Imprinting is a dynamic process. It must be possible to erase and re-establish imprints through each generation so that genes that are imprinted in an adult may still be expressed in that adult's offspring. (For example, the maternal genes that control insulin production will be imprinted in a male but will be expressed in any of the male's offspring that inherit these genes.) The nature of imprinting must therefore be  epigenetic  rather than DNA sequence dependent. In  germline  cells the imprint is erased and then re-established according to the  sex  of the individual, i.e. in the developing sperm (during  spermatogenesis ), a paternal imprint is established, whereas in developing oocytes ( oogenesis ), a maternal imprint is established. This process of erasure and  reprogramming [ 45 ]  is necessary such that the germ cell imprinting status is relevant to the sex of the individual. In both plants and mammals there are two major mechanisms that are involved in establishing the imprint; these are  DNA methylation  and  histone  modifications.


Recently, a new study [ 46 ]  has suggested a novel inheritable imprinting mechanism in humans that would be specific of  placental  tissue and that is independent of DNA methylation (the main and classical mechanism for genomic imprinting). This was observed in humans, but not in mice, suggesting development after the evolutionary divergence of humans and mice, ~80  Mya . Among the hypothetical explanations for this novel phenomenon, two possible mechanisms have been proposed: either a histone modification that confers imprinting at novel placental-specific imprinted  loci  or, alternatively, a recruitment of  DNMTs  to these loci by a specific and unknown  transcription factor  that would be expressed during early trophoblast differentiation.


The grouping of imprinted genes within clusters allows them to share common regulatory elements, such as  non-coding RNAs  and  differentially methylated regions (DMRs) . When these regulatory elements control the imprinting of one or more genes, they are known as imprinting control regions (ICR). The expression of  non-coding RNAs , such as  antisense Igf2r RNA  ( Air ) on mouse chromosome 17 and  KCNQ1OT1  on human chromosome 11p15.5, have been shown to be essential for the imprinting of genes in their corresponding regions. [ 47 ]


Differentially methylated regions are generally segments of DNA rich in  cytosine  and  guanine  nucleotides, with the cytosine nucleotides methylated on one copy but not on the other. Contrary to expectation, methylation does not necessarily mean silencing; instead, the effect of methylation depends upon the default state of the region. [ 48 ]


The control of expression of specific genes by genomic imprinting is unique to  therian  mammals ( placental mammals  and  marsupials ) and flowering plants. Imprinting of whole chromosomes has been reported in mealybugs (Genus:  Pseudococcus ) [ 15 ] [ 16 ] [ 17 ] [ 18 ]  and a  fungus gnat  ( Sciara ). [ 49 ]  It has also been established that  X-chromosome  inactivation occurs in an imprinted manner in the extra-embryonic tissues of mice and all tissues in marsupials, where it is always the paternal X-chromosome which is silenced. [ 5 ] [ 50 ]


The majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta. [ 27 ] [ 51 ]  Other imprinted genes are involved in post-natal development, with roles affecting suckling and metabolism. [ 51 ] [ 52 ]


A widely accepted hypothesis for the evolution of genomic imprinting is the "parental conflict hypothesis". [ 53 ]  Also known as the kinship theory of genomic imprinting, this hypothesis states that the inequality between parental genomes due to imprinting is a result of the  differing interests of each parent  in terms of the  evolutionary fitness of their genes . [ 54 ] [ 55 ]  The  father 's genes that encode for imprinting gain greater fitness through the success of the offspring, at the expense of the  mother . The mother's evolutionary imperative is often to conserve resources for her own survival while providing sufficient nourishment to current and subsequent litters. Accordingly, paternally expressed genes tend to be growth-promoting whereas maternally expressed genes tend to be growth-limiting. [ 53 ]  In support of this hypothesis, genomic imprinting has been found in all placental mammals, where post-fertilisation offspring resource consumption at the expense of the mother is high; although it has also been found in  oviparous  birds [ 56 ] [ 57 ]  where there is relatively little post-fertilisation resource transfer and therefore less parental conflict. A small number of imprinted genes are fast evolving under positive Darwinian selection possibly due to antagonistic co-evolution. [ 58 ]  The majority of imprinted genes display high levels of micro- synteny  conservation and have undergone very few duplications in placental mammalian lineages. [ 58 ]


However, our understanding of the molecular mechanisms behind genomic imprinting show that it is the maternal genome that controls much of the imprinting of both its own and the paternally-derived genes in the zygote, making it difficult to explain why the maternal genes would willingly relinquish their dominance to that of the paternally-derived genes in light of the conflict hypothesis. [ 59 ]


Another hypothesis proposed is that some imprinted genes act coadaptively to improve both fetal development and maternal provisioning for nutrition and care. [ 9 ] [ 59 ] [ 60 ]  In it, a subset of paternally expressed genes are co-expressed in both the placenta and the mother's hypothalamus. This would come about through selective pressure from parent-infant coadaptation to improve infant survival. Paternally expressed 3 ( PEG3 ) is a gene for which this hypothesis may apply. [ 9 ]


Others have approached their study of the origins of genomic imprinting from a different side, arguing that  natural selection  is operating on the role of epigenetic marks as machinery for homologous chromosome recognition during meiosis, rather than on their role in differential expression. [ 61 ]  This argument centers on the existence of epigenetic effects on chromosomes that do not directly affect gene expression, but do depend on which parent the chromosome originated from. [ 62 ]  This group of epigenetic changes that depend on the chromosome's parent of origin (including both those that affect gene expression and those that do not) are called parental origin effects, and include phenomena such as paternal  X inactivation  in the  marsupials , nonrandom parental  chromatid  distribution in the ferns, and even mating type switching in yeast. [ 62 ]  This diversity in organisms that show parental origin effects has prompted theorists to place the evolutionary origin of genomic imprinting before the last common ancestor of plants and animals, over a billion years ago. [ 61 ]


Natural selection for genomic imprinting requires genetic variation in a population. A hypothesis for the origin of this genetic variation states that the host-defense system responsible for silencing foreign DNA elements, such as genes of viral origin, mistakenly silenced genes whose silencing turned out to be beneficial for the organism. [ 63 ]  There appears to be an over-representation of  retrotransposed genes , that is to say genes that are inserted into the genome by  viruses , among imprinted genes. It has also been postulated that if the retrotransposed gene is inserted close to another imprinted gene, it may just acquire this imprint. [ 64 ]


Unfortunately, the relationship between the phenotype and genotype of imprinted genes is solely conceptual. The idea is frameworked using two alleles on a single locus and hosts three different possible classes of genotypes. [ 65 ]  The reciprocal heterozygotes genotype class contributes to understanding how imprinting will impact genotype to phenotype relationship. Reciprocal heterozygotes have a genetically equivalent, but they are phenotypically nonequivalent. [ 66 ]  Their phenotype may not be dependent on the equivalence of the genotype. This can ultimately increase diversity in genetic classes, expanding flexibility of imprinted genes. [ 67 ]  This increase will also force a higher degree in testing capabilities and assortment of tests to determine the presences of imprinting.


