Yeomans Canyon. The 33 service to Gloucester and 36 service to Monmouth are operated by Stagecoach West, services historically in the hands of Red & White. Other bus services are operated by various operators. TrawsCymru links Hereford railway station to Hay-on-Wye and Brecon on the T14 service. Stagecoach South Wales has the 23 which runs to Abergavenny and Newport

Military associations
In 1999, the British Army Special Air Service (SAS) moved from their base at Stirling Lines (formerly Bradbury Lines) in Hereford, their home since 1960, to a former Royal Air Force base RAF Credenhill in Credenhill that had been redeveloped and was designated as Stirling Lines in 2000. The clock tower on which the names of deceased SAS soldiers are inscribed was re-located.

Economy
The main public service employers in Hereford include:
 * Herefordshire Council
 * NHS Herefordshire

In 2005 Hereford was granted Fairtrade City status.

Major employers in the city include:
 * Bulmers, now owned by Heineken – Cider and alcoholic beverages producer. Brands include Woodpecker Cider, Strongbow and Bulmers Cider
 * Special Metals Wiggin Ltd – Manufacturers of nickel alloys
 * Cargill Meats Europe (formerly Sun Valley) – Manufacturers and suppliers of food products for retailers and foodservice operators
 * Painter Brothers – Manufacturers of galvanized steel towers including The Skylon

Herefordshire is a centre for cider production as it supports many acres of orchards, so many breweries and associated organisations exist here, along with other heavy and light industries. Within the city, many are based at the Rotherwas Industrial Estate.

Regeneration
Many of the schools in Hereford have been rebuilt and improved. The Herefordshire and Ludlow College has also been rebuilt to a 21st-century standard. In September 2021 a new higher education institution NMITE (New Model Institute for Technology and Engineering) welcomed its first students who are undertaking an MEng Integrated Engineering. There have been a number of improvements at Hereford Sixth Form College, where a new business block extension was completed in 2013 and a new reception area was completed in 2015.

Hereford benefitted from the PFI reconstruction schemes for NHS hospitals, with the former County Hospital site having £60 million spent on a brand new, one-site hospital to replace the former 3 hospitals: the General, the Eye Hospital, and the County Hospital. The new Hereford County Hospital was the single largest investment in Herefordshire at that point. In 2015, further funds for more improvements at the hospital were granted.

Current and future projects
A major regeneration project is taking place in Hereford city centre, formerly known as the Edgar Street Grid. This covers an area of around 100 acre just north of the old city walls. Work started on 8 October 2012, and should take around 15 years to complete the whole project. The regeneration includes the rebuilding of the canal basin at the end of the currently disused Herefordshire and Gloucestershire Canal. The £80 million phase 1 includes a supermarket, department store, multiplex cinema, shops, restaurants, and other facilities and opened in late Spring 2014.

The Butter Market is due for refurbishment and proposals are being examined.

A proposed bypass has been drawn up to circulate the city, which suffers from rush hour traffic, with potential routes either to the east or west of the city. Both routes would connect with the Rotherwas Access Road which was recently completed, connecting the Rotherwas Industrial Estate to the A49. Rotherwas itself has recently been awarded an Enterprise Zone status by the government which is expected to boost the economy and bring in thousands of new jobs.

A second railway station for Hereford has been discussed, which would be situated in Rotherwas as part of the Enterprise Zone.

Hereford is due to receive half of the 20,600 new homes expected to be built in the county by 2026 as part of the Regional Spatial Strategy.

Sport
Hereford is the home of the football club, Hereford FC who play at Edgar Street in the National League North. They are a phoenix club that was set up in the wake of the demise of Hereford United Football Club in 2014. United were best known for beating Newcastle 2–1 in an FA Cup replay in January 1972, when they were still a non-league side and Newcastle were in the top division of English football. Other city clubs include Westfields, Hereford Pegasus and Hereford Lads Club, all of whom play in the Hellenic Football League.

Hereford Rugby Club announced plans in 2012 for a £6 million move to a new home. Also based at the Rugby club are Hereford Stampede who are an American football team who play in the BAFA National Leagues and made their full League debut in 2021.

Hereford Hockey Club is based at the Hereford City Sports Club, with teams entered into leagues in the West Hockey Association.

The city is home to Hereford Racecourse, a traditional National Hunt course to the north of the city centre which hosted around twenty meetings a year. The company who leased the site decided in 2012 that the site was not viable. What many thought to be the last meeting was held on 16 December 2012, however the course reopened for racing in October 2016.

