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. [ 4 ]


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 H3R8 site is methylated by PRMT5 and linked to transcriptional repression. PRMT5 is recruited by several transcriptional repressors, such as Snail,  ZNF224  and Ski. A prior acetylation of H3K9 or H3K14 prevents methylation of H3R8 by PRMT5. [ 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 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 comes 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 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. [ 8 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 9 ]  A look in to 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.


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. [ 11 ]


PRMT2 was shown to mediate the dorsal developmental program through methylation of H3R8me2a. [ 12 ]


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. [ 13 ]


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. [ 14 ]


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. [ 15 ] [ 16 ] [ 17 ]


H3R17me2  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the di- methylation  at the 17th  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 17 on histone H3 protein subunit:
 [ 2 ]


Arginine methylation plays a major role in gene regulation because of the ability of the PRMTs to deposit key activating (histone  H4R3me2 ,  H3R2me2 , H3R17me2,  H3R26me2a ) or repressive (  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 .


Methylation of H3R17 is mediated by  CARM1  and is recruited to promoter upon gene activation along with acetyltransferases and activates transcription.  When CARM1 is recruited to transcriptional promoters the histone H3 is methylated (H3R17me2 & H3R26me2). H3R17 dimethylation as a critical epigenetic mark in starvation-induced  autophagy [ 4 ]


CARM1 knockout mice are smaller and die shortly after birth. CARM1 is required for the epigenetic maintenance of pluripotency and self-renewal, as it methylates H3R17 and H3R26 at core pluripotency genes such as  Oct4 ,  Sox2 , and  Nanog . [ 1 ]


CARM1-mediated methylation of H3R17 is needed to establish and maintain the astroglial lineage. The absence of H3R17me2a downregulates  miR-92a  levels, and this miRNA is known to participate in neural development. [ 1 ]


CARM1 was indirectly associated with  diabetic retinopathy  progression, as it and its associated H3R17me2a mark increased with high glucose, promoting  apoptosis  of the retinal pigment epithelial cells. [ 1 ]


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 ]


H3R26me2  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the di- methylation  at the 26th  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 26 on histone H3 protein subunit:
 [ 2 ]


Arginine methylation plays a major role in gene regulation because of the ability of the PRMTs to deposit key activating (histone  H4R3me2 ,  H3R2me2 ,  H3R17me2a , H3R26me2) or repressive (H3R2me2,  H3R8me2 ,  H4R3me2 ) histone marks.


Methylation of H3R26me2 is mediated by  CARM1  and is recruited to promoter upon gene activation along with acetyltransferases and activates transcription.  When CARM1 is recruited to transcriptional promoters the histone H3 is methylated (H3R17me2 & H3R26me2). [ 4 ]


H3R26 lies close to  H3K27 , which is a repressive mark when methylated. There are several ways that  H3R26 could change gene expression. [ 5 ]


CARM1 knockout mice are smaller and die shortly after birth. CARM1 is required for the epigenetic maintenance of pluripotency and self-renewal, as it methylates H3R17 and H3R26 at core pluripotency genes such as  Oct4 ,  SOX2 , and  Nanog . [ 1 ]


It is possible that H3R26me2 levels are changed before pre-implantation of bovine embryos and their development. [ 12 ]


H3R42me  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the mono- methylation  at the 42nd  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 ]


H3K4me1 indicates  monomethylation  of  lysine  4 on histone H3 protein subunit:
 [ 2 ]


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 .


R42 is located within the core region of histone H3. Inside the nucleosomal structure, R42 overlaps the point where DNA enters and exits the nucleosome. [ 4 ]


The addition of a methyl group at arginine enhances steric hindrance and also removes a hydrogen bond donor, which slightly decreases nucleosome stability to allow RNA polymerase II to migrate more easily through the template. [ 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 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 comes 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. Use of  ChIP-sequencing  revealed regions in the genome characterised by different banding. [ 8 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 9 ]  A look in to 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.


Mycobacteria can reduce a host's immune response through, a secreted mycobacterial protein Rv1988. Rv1988 is a methyltransferase that methylates histone H3 at H3R42 and represses the genes that help defense against mycobacteria. [ 12 ]


H3S10P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the  phosphorylation  the 10th  serine  residue of the histone H3 protein.


Depending on the environment in which it happens, the same phosphorylated residue might have drastically different consequences on chromatin structure. H3S10 and H3S28 phosphorylation is an excellent illustration of this duality: both phosphorylated residues are involved in chromatin compaction during mitosis and meiosis, as well as chromatin relaxation after transcription activation. [ 1 ]  Because of the diverse roles that these phosphorylation events play, individual residue phosphorylation can't be examined in isolation. The impact is determined by the cellular environment and interplay with other cis or trans changes. [ 1 ]


The S10 phosphorylation is involved in mitosis, transcription, chromatin condensation, and UVB response. [ 1 ]  H3S10p causes chromosome condensation and segregation during cell mitosis. [ 2 ]  H3S10p temporarily increases during mitosis while  H3K9me3  decreases and H3K9me3 recovers upon mitotic exit. [ 2 ]


R loops  are linked to H3S10P and  chromatin condensation . [ 3 ]


The name of this modification indicates the  protein phosphorylation  of serine 10 on histone H3 protein subunit:
 [ 4 ]


The addition of a negatively charged phosphate group can lead to major changes in protein structure, leading to the well-characterized role of  phosphorylation  in controlling protein function. It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification.


Post-translational modification of histones such as histone phosphorylation has been shown to modify the chromatin structure by changing protein:DNA or protein:protein interactions. [ 5 ]  Histone post-translational modifications modify the chromatin structure. The most commonly associated histone phosphorylation occurs during cellular responses to DNA damage, when phosphorylated histone H2A separates large chromatin domains around the site of DNA breakage. [ 6 ]  Researchers investigated whether modifications of histones directly impact RNA polymerase II directed transcription. Researchers choose proteins that are known to modify histones to test their effects on transcription, and found that the  stress-induced kinase, MSK1, inhibits RNA synthesis. Inhibition of transcription by MSK1 was most sensitive when the template was in chromatin, since DNA templates not in chromatin were resistant to the effects of MSK1. It was shown that MSK1 phosphorylated histone H2A on serine 1, and mutation of serine 1 to alanine blocked the inhibition of transcription by MSK1. Thus results suggested that the acetylation of histones can stimulate transcription by suppressing an inhibitory phosphorylation by a kinase as MSK1. [ 7 ]


Phosphorylation introduces a charged and hydrophilic group in the side chain of amino acids, possibly changing a protein's structure by altering interactions with nearby amino acids. Some proteins such as  p53  contain multiple phosphorylation sites, facilitating complex, multi-level regulation. Because of the ease with which proteins can be phosphorylated and dephosphorylated, this type of modification is a flexible mechanism for cells to respond to external signals and environmental conditions. [ 8 ]


Kinases  phosphorylate proteins and  phosphatases  dephosphorylate proteins. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a  conformational change  in the structure in many  enzymes  and  receptors , causing them to become activated or deactivated. Phosphorylation usually occurs on  serine ,  threonine ,  tyrosine  and  histidine  residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phosphorylation. [ 9 ]  In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or  arginine  or  lysine  residues. [ 9 ] [ 10 ]  The addition of a phosphate (PO 4 3- ) molecule to a non-polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of a molecule. In this way  protein dynamics