When a locus is identified as imprinted, two different classes express different alleles. [ 65 ]  Inherited imprinted genes of offspring are believed to be monoallelic expressions. A single locus will entirely produce one's phenotype although two alleles are inherited. This genotype class is called parental imprinting, as well as dominant imprinting. [ 68 ]  Phenotypic patterns are variant to possible expressions from paternal and maternal genotypes. Different alleles inherited from different parents will host different phenotypic qualities. One allele will have a larger phenotypic value and the other allele will be silenced. [ 65 ]  Underdominance of the locus is another possibility of phenotypic expression. Both maternal and paternal phenotypes will have a small value rather than one hosting a large value and silencing the other.


Statistical frameworks and mapping models are used to identify imprinting effects on genes and complex traits. Allelic parent-of-origin influences the vary in phenotype that derive from the imprinting of genotype classes. [ 65 ]  These models of mapping and identifying imprinting effects include using unordered genotypes to build mapping models. [ 67 ]  These models will show classic quantitative genetics and the effects of dominance of the imprinted genes.


Imprinting may cause problems in  cloning , with clones having DNA that is not  methylated  in the correct positions. It is possible that this is due to a lack of time for reprogramming to be completely achieved. When a  nucleus  is added to an egg during  somatic cell nuclear transfer , the egg starts dividing in minutes, as compared to the days or months it takes for reprogramming during  embryonic  development. If time is the responsible factor, it may be possible to delay cell division in clones, giving time for proper reprogramming to occur. [ citation needed ]


In vitro fertilisation , including  ICSI , is associated with an increased risk of imprinting disorders, with an  odds ratio  of 3.7 (95%  confidence interval  1.4 to 9.7). [ 69 ]


Epigenetic deregulations at  H19  imprinted gene in sperm have been observed associated with male  infertility . [ 70 ]  Indeed, methylation loss at H19 imprinted gene has been observed associated with  MTHFR  gene promoter  hypermethylation  in semen samples from  infertile  males.  [ 70 ]


The first imprinted  genetic disorders  to be described in humans were the reciprocally inherited  Prader-Willi syndrome  and  Angelman syndrome . Both syndromes are associated with loss of the chromosomal region 15q11-13 (band 11 of the long arm of chromosome 15). This region contains the paternally expressed genes  SNRPN  and  NDN  and the maternally expressed gene  UBE3A .


The  imprinted brain hypothesis  is an unsubstantiated  hypothesis  in  evolutionary psychology  regarding the causes of  autism spectrum  and  schizophrenia spectrum disorders , first presented by  Bernard Crespi  and  Christopher Badcock  in 2008. It claims that certain autistic and  schizotypal  traits are opposites, and that this implies the  etiology  of the two conditions must be at odds.


The imprinted brain hypothesis is based around genomic imprinting, an  epigenetic  process through which genes are  expressed  differently by way of one parent's contribution having more effect than the other. Specifically, proponents of the imprinted brain hypothesis propose that autism spectrum disorders are caused by paternal overimprinting, while schizophrenia spectrum disorders are caused by maternal overimprinting; they point to a number of supposed  correlations  and anticorrelations seen between the disorders and other traits to support the hypothesis.


DIRAS3  is a paternally expressed and maternally imprinted gene located on chromosome 1 in humans. Reduced DIRAS3 expression is linked to an increased risk of ovarian and breast cancers; in 41% of breast and ovarian cancers the protein encoded by DIRAS3 is not expressed, suggesting that it functions as a  tumor suppressor gene . [ 74 ]  Therefore, if uniparental disomy occurs and a person inherits both chromosomes from the mother, the gene will not be expressed and the individual is put at a greater risk for breast and ovarian cancer.


Other conditions involving imprinting include  Beckwith-Wiedemann syndrome ,  Silver-Russell syndrome , and  pseudohypoparathyroidism . [ 75 ]


Transient neonatal diabetes mellitus  can also involve imprinting. [ 76 ]


The " imprinted brain hypothesis " argues that unbalanced imprinting may be a cause of  autism  and  psychosis .


In insects, imprinting affects entire chromosomes. In some insects the entire paternal genome is silenced in male offspring, and thus is involved in sex determination. The imprinting produces effects similar to the mechanisms in other insects that eliminate paternally inherited chromosomes in male offspring, including  arrhenotoky . [ 77 ]


In social honey bees, the parent of origin and allele-specific genes has been studied from reciprocal crosses to explore the epigenetic mechanisms underlying aggressive behavior. [ 78 ]


In placental species, parent-offspring conflict can result in the evolution of strategies, such as genomic imprinting, for embryos to subvert maternal nutrient provisioning. Despite several attempts to find it, genomic imprinting has not been found in the platypus, reptiles, birds, or fish. The absence of genomic imprinting in a placental reptile, the  Pseudemoia entrecasteauxii , is interesting as genomic imprinting was thought to be associated with the evolution of viviparity and placental nutrient transport. [ 79 ]


Studies in domestic livestock, such as dairy and beef cattle, have implicated imprinted genes (e.g. IGF2) in a range of economic traits, [ 80 ] [ 81 ] [ 35 ]  including dairy performance in Holstein-Friesian cattle. [ 82 ]


In sheep, the CLPG gene ("callipyge" from  Greek , meaning "beautiful buttocks") produces a large buttocks consisting of muscle with very little fat. The large-buttocked phenotype only occurs when the allele is present on the copy of chromosome 18 inherited from a sheep's father and is  not  on the copy of chromosome 18 inherited from that sheep's mother. [ 83 ]  The CLPG locus is encompassed by  Dlk1 -Gtl2, an imprinted region of the mammalian genome, and the atypical presentation of this gene is a result of this imprinting. [ 84 ]


Foraging behavior in mice studied is influenced by a sexually dimorphic allele expression implicating a cross-gender imprinting influence that varies throughout the body and may dominate expression and shape a behavior. [ 85 ] [ 86 ]


A similar imprinting phenomenon has also been described in  flowering plants  (angiosperms). [ 87 ]  During fertilization of the egg cell, a second, separate fertilization event gives rise to the  endosperm , an extraembryonic structure that nourishes the embryo in a manner analogous to the mammalian  placenta . Unlike the embryo, the endosperm is often formed from the fusion of two maternal cells with a male  gamete . This results in a  triploid  genome. The 2:1 ratio of maternal to paternal genomes appears to be critical for seed development. Some genes are found to be expressed from both maternal genomes while others are expressed exclusively from the lone paternal copy. [ 88 ]  It has been suggested that these imprinted genes are responsible for the  triploid block  effect in flowering plants that prevents hybridization between diploids and autotetraploids. [ 89 ]  Several computational methods to detect imprinting genes in plants from reciprocal crosses have been proposed.  [ 90 ] [ 91 ] [ 92 ]


G lal hydrolysis and  L igation  A dapter  D ependent  PCR  assay ( GLAD-PCR assay [ 1 ] ) is the novel method to determine R(5mC)GY sites produced in the course of  de novo   DNA methylation  with DNMTЗA and DNMTЗB  DNA methyltransferases . GLAD-PCR assay do not require bisulfite treatment of the DNA.