Golf courses surround the city at Wormsley (Herefordshire GC), Kington, Burghill and Brockington. The racecourse surrounds a golf course in Holmer.

Public leisure
Hereford's public leisure facilities are managed by a not-for-profit trust HALO Leisure, which runs the Hereford Leisure Centre (that includes sports halls, gymnasium, squash courts, golf course and an outdoor athletics facility), and the Hereford Leisure Pool (which includes a gymnasium, full size swimming pool, leisure pool, diving pool, and learners pool).

Clubs and societies
The Hereford Rowing Club (along with the Kayak Club) uses the River Wye. The stretch of river is also used for other water sports. Hereford has a nine pin skittle league, formed on 24 October 1902, and today consists of five divisions.

Hereford has other clubs and societies including the Railway Club, Welsh Club, Military Club, Richmond Place Club and the Whitecross Squash & Lawn Tennis Club.

Hereford has several music clubs/societies such as Herefordshire Youth Orchestra, a group for those up to the age of 21.

University
A new higher education institution, the New Model Institute for Technology and Engineering (NMITE), has been created in Hereford, which had its first intake of students in September 2021. It is envisioned as a seed institution for a future University of Hereford within a decade.

Colleges
Hereford is home to five colleges, including:
 * Hereford College of Arts – a publicly funded art school located on Folly Lane, with a Higher Education centre on College Road in the former main buildings of the Royal National College for the Blind. The University of Wales Trinity St Davids co-operate to provide degree qualifications.
 * Herefordshire and Ludlow College (HLC) formerly known as Hereford College of Technology – The Folly Lane facility includes a university centre for the University of Worcester.

The National School of Blacksmithing is the oldest established Blacksmithing college in the UK, also the largest facility for training smiths in Europe. This is also part of HLC.

 * Hereford Sixth Form College
 * The Royal National College for the Blind – One of the top colleges in Europe for blind and visually impaired students, and one of only two in Britain. The college occupies the former Hereford College of Education campus. The college often plays host to major blind sporting competitions like the Blind World Cup 2010 and Euro 2015 Blind Football Championships, and currently hosts the England Blind Football squad training camps.
 * Holme Lacy College – An agricultural college that was part of the Pershore Group of Colleges (now Warwickshire College), but currently belongs to Herefordshire and Ludlow College (HLC).

Schools
Hereford's many secondary schools include:

 * The Steiner Academy Hereford – The first Rudolf Steiner school in England to become an academy.
 * Aylestone Business and Enterprise College – A co-educational comprehensive school for pupils aged between 11 and 16, created in 1976 by merging two former grammar schools, the Hereford High School for Boys and the Hereford High School for Girls. Specialises in Business and Enterprise.
 * The Bishop of Hereford's Bluecoat School – A co-educational voluntary aided comprehensive school for pupils aged between 11 and 16, formed in 1973 from two former church secondary schools, the Bluecoat foundation, dating back to 1710 and the Bishop's School, a secondary modern school founded in 1958. It is now a Technology College with a second specialism in Languages.
 * The Hereford Academy – A high school for pupils aged between 11 and 19. It was known as Haywood High School in the late seventies until 2006, when it was renamed as Wyebridge Sports College. As of 1 September 2009 it was renamed The 'Hereford Academy'. It has been, like Whitecross High School, re-classified as a 'Sports College'. The academy's new building opened in September 2011, and the demolition of the old school site, making way for new playing fields to be laid out, was completed in Spring 2012.
 * Hereford Cathedral School – A co-educational independent school and sixth form, and a member of the Headmasters' and Headmistresses' Conference. The earliest existing records date from 1384 though it is likely that a school was associated with the cathedral from its foundation in the late 7th century. HCS, together with HCJS (see below) educates the choristers for Hereford Cathedral Choir.
 * St Marys RC High School – A Roman Catholic Comprehensive School for boys and girls aged 11–16. The school primarily serves the Catholic Communities of Herefordshire and is situated in a very attractive rural location close to the River Lugg, a few miles to the east of the City of Hereford in the village of Lugwardine.
 * Whitecross Hereford High School – A specialist Sports College, which moved to a brand new PFI building in June 2006. The college for pupils aged between 11 and 16 aims to use the new facility to provide the best high school education for its pupils in the topic of Sports & Fitness.

Primary schools in the city include Hereford Cathedral Junior School, a co-educational independent school. Hereford Cathedral Junior School is, with Hereford Cathedral School, part of the ancient Hereford Cathedral Foundation dating back to 676. The Junior School was founded as an independent school in 1898. The city's other primary schools are: Lord Scudamore Academy, St James C of E, St Francis Xavier R.C, Trinity, Holmer C of E, Marlbrook, Riverside, St Martin's, Broadlands, Riverside, Hampton Dene and St Paul's C of E.