Method was specially designed to determine methylation of RCGY site of interest in human and mammalian genomes in excess of corresponding unmethylated sites. This is a typical situation for DNA preparations from clinical samples of blood and tissues.


GLAD-PCR assay is based on the new type of enzymes - site-specific methyl-directed DNA-endonucleases (MD DNA endonucleases). These enzymes are very similar to  restriction enzymes  in biochemical properties and cleave DNA completely, but act in opposite way: they cleave only methylated DNA and do not cleave unmethylated DNA at all.


Mammalian DNA-methyltransferases DNMT1, DNMT3a and DNMT3b catalyze a reaction of DNA methylation.


It is well known that  hypermethylation  of  CpG-islands  in regulatory regions of  promoter  and/or first exon in a variety of genes often occurs at early stages of sporadic  carcinogenesis . This leads to downregulation of the  genes expression  in tumor cells, whereas in a healthy tissue the corresponding genes remain to be active. [ 2 ]  Thus, the detection of such epigenetic biomarkers is one of the most promising diagnostic and prognostic tools [ 3 ]


Study of DNMT3a and DNMT3b substrate specificity has shown that both enzymes predominantly recognize RCGY site and modify internal CG-dinucleotide to form 5’-R(5mC)GY-3’/3’-YG(5mC) R-5’ sequence. [ 4 ]  One of new enzymes GlaI recognizes and cleaves site R(5mC)GY. [ 5 ]  Due to this unique substrate specificity, GlaI is a convenient tool for identification of  de novo  methylated sites in the human and mammalian DNA.


GLAD-PCR assay includes 3 simple steps:


Assay is performed in one tube, takes about 2–3 hours and determines even several copies of DNA with R(5mC)GY site of interest.


H2BK5ac   is an  epigenetic  modification to the DNA packaging protein  Histone H2B . It is a mark that indicates the  acetylation  at the 5th  lysine  residue of the histone H2B protein. H2BK5ac is involved in maintaining stem cells and colon cancer.


Proteins are typically acetylated on  lysine  residues and this reaction relies on  acetyl-coenzyme A  as the acetyl group donor.
In  histone acetylation and deacetylation , histone proteins are acetylated and deacetylated on lysine residues in the N-terminal tail as part of  gene regulation . Typically, these reactions are catalyzed by  enzymes  with  histone acetyltransferase  (HAT) or  histone deacetylase  (HDAC) activity, although HATs and HDACs can modify the acetylation status of non-histone proteins as well. [ 1 ]


The regulation of transcription factors, effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism [ 2 ]  These regulatory mechanisms are analogous to phosphorylation and dephosphorylation by the action of  kinases  and  phosphatases . Not only can the acetylation state of a protein modify its activity but there has been recent suggestion that this  post-translational modification  may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 3 ] [ 4 ] [ 5 ]


In the field of  epigenetics ,  histone acetylation  (and  deacetylation ) have been shown to be important mechanisms in the regulation of gene transcription. Histones, however, are not the only proteins regulated by  posttranslational  acetylation.


H2BK5ac indicates acetylation of  lysine  5 on histone H2B protein subunit:
 [ 6 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in  H3K36me3 . [ 7 ] [ 8 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodeling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 9 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 10 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 11 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 12 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 13 ]


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 14 ]


MAP3K4  controls the activity of  CBP histone acetyltransferase  which acetylates histones H2A and H2B to maintain the  trophoblast  stem cell  epithelial  phenotype. [ 15 ]


Trophoblast are cells forming the outer layer of a  blastocyst , which provide nutrients to the embryo and develop into a large part of the placenta.  They are formed during the first stage of pregnancy and are the first cells to  differentiate  from the  fertilized  egg. [ 16 ]  or, after  gastrulation , [ 17 ]


The histone mark acetylation can be detected in a variety of ways:


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 18 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 19 ]


3. Assay for transposase accessible chromatin sequencing  (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 20 ] [ 21 ] [ 22 ]


H3K4me1  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the mono- methylation  at the 4th  lysine  residue of the histone H3 protein and often associated with  gene enhancers .


H3K4me1 indicates  monomethylation  of  lysine  4 on histone H3 protein subunit:
 [ 1 ]


(counting from  N-terminus )


This diagram shows the progressive methylation of a lysine residue. The mono-methylation (second from left) denotes the methylation present in H3K4me1.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The  carboxyl (C) terminal  end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The  amino (N) terminal  charged tails are the site of the post-translational modifications, such as the one seen in H3K4me1. [ 2 ] [ 3 ]


H3K4me1 is enriched at active and primed enhancers. [ 4 ]   Transcriptional enhancers control the cell-identity gene expression and are important in the cell identity. Enhancers are primed by histone  H3K4  mono-/di-methyltransferase  MLL4  and then are activated by histone H3K27 acetyltransferase  p300 . [ 5 ]   H3K4me1 fine-tunes the enhancer activity and function rather than controls. [ 4 ]   H3K4me1 is put down by  KMT2C  (MLL3) and  KMT2D  (MLL4) [ 6 ]


LSD1 , and the related LSD2/KDM1B demethylate H3K4me1 and H3K4me2. [ 7 ]


Marks associated with active gene transcription like H3K4me1 and H3K9me1 have very short half-lives. [ 8 ]


H3K4me1 with MLL3/4 can also act at promoters and repress genes. [ 8 ]


H3K4me1 is a chromatin signature of enhancers, H3K4me2 is highest toward the  5′ end  of transcribing genes and H3K4me3 is highly enriched at promoters and in poised genes.  H3K27me3 ,  H4K20me1  and H3K4me1 silence transcription in embryonic fibroblasts, macrophages, and human embryonic stem cells (ESCs). [ 7 ]


Enhancers that have two opposing marks like the active mark H3K4me1 and repressive mark H3K27me3 at the same time are called bivalent or poised. These bivalent enhancers convert and become enriched with H3K4me1 and acetylated H3K27 ( H3K27ac ) after differentiation. [ 8 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 9 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 10 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 11 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 12 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 13 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


Suppression of the H3K4 mono- and di-demethylase LSD-1 might extend lifespan in various species. [ 15 ]


H3K4me allows binding of MDB and increased activity of  DNMT1  which could give rise to  CpG island methylator phenotype  (CIMP). CIMP is a type of colorectal cancers caused by the inactivation of many tumor suppressor genes from epigenetic effects. [ 16 ]


The histone mark H3K4me1 can be detected in a variety of ways:


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and  immunoprecipitated . It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 17 ]


2. Micrococcal Nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 18 ]


3. Assay for transposase accessible chromatin sequencing  ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 19 ] [ 20 ] [ 21 ]


H3K4me3  is an  epigenetic  modification to the DNA packaging protein  Histone H3  that indicates tri- methylation  at the 4th  lysine  residue of the histone H3 protein and is often involved in the  regulation of gene expression . [ 1 ]  The name denotes the addition of three  methyl groups  ( trimethylation ) to the  lysine  4 on the  histone H3  protein.


H3 is used to package  DNA  in  eukaryotic  cells (including human cells), and modifications to the histone alter the accessibility of  genes  for transcription. H3K4me3 is commonly associated with the activation of  transcription  of nearby genes. H3K4 trimethylation regulates gene expression through  chromatin remodeling  by the  NURF  complex. [ 2 ]  This makes the DNA in the  chromatin  more accessible for  transcription factors , allowing the genes to be  transcribed  and expressed in the cell. More specifically, H3K4me3 is found to positively regulate transcription by bringing  histone acetylases  and nucleosome remodelling enzymes (NURF). [ 3 ]  H3K4me3 also plays an important role in the genetic regulation of  stem cell   potency  and  lineage . [ 4 ]  This is because this histone modification is found more in areas of the DNA that are associated with development and establishing cell identity. [ 5 ]


H3K4me3 indicates  trimethylation  of  lysine  4 on histone H3 protein subunit:


This diagram shows the progressive methylation of a lysine residue. The tri-methylation (right) denotes the methylation present in H3K4me3.


The H3K4me3 modification is created by a lysine-specific  histone methyltransferase  (HMT) transferring three  methyl groups  to histone H3. [ 6 ]  H3K4me3 is methylated by methyltransferase complexes containing a protein  WDR5 , which contains the  WD40 repeat  protein  motif . [ 7 ]  WDR5 associates specifically with dimethylated H3K4 and allows further methylation by methyltransferases, allowing for the creation and readout of the H3K4me3 modification. [ 8 ]  WDR5 activity has been shown to be required for developmental genes, like the  Hox genes , that are regulated by histone methylation. [ 7 ]


H3K4me3 is a commonly used histone modification. H3K4me3 is one of the least abundant histone modifications; however, it is highly enriched at active promoters near  transcription start sites  (TSS)  [ 9 ]  and positively correlated with transcription. H3K4me3 is used as a  histone code  or histone mark in  epigenetic  studies (usually identified through  chromatin immunoprecipitation ) to identify active  gene promoters .


H3K4me3 promotes gene activation through the action of the NURF complex, a protein complex that acts through the PHD finger protein motif to remodel chromatin. [ 2 ]  This makes the DNA in the  chromatin  accessible for  transcription factors , allowing the genes to be  transcribed  and expressed in the cell.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in H3K4me1. [ 10 ] [ 11 ]


Regulation of gene expression through H3K4me3 plays a significant role in stem cell fate determination and early embryo development.  Pluripotent cells  have distinctive patterns of methylation that can be identified through  ChIP-seq . This is important in the development of  induced pluripotent stem cells . A way of finding indicators of successful pluripotent induction is through comparing the epigenetic pattern to that of  embryonic stem cells . [ 12 ]


In  bivalent chromatin , H3K4me3 is co-localized with the repressive modification  H3K27me3  to control gene regulation. [ 13 ]  H3K4me3 in embryonic cells is part of a bivalent chromatin system, in which regions of DNA are simultaneously marked with activating and repressing histone methylations. [ 13 ]  This is believed to allow for a flexible system of gene expression, in which genes are primarily repressed, but may be expressed quickly due to H3K4me3 as the cell progresses through development. [ 4 ]  These regions tend to coincide with transcription factor genes expressed at low levels. [ 4 ]  Some of these factors, such as the  Hox genes , are essential for control development and cellular differentiation during  embryogenesis . [ 2 ] [ 4 ]


H3K4me3 is present at sites of DNA double-strand breaks where it promotes  repair  by the  non-homologous end joining  pathway. [ 14 ]  It has been implicated that the binding of H3K4me3 is necessary for the function of genes such as  inhibitor of growth protein 1 (ING1) , which act as a  tumor suppressors  and enact DNA repair mechanisms. [ 15 ]


When DNA damage occurs, DNA damage signalling and repair begins as a result of the modification of histones within the chromatin. Mechanistically, the demethylation of H3K4me3 is used required for specific protein binding and recruitment to DNA damage [ 16 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 17 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 18 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 19 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 20 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 21 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as  enhancers . This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 22 ]


The histone mark H3K4me3 can be detected in a variety of ways:


1.  Chromatin immunoprecipitation  sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and  immunoprecipitated . It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 23 ]


2. Micrococcal nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 24 ]


3. Assay for transposase accessible chromatin sequencing  ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 25 ] [ 26 ] [ 27 ]


H3K9ac  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the  acetylation  at the 9th  lysine  residue of the histone H3 protein.


The H3K9 histone has two jobs. Genes get turned on if this mark is acetylated and silences them if methylated. H3K9ac is an important acetylation and connected with active promoters.  H3K9ac and  H3K14ac  have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers.


This is also a mark for liver cancer through a defect in the H3K9ac/ H3K9me3  transition.


H3K9ac indicates acetylation of  lysine  9 on histone H3 protein subunit:
 [ 6 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 9 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 10 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 11 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 12 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 13 ]


H3K9ac and H3K14ac have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers. [ 15 ]


The H3K9 histone has two jobs. Genes get turned on if this mark is acetylated and silences them if methylated. H3K9ac is an important acetylation and connected with active promoters. [ 16 ]


This is also a mark for liver cancer through a defect in the H3K9ac/H3K9me3 transition. [ 17 ]   Also, lower acetylation at this mark shows a poor prognosis in oral cancer. [ 18 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 19 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 20 ]


3. Assay for transposase accessible chromatin sequencing  (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 21 ] [ 22 ] [ 23 ]


H3K9me2  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the di- methylation  at the 9th  lysine  residue of the histone H3 protein. H3K9me2 is strongly associated with  transcriptional repression . [ 1 ] [ 2 ] [ 3 ]  H3K9me2 levels are higher at silent compared to active genes in a 10kb region surrounding the transcriptional start site. [ 4 ]  H3K9me2 represses gene expression both passively, by prohibiting  acetylation [ 5 ]  as therefore binding of  RNA polymerase  or its regulatory factors, and actively, by recruiting transcriptional repressors. [ 6 ] [ 7 ]  H3K9me2 has also been found in megabase blocks, termed Large Organised Chromatin K9 domains (LOCKS), which are primarily located within gene-sparse regions but also encompass genic and  intergenic  intervals. [ 8 ] [ 9 ] [ 10 ] [ 11 ]  Its synthesis is catalyzed by  G9a ,  G9a-like protein , and  PRDM2 . [ 1 ] [ 3 ] [ 12 ]  H3K9me2 can be removed by a wide range of histone lysine demethylases (KDMs) including KDM1, KDM3, KDM4 and KDM7 family members. [ 13 ] [ 6 ]  H3K9me2 is important for various biological processes including  cell lineage  commitment, [ 10 ] [ 14 ]  the reprogramming of  somatic cells  to  induced pluripotent stem cells , [ 15 ]  regulation of the  inflammatory response , [ 16 ] [ 17 ]  and  addiction  to drug use. [ 2 ] [ 18 ] [ 19 ] [ 20 ]


H3K9me2 indicates  dimethylation  of  lysine  9 on histone H3 protein subunit: [ 21 ]


(counting from N-terminus)