Health and social care
In early 2008, Herefordshire Council and NHS Herefordshire became the first local authority and primary care trust to form a new kind of partnership.

The major hospital in Hereford is the Hereford County Hospital. Ambulance services are provided by the West Midlands Ambulance Service NHS Trust. The Midlands Air Ambulance charity provides air ambulance services across Herefordshire.

A private national firm operates a hospital in Hereford, and the city is well-populated with council-funded, private and charity based nursing, residential and other elderly care homes and facilities.

Agriculture
Farming has played a major part in the history of the county of Herefordshire, and for many years the City of Hereford was the epicentre, playing host to the Cattle Market; a major market site.

With the 2001 foot-and-mouth outbreak the market suffered with trade reduced. Established by Act of Parliament, the market had to be provided, and so a Bill was introduced in 2003 to move the site to the outskirts of the city. The inner city site would then be available for redevelopment, a process that has now finished.

The new Hereford Cattle Market opened its doors in August 2011 on the site just outside the city and has already proved so successful that trading and business is up on the previous site's record.

Music
The annual Three Choirs Festival, originating in the 18th century and one of the oldest music festivals in the British Isles, is held in Hereford every third year, the other venues being Gloucester and Worcester.

The hymn tune 'Hereford' was written by Samuel Sebastian Wesley (1810–1876). He was an organist at Hereford Cathedral (1832–1835). This tune is often sung to the words 'O Thou who camest from above'.

Composer Sir Edward Elgar lived at Plas Gwyn, Eign Hill, in Hereford between 1904 and 1911, writing some of his most famous works during that time. He is commemorated with a statue on the Cathedral Close. One of his Enigma Variations was inspired by a bulldog named Dan falling into the River Wye at Hereford, and the dog is similarly honoured with a wooden statue beside the river. Not long after moving into the city he was (despite not being a city council member) offered but declined the office of mayor of the city. He visited the city as a conductor at the Three Choirs Festival, the last occasion in 1933 prior to his death.

Hereford is home to the Hereford Police Male Voice Choir who competed on the BBC TV show "Last Choir Standing", and the Railway Choir.

A charity music school is based in Hereford.

Art
H.Art, or Herefordshire Art Week, is an annual county-wide exhibition held in September, displaying the work of local artists. Many places usually closed to the public are opened during this week, such as the Bishop's Palace at the cathedral.

Polish-born sculptor Walenty Pytel has had studios in Hereford since 1963 after training at Hereford College of Art.

There is a statue of a Bronze Hereford bull designed by Brian Alabaster ARBS in front of The Old House.

Literature
The troops of the fictional commando squad Rainbow were based at RAF Hereford, as detailed in the novel Rainbow Six.

The action of the fictional novels Shades of Grey and The Last Dragonslayer by Jasper Fforde take place in Hereford.

Phil Rickman's Merrily Watkins series of supernatural and mystery novels is set in and around Hereford.

Comedy writer Aaron Gillies began writing using Twitter while working as a sound technician at The Courtyard.

Media
The local radio stations include Free Radio Herefordshire & Worcestershire (formerly known as Wyvern) which broadcasts on 97.6–96.7–102.8 FM, Sunshine Radio on 106.2 FM, and BBC Hereford and Worcester which broadcasts on 94.7FM. Hereford FC has its own online Radio station, RadioHerefordFC covering all its matches Home and Away. It has a 24/7 eclectic music output.

The Hereford Times is the city's only remaining weekly local newspaper as the 'Hereford Journal' ceased publication on 11 June 2014 and the 'Hereford admag' ceased publication in September 2018.

Local TV content is currently provided by BBC Midlands Today and ITV News Central.

Entertainment
The city's main theatre and cultural venue is the Courtyard Centre for the Arts which was opened in 1998, replacing the New Hereford Theatre.

There is also a multi screen Odeon cinema in the Old Market precinct.

MFA Bowl (formerly known as TGS), home to a Ten Pin Bowling alley and Mini Golf course is located near the railway station.

There is a dedicated Skatepark on Holmer Road.