This diagram shows the progressive methylation of a lysine residue. The di-methylation (third from left) denotes the methylation presentpresent in H3K9me2.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the  post-translational modifications , such as the one seen in H3K9me2. [ 22 ] [ 23 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 24 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 25 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  chromatin immunoprecipitation (ChIP)-sequencing  revealed regions in the genome characterised by different banding. [ 26 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 27 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 28 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 29 ]


Chronic addictive drug exposure results in  ΔFosB -mediated  repression  of  G9a  and reduced H3K9 dimethylation in the  nucleus accumbens , which in turn causes  dendritic arborization , altered synaptic protein expression, and increased drug seeking behavior. [ 2 ] [ 18 ]  In contrast, accumbal G9a hyperexpression results in markedly increased H3K9 dimethylation and blocks the induction of this  neural  and  behavioral plasticity  by chronic drug use, [ 2 ] [ 19 ] [ 20 ] [ 30 ]  which occurs via H3K9me2-mediated repression of  transcription factors  for ΔFosB and H3K9me2-mediated repression of various ΔFosB transcriptional targets (e.g.,  CDK5 ). [ 2 ] [ 18 ] [ 19 ]  Due to the involvement of H3K9me2 in these feedback loops and the central  pathophysiological  role of ΔFosB  overexpression  as the mechanistic trigger for  addiction , [ 2 ] [ 31 ]  the reduction of accumbal H3K9me2 following repeated drug exposure directly mediates the development of drug addictions. [ 18 ] [ 19 ]


R-loop 's are found with H3K9me2 mark at  FXN  in  Friedreich's ataxia  cells. [ 32 ]


H3K9me2 is present at a subset of  cardiovascular disease -associated gene promoters in  vascular smooth muscle cells [ 16 ]  to block binding of  NFκB  and  AP-1  (activator protein-1)  transcription factors . [ 16 ]  Reduced levels of H3K9me2 have been observed in vascular smooth muscle cells from human atherosclerotic lesions compared to healthy aortic tissue in patients. [ 33 ]  Vascular smooth muscle cells from diabetic patients display reduced levels of H3K9me2 compared to non-diabetic controls; it has therefore been suggested that dysregulation of H3K9me2 might underlie the vascular complications associated with diabetes. [ 34 ] [ 35 ]  Loss of H3K9me2 in vascular smooth muscle cells exacerbates upregulation of a subset of cardiovascular disease-associated genes in vascular disease models. [ 16 ] [ 34 ] [ 36 ]


Histone modifications, including H3K9me2, can be detected using a variety of methods:


H3K9me3  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the tri- methylation  at the 9th  lysine  residue of the histone H3 protein and is often associated with  heterochromatin .


H3K9me3  indicates  trimethylation  of  lysine  9 on histone H3 protein subunit:
 [ 1 ]


This diagram shows the progressive methylation of a lysine residue. The tri-methylation (right) denotes the methylation present in H3K9me3 .


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  Histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in H3K9me3 . [ 2 ] [ 3 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 4 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 5 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 6 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 7 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 8 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 9 ]


Heterochromatin  marked with H3K9me3 has a pivotal role in embryonic  stem cells  at the onset of  organogenesis  during lineage commitment, and also a role in lineage fidelity maintenance. [ 10 ]


The histone mark can be detected in a variety of ways:


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 11 ]


2. Micrococcal Nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 12 ]


3. Assay for transposase accessible chromatin sequencing  ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 13 ] [ 14 ] [ 15 ]


H3K14ac  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the  acetylation  at the 14th  lysine  residue of the histone H3 protein.


H3K14ac has not been widely studied partly due to previous lack of commercially available antibody.  H3K9ac  and H3K14ac have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers. H3K14ac is also enriched over a subset of inactive promoters.


The  Tudor domain  of the H3K9 methyltransferase  SETDB1  binds to methylated H3 with both K14 acetylation and K9 methylation. SETDB1 silences retroviruses and gene regulation.


The regulation of transcription factors, effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism. [ 2 ]  These regulatory mechanisms are analogous to phosphorylation and dephosphorylation by the action of  kinases  and  phosphatases . Not only can the acetylation state of a protein modify its activity but there has been recent suggestion that this  post-translational modification  may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 3 ] [ 4 ] [ 5 ]


H3K14acindicates acetylation of  lysine  14on histone H3 protein subunit:
 [ 6 ]


H3K14ac has not been widely studied partly due to previous lack of commercially available antibody.  H3K9ac  and H3K14ac have been shown to be part of the active promoter state. They are also present over bivalent promoters and active enhancers. H3K14ac is also enriched over a subset of inactive promoters. [ 15 ]


The  Triple Tudor  domain of the H3K9 methyltransferase  SETDB1  binds to methylated H3 with both K14 acetylation and K9 methylation. SETDB1 silences retroviruses and gene regulation. [ 16 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 17 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 18 ]


3. Assay for transposase accessible chromatin sequencing  (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 19 ] [ 20 ] [ 21 ]


H3K23ac  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the  acetylation  at the 23rd  lysine  residue of the histone H3 protein.


H3K23ac is not well studied but is correlated to  TRIM24  in breast cancer.


H3K23ac indicates acetylation of  lysine  23 on histone H3 protein subunit:
 [ 6 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  Histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in  H3K36me3 . [ 7 ] [ 8 ]


H3K23ac and the oncoprotein TRIM24 are higher in  HER2-positive  breast cancer patients and is a poor prognosis. [ 15 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 16 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 17 ]


3. Assay for transposase accessible chromatin sequencing  (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 18 ] [ 19 ] [ 20 ]


H3K27ac  is an  epigenetic  modification to the DNA packaging protein   histone H3 . It is a mark that indicates  acetylation  of the  lysine  residue at  N-terminal  position 27 of the histone H3 protein.


H3K27ac is associated with the higher activation of  transcription  and therefore defined as an  active  enhancer  mark. H3K27ac is found at both proximal and distal regions of  transcription start site  (TSS).


Proteins are typically acetylated on  lysine  residues, and the acetylation reaction relies on  acetyl-coenzyme A  as the acetyl group donor.
In  histone acetylation and deacetylation , histone proteins are acetylated and deacetylated on lysine residues in the N-terminal tail as part of  gene regulation . Typically, these reactions are catalyzed by  enzymes  with  histone acetyltransferase  (HAT) or  histone deacetylase  (HDAC) activity, although HATs and HDACs can modify the acetylation status of non-histone proteins as well. [ 1 ]


The regulation of  transcription factors , effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism [ 2 ]  These regulatory mechanisms are analogous to phosphorylation and dephosphorylation by the action of  kinases  and  phosphatases . Not only can the acetylation state of a protein modify its activity, but there has been a recent suggestion that this  post-translational modification  may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 3 ] [ 4 ] [ 5 ]


In the field of  epigenetics ,  histone acetylation  (and  deacetylation ) have been shown to be important mechanisms in the regulation of gene transcription. Histones, however, are not the only proteins regulated by  post-translational  acetylation.


H3K27ac indicates acetylation of  lysine  27 on histone H3 protein subunit:
 [ 6 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as   histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The  carboxyl (C) terminal  end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in  H3K36me3 . [ 7 ] [ 8 ]


The posttranslational modification of histone tails by either histone-modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to the complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 9 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 10 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 11 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 12 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 13 ]


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as  enhancers . This additional level of annotation allows for a deeper understanding of cell-specific gene regulation. [ 14 ]


Since the H3K27ac and  H3K27me3  modification is at the same location on the histone tail, they antagonize each other. [ 15 ]  H3K27ac is often used to find active enhancers and poised enhancers subtracting from another enhancer mark  H3K4me1  that contains all enhancers. [ 16 ]


Acetylation is usually linked to the upregulation of genes. This is the case in H3K27ac which is an active enhancer mark. It is found in distal and proximal regions of genes. It is enriched in  Transcriptional start sites  (TSS). H3K27ac shares a location with  H3K27me3  and they interact in an antagonistic manner.


H3K27ac is enriched in the regulatory regions of genes implicated in  Alzheimer's disease , including those in tau and amyloid neuropathology.  [ 17 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and  immunoprecipitated . It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 18 ]


2. Micrococcal Nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well-positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well-positioned nucleosomes are seen to have enrichment of sequences. [ 19 ]


3. Assay for transposase accessible chromatin sequencing  ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 20 ] [ 21 ] [ 22 ]


H3K27me3  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the tri- methylation  of  lysine  27 on histone H3 protein.


This tri-methylation is associated with the  downregulation  of nearby genes via the formation of  heterochromatic  regions. [ 1 ]


H3K27me3 indicates  trimethylation  of  lysine  27 on histone H3 protein subunit:


This diagram shows the progressive methylation of a lysine residue. The tri-methylation (right) denotes the methylation present in H3K27me3.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The  carboxyl (C) terminal end  of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The  amino (N) terminal charged tails   are the site of the  post-translational modifications , such as the one seen in H3K27me3. [ 2 ] [ 3 ]


The placement of a repressive mark on lysine 27 requires the recruitment of chromatin regulators by  transcription factors . These modifiers are either histone modification complexes which covalently modify the histones to move around the nucleosomes and open the chromatin, or chromatin remodelling complexes which involve movement of the nucleosomes without directly modifying them. [ 4 ]  These histone marks can serve as docking sites of other co-activators as seen with H3K27me3.
This occurs through polycomb mediated gene silencing via histone methylation and chromodomain interactions. A polycomb repressive complex (PRC);  PRC2 , mediates the tri-methylation of histone 3 on lysine 27 through histone methyl transferase activity. [ 5 ]  This mark can recruit  PRC1  which will bind and contribute to the compaction of the chromatin. [ 6 ]


The inflammatory  transcription factor   NF-κB  can cause demethylation of H3K27me3 via  Jmjd3 . [ 7 ]


H3K27me3 is linked to the  repair of DNA damages , particularly repair of double-strand breaks by  homologous recombinational  repair. [ 8 ]


H3K27 can undergo a variety of other modifications. It can exist in mono- as well as di-methylated states. The roles of these respective modifications are not as well characterised as tri-methylation. PRC2 is however believed to be implicated in all the different methylations associated with H3K27me.


H3K27me1 is linked to promotion of transcription and is seen to accumulate in transcribed genes. Histone-histone interactions play a role in this process. Regulation occurs via Setd2-dependent  H3K36me3  deposition. [ 9 ]


H3K27me2 is broadly distributed within the core histone H3 and is believed to play a protective role by inhibiting non-cell-type specific enhancers. Ultimately, this leads to the inactivation of transcription. [ 10 ]


Acetylation is usually linked to the upregulation of genes. This is the case in  H3K27ac  which is an active enhancer mark. It is found in distal and proximal regions of genes. It is enriched in  transcriptional start sites  (TSS). H3K27ac shares a location with H3K27me3 and they interact in an antagonistic manner.


H3K27me3 is often seen to interact with  H3K4me3  in bivalent domains . [ 11 ]  These domains are usually found in embryonic stem cells and are pivotal for proper cell differentiation. H3K27me3 and H3K4me3 determine whether a cell will remain unspecified or will eventually differentiate. [ 12 ] [ 13 ]  The Grb10 gene in mice makes use of these bivalent domains. Grb10 displays imprinted gene expression. Genes are expressed from one parental allele while simultaneously being silenced in the other parental allele. [ 14 ]  Demethylation of H3K27me3 can lead to up-regulation of genes controlling the  senescence-associated secretory phenotype  (SASP). [ 7 ]


Other well characterised modifications are H3K9me3 as well as  H4K20me 3 which—just like H3K27me3—are linked to transcriptional repression via formation of heterochromatic regions. Mono-methylations of H3K27, H3K9, and H4K20 are all associated with gene activation. [ 15 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 16 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 17 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP sequencing  revealed regions in the genome characterised by different banding. [ 18 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 19 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 20 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 21 ]


Cause-and-effect relationship between  sperm -transmitted histone marks and  gene expression  and development is in
offspring and grandoffspring. [ 22 ]


H3K27me3 is believed to be implicated in some diseases due to its regulation as a repressive mark.


Cohen–Gibson syndrome  is a disorder linked to overgrowth and is characterised by dysmorphic facial features and variable intellectual disability. In some cases, a  de novo   missense mutation  in  EED  was associated with decreased levels of H3K27me3 in comparison to  wild type . This decrease was linked to loss of PRC2 activity. [ 23 ]


Diffuse midline glioma, H3K27me3-altered  (DMG), also known as diffuse intrinsic  pontine  glioma (DIPG) is a type of highly aggressive  brain tumor  mostly found in children. All DMGs exhibit loss of H3K27me3, in about 80% of cases due to a genetic mutation receplacing lysine with  methionine  (M), known as H3K27M. In rare forms, H3Kme3-loss is mediated by overexpression of the  EZH inhibiting protein , decreasing PRC2-activity. [ 24 ]


There is evidence that implicates the downregulation of expression of H3K27me3 in conjunction with differential expression of H3K4me3 AND DNA methylation may play a factor in  fetal alcohol spectrum disorder  (FASD) in C57BL/6J mice. This histone code is believed to affect the peroxisome associated pathway and induce the loss of the peroxisomes to ameliorate oxidative stress. [ 25 ]


The histone mark H3K27me3 can be detected in a variety of ways:


1. Chromatin Immunoprecipitation Sequencing ( ChIP sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 26 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 27 ]


3. Assay for transposase accessible chromatin sequencing ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 28 ] [ 29 ] [ 30 ]


H3K36ac  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the  acetylation  at the 36th  lysine  residue of the histone H3 protein.


H3K36ac has not been widely studied but it is very widely conserved across mammals and yeast and marks genes. Specifically, it marks promoters of  RNA polymerase  II-transcribed genes which is opposite of  H3K36me3 .