Notable people

 * See Category:People from Hereford

 * Richard Hakluyt (1553–1616), an English writer who promoted the English colonization of North America was born in the town.
 * John Kemble (c. 1599–1679), Catholic priest and martyr, was born at Rhydicar Farm, St Weonards, near Hereford.
 * Thomas Traherne (1636 or 1637 – 1674), English metaphysical poet, cleric, theologian, and writer.
 * Nell Gwyn (1650–1687), David Garrick (1717–1779) and Sarah Siddons (1755–1831), actors and actresses, are all historical figures popularly associated with Hereford.
 * The highwayman William Spiggot (1691–1721) declared before his execution to the Ordinary's Accounts of Newgate Prison in London that he was the son of an innkeeper from Hereford.
 * Major-General Stringer Lawrence (1698–1775), first commander-in-chief of British troops in India, under whose command Robert Clive (1725–1774) served, was born in Hereford.
 * William Samuel Symonds (1818–1887), was an English cleric, geologist and author from Hereford.
 * Henry James, 1st Baron James of Hereford (1828–1911), known as Sir Henry James was an Anglo-Welsh lawyer and statesman.
 * The composer Sir Edward Elgar (1857–1934) lived in Hereford 1904–1911, during which time he was offered but declined the city mayoralty.
 * The rugby union player and sports broadcaster Teddy Wakelam (1893–1963), was born in Hereford.
 * Broadcaster Gilbert Harding (1907–1960) was born there when his father was master of the local workhouse, as was contemporary actress Beryl Reid OBE (1919–1996).
 * Al Vandenberg (1932–2012), American photographer, worked and died in Hereford.
 * John Williamson (1937–2021), international economist and author of "What Washington Means by Policy Reform" was born in Hereford.
 * Mike Osborne (1941–2007), notable jazz saxophonist active from 1966 to 1981, was born and spent the last decades of his life in Hereford suffering from mental illness.
 * Frank Oz (born 1944), puppeteer for The Muppets and Yoda of Star Wars was born in Hereford and lived there for the first five years of his life.
 * Simon Carroll (1964–2009), studio potter was born in Hereford.
 * The original lineup of The Pretenders (formed 1978), with the exception of lead singer Chrissie Hynde, were from Hereford, as were the rock band Mott the Hoople (formed 1966).
 * Ellie Goulding (born 1986), pop singer and songwriter was born in Hereford.
 * Lucy Letby (born 1990), serial killer grew up in Hereford.
 * Footballer Connor Wickham (born 1993) was born in the city.
 * Jordan James (born 2004), professional footballer with Birmingham City and Wales national team.

Tourism and attractions
Hereford Cathedral dates from 1079 and contains the Mappa Mundi, a medieval map of the world dating from the 13th century which was restored in the late 20th century. It also has a chained library.

The Old House, Hereford is an historic black and white house in the centre of High Town in Hereford. It is now a museum about life in the Jacobean era of the 1600s when it was built.

The Hereford Museum and Art Gallery, housed in a Victorian Gothic building and opened in 1874, presents artefacts, fine art, and decorative art associated with the local area.

The Hereford Cider Museum is in the city, with a shop, and an interactive guide to producing the drink. It is a registered Charity Trust founded in the early 1970s by people who wanted to record the past, and the disappearing traditional art of cider making that had been practised for generations on the farms in the "Cider Counties". Situated in an old cider factory, it opened in 1980 and 1981. In the spring/summer a cider festival is held, started in the mid-1980s, by the Friends of the Museum with the advice of Long Ashton Research station near Bristol. It has a display of named cider apples, and the apples are pressed in the old way. The Museum holds in its Pomological Archive a number of records pertaining to apples and cider.

The Violette Szabo Museum is in Wormelow village, outside the city.

Holme Lacy House, now a hotel for a national chain, was built near the city by John Scudamore in the 1500s. It has played host to famous historical figures in its time.

Festivals
Several festivals are hosted in Hereford including the Beer on the Wye festival, the Hereford Food Festival, and the Three Choirs Festival.

Twin towns

 * Dillenburg, Germany
 * Vierzon, France (since 1994)

Freedom of the City
The following people and military units have received the Freedom of the City of Hereford.

Individuals

 * John Edward Masefield: 1930.
 * Graham John Turner: 31 October 2010.

Military units
Source:
 * The Herefordshire Light Infantry: September 1945.
 * RAF Hereford: April 1959.
 * The King's Shropshire Light Infantry: April 1960.
 * The Light Infantry: July 1971.
 * HMS Antelope, RN: March 1976.
 * The Royal British Legion: April 1976.
 * The 22nd Special Air Services Regiment: April 1981.
 * The Burma Star Association: April 1982.
 * The Rifles: July 2008.

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title: Hereford