H3K36ac indicates acetylation of  lysine  36th histone H3 protein subunit:
 [ 6 ]


H3K36ac has not been widely studied but it is very widely conserved across mammals and yeast and marks genes. Specifically, it marks promoters of  RNA polymerase  II-transcribed genes which is opposite of  H3K36me3 . [ 15 ] [ 16 ]


1.  Chromatin Immunoprecipitation  Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and  immunoprecipitated . It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 17 ]


H3K36me  is an  epigenetic  modification to the DNA packaging protein  Histone H3 , specifically, the mono- methylation  at the 36th  lysine  residue of the histone H3 protein.


There are diverse modifications at H3K36, such as phosphorylation, methylation, acetylation, and ubiquitylation, which have many important biological processes. [ 1 ]  The methylation of H3K36 has particularly had effects in transcriptional repression, alternative splicing, dosage compensation, DNA replication and repair, DNA methylation, and the transmission of the memory of gene expression from parents to offspring during development. [ 1 ]


H3K36me2 indicates  dimethylation  of  lysine  36 on histone H3 protein subunit: [ 2 ]


This diagram shows the progressive methylation of a lysine residue. The mono-methylation (second from left) denotes the methylation present in H3K36me1.


Lysine methylation is the addition of a methyl group to the lysine of histone proteins. [ 3 ]  This occurs via histone lysine methyltransferase (HMTase) that utilize  S -adenosylmethionine to specifically place the methyl group on histone Lys or Arg residues. [ 1 ]  So far, there have only been eight specific mammalian enzymes discovered that can methylate H3K36 in vitro and/or in vivo, all of which have identical catalytic SET domains but, different preferences for Lys36 residues in different methylation states. [ 1 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome , which consists of the core octamer of histones ( H2A ,  H2B ,  H3 , and  H4 ) as well as a linker histone and about 180 base pairs of DNA wrapped around it. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in H3K36me3. [ 4 ] [ 5 ]


The post-translational modification of histone tails by either histone-modifying complexes or chromatin remodeling complexes is interpreted by the cell and leads to the complex, combinatorial transcriptional output. It is thought that a  histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 6 ]  The current understanding and interpretation of histones come from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 7 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together. Chromatin states were investigated in  Drosophila  cells by looking at the binding location of proteins in the genome. The use of  ChIP-sequencing  revealed regions in the genome characterized by different banding. [ 8 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 9 ]  A look into the data obtained led to the definition of chromatin states based on histone modifications. [ 10 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell-specific gene regulation. [ 11 ]


The histone mark H3K36me can be detected in a variety of ways:


H3K36me2  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the di- methylation  at the 36th  lysine  residue of the histone H3 protein.


There are diverse modifications at H3K36 and have many important biological processes. H3K36 has different acetylation and methylation states with no similarity to each other. [ 1 ]


H3K36me2 indicates  dimethylation  of  lysine  36 on histone H3 protein subunit:
 [ 2 ]


This diagram shows the progressive methylation of a lysine residue. The di-methylation (third from left) denotes the methylation present in H3K36me2.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  Histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in H3K36me3. [ 3 ] [ 4 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 5 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 6 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 7 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 8 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 9 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 10 ]


The histone mark H3K36me2 can be detected in a variety of ways:


1.  Chromatin Immunoprecipitation  Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 11 ]


H3K36me3  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the tri- methylation  at the 36th  lysine  residue of the histone H3 protein and often associated with  gene bodies .


H3K36me3 indicates  trimethylation  of  lysine  36 on histone H3 protein subunit:
 [ 2 ]


This diagram shows the progressive methylation of a lysine residue. The tri-methylation (right) denotes the methylation present in H3K36me3.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  Histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The  carboxyl (C) terminal  end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino  (N) terminal  charged tails are the site of the post-translational modifications, such as the one seen in H3K36me3. [ 3 ] [ 4 ]


H3K36me3 can bind  chromodomain  proteins such as MSL3 hMRG15 and scEaf3. [ 5 ]  It can bind  PWWP  proteins such as BRPF1  DNMT3A ,  HDGF2  and  Tudor domains  such as PHF19 and PHF1. [ 5 ]


H3K36me3 is required for  homologous recombinational   repair of DNA damage  such as double-strand breaks. [ 6 ]   The trimethylation is catalyzed by  SETD2   methyltransferase .


H3K36me3 acts as a mark for  HDACs  to bind and deacetylate the histone which would prevent run-away transcription. [ 1 ]   It is associated with both facultative and constitutive  heterochromatin . [ 7 ]


H3K36me3 might define  exons . Nucleosomes in the exons have more histone modifications such as H3K79, H4K20, and especially H3K36me3. [ 1 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 8 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 9 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 10 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 11 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 12 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions. Five core histone modifications were found with each respective one being linked to various cell functions.


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 13 ]


This histone methylation is responsible for maintaining gene expression stability. It is important throughout aging and has an impact on longevity. Genes that change their expression during aging have much lower levels of H3K36me3 in their gene bodies. [ 14 ]


There is reduced levels of H3K36me3 and  H3K79me2  at the upstream GAA region of the  FXN , indicative of a defect
of transcription elongation in  Friedreich's ataxia . [ 15 ]


The histone mark H3K36me3 can be detected in a variety of ways:


H3K56ac  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the  acetylation  at the 56th  lysine  residue of the histone H3 protein.


It is a  covalent  modification known as a mark of newly replicated  chromatin  as well as replication-independent histone replacement.


H3K56ac is catalyzed by Rtt109, is important for nucleosome assembly and serves as a marker of new nucleosomes during DNA replication. The levels of H3K56ac are regulated during the cell cycle, peaking in S phase and removed by Hst3 and Hst4.


Lysine 56 is located at the amino-terminal αN-helix and close to the site where the DNA enters and exits the nucleosome.  The studies on yeast might not apply to the mammals. Mammalian cells do not express  HATs  with high specificity to K56.


Sirtuins  can catalyze the removal of the acetyl group from K56 [ 1 ]   H3K56ac levels are elevated in cancer and  pluripotent  cells. TRIM66  reads unmodified  H3R2K4  and H3K56ac to respond to DNA damage.


Proteins are typically acetylated on  lysine  residues and this reaction relies on  acetyl-coenzyme A  as the acetyl group donor.
In  histone acetylation and deacetylation , histone proteins are acetylated and deacetylated on lysine residues in the N-terminal tail as part of  gene regulation . Typically, these reactions are catalyzed by  enzymes  with  histone acetyltransferase  (HAT) or  histone deacetylase  (HDAC) activity, although HATs and HDACs can modify the acetylation status of non-histone proteins as well. [ 2 ]


The regulation of transcription factors, effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism [ 3 ]  These regulatory mechanisms are analogous to phosphorylation and dephosphorylation by the action of  kinases  and  phosphatases . Not only can the acetylation state of a protein modify its activity but there has been recent suggestion that this  post-translational modification  may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 4 ] [ 5 ] [ 6 ]


H3K56ac indicates acetylation of  lysine  56th histone H3 protein subunit:
 [ 7 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in  H3K36me3 . [ 8 ] [ 9 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 10 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 11 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 12 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 13 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 14 ]


The human genome was annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 15 ]


H3K56ac is a covalent modification known as a mark of newly replicated chromatin as well as replication-independent histone replacement. [ 16 ]


H3K56ac is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication but its role in the cell cycle is debated. [ 1 ]


Lysine 56 is located at the amino-terminal αN-helix and close to the site where the DNA enters and exits the nucleosome. [ 1 ]  due to its location on the lateral surface of the nucleosome, which is close to the DNA entry/exit site and interacts with DNA29. [ 17 ]


The studies on yeast might not apply to the mammals. Mammalian cells do not express HATs with high specificity to K56. [ 1 ]


Sirtuins can catalyze the removal of the acetyl group from K56 [ 1 ]   H3K56ac levels are elevated in cancer and pluripotent cells [ 1 ]   TRIM66  reads unmodified H3R2K4 and H3K56ac to respond to DNA damage. [ 1 ]


H3T45P  promotes H3K56 acetylation. [ 18 ]  Phosphorylation of the nucleosome DNA entry-exit region improves access to DNA binding complexes, and the combination of phosphorylation and acetylation has the ability to alter DNA accessibility to transcription regulatory complexes dramatically. [ 19 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 20 ]


2. Micrococcal Nuclease sequencing (MNase-seq) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 21 ]


3. Assay for transposase accessible chromatin sequencing  (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 22 ] [ 23 ] [ 24 ]


H3K79me2  is an  epigenetic  modification to the DNA packaging protein  Histone H3 . It is a mark that indicates the di- methylation  at the 79th  lysine  residue of the histone H3 protein. H3K79me2 is detected in the transcribed regions of active genes.


H3K79me2 indicates  dimethylation  of  lysine  79 on histone H3 protein subunit:
 [ 1 ]


This diagram shows the progressive methylation of a lysine residue. The di-methylation (third from left) denotes the methylation present in H3K79me2. [ 2 ]


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  Histones . The complexes formed by the looping of the DNA are known as  chromatin . The basic structural unit of chromatin is the  nucleosome : this consists of the core octamer of histones (H2A, H2B, H3 and H4) as well as a linker histone and about 180 base pairs of DNA. These core histones are rich in lysine and arginine residues. The carboxyl (C) terminal end of these histones contribute to histone-histone interactions, as well as histone-DNA interactions. The amino (N) terminal charged tails are the site of the post-translational modifications, such as the one seen in  H3K36me3 . [ 3 ] [ 4 ]


The post-translational modification of histone tails by either histone modifying complexes or chromatin remodelling complexes are interpreted by the cell and lead to complex, combinatorial transcriptional output. It is thought that a  Histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 5 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 6 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states which define genomic regions by grouping the interactions of different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 7 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 8 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 9 ]


Three forms of H3K79 methylation (H3K79me1; H3K79me2; H3K79me3) are catalyzed by DOT1 in yeast or DOT1L in mammals.  H3K79 methylation participates in the DNA damage response and has multiple roles in nucleotide excision repair and sister chromatid recombinational repair. [ 11 ]


H3K79 dimethylation has been detected in the transcribed regions of active genes. [ 2 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and immunoprecipitated. It results in good optimization and is used in vivo to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 12 ]


2. Micrococcal Nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well positioned nucleosomes are seen to have enrichment of sequences. [ 13 ]


3. Assay for transposase accessible chromatin sequencing  ( ATAC-seq ) is used to look in to regions that are nucleosome free (open chromatin). It uses hyperactive  Tn5 transposon  to highlight nucleosome localisation. [ 14 ] [ 15 ] [ 16 ]


H3R2me2  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the di- methylation  at the 2nd  arginine  residue of the histone H3 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial. [ 1 ]


The name of this modification indicates  dimethylation  of arginine 2 on histone H3 protein subunit:
 [ 2 ]


Arginine can be methylated once (monomethylated arginine) or twice (dimethylated arginine). Methylation of arginine residues is catalyzed by three different classes of protein arginine methyltransferases. [ 1 ]


Arginine methylation affects the interactions between proteins and has been implicated in a variety of cellular processes, including protein trafficking, signal transduction, and transcriptional regulation. [ 3 ]


Arginine methylation plays a major role in gene regulation because of the ability of the PRMTs to deposit key activating (histone  H4R3me2 , H3R2me2,  H3R17me2 ,  H3R26me2 ) or repressive (H3R2me2,  H3R8me2 ,  H4R3me2 ) histone marks.


The genomic DNA of eukaryotic cells is wrapped around special protein molecules known as  histones . The complexes formed by the looping of the DNA are known as  chromatin .


JMJD6 , a  Jumonji  domain-containing protein, was reported to demethylate H3R2me2.
 [ 4 ]   H3R2me2 is a major mark deposited by  PRMT6 .   [ 4 ]  H3R2me1 and H3R2me2 marks are associated with highly expressed genes although H3R2me2 can block H3K4me3 effector molecules. [ 4 ]


The post-translational modification of histone tails by either histone-modifying complexes or chromatin remodeling complexes is interpreted by the cell and leads to complex, combinatorial transcriptional output. It is thought that a  histone code  dictates the expression of genes by a complex interaction between the histones in a particular region. [ 5 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 6 ]  The purpose of the epigenomic study was to investigate epigenetic changes across the entire genome. This led to chromatin states, which define genomic regions by grouping different proteins and/or histone modifications together.
Chromatin states were investigated in Drosophila cells by looking at the binding location of proteins in the genome. Use of  ChIP-sequencing  revealed regions in the genome characterized by different banding. [ 7 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 8 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 9 ]  Certain modifications were mapped and enrichment was seen to localize in certain genomic regions.


The human genome is annotated with chromatin states. These annotated states can be used as new ways to annotate a genome independently of the underlying genome sequence. This independence from the DNA sequence enforces the epigenetic nature of histone modifications. Chromatin states are also useful in identifying regulatory elements that have no defined sequence, such as enhancers. This additional level of annotation allows for a deeper understanding of cell specific gene regulation. [ 10 ]


As of March 2021, PRMT6-mediated H3R2me2 role in early embryonic development and ES cell identity are unclear. [ 11 ]


1. Chromatin Immunoprecipitation Sequencing ( ChIP-sequencing ) measures the amount of DNA enrichment once bound to a targeted protein and  immunoprecipitated . It results in good optimization and is used  in vivo  to reveal DNA-protein binding occurring in cells. ChIP-Seq can be used to identify and quantify various DNA fragments for different histone modifications along a genomic region. [ 12 ]


2. Micrococcal Nuclease sequencing ( MNase-seq ) is used to investigate regions that are bound by well-positioned nucleosomes. Use of the micrococcal nuclease enzyme is employed to identify nucleosome positioning. Well-positioned nucleosomes are seen to have enrichment of sequences. [ 13 ]


H3R8me2  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the di- methylation  at the 8th  arginine  residue of the histone H3 protein. In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus higher levels of transcription. The existence of arginine demethylases that could reverse arginine methylation is controversial. [ 1 ]


H3R8me2 is associated with transcriptional repression, and modified by PRMT5, but not CARM1.


As of March 2021, there are no disease associations known for H3R8me2. [ 2 ]


The name of this modification indicates  dimethylation  of arginine 8 on histone H3 protein subunit:
 [ 3 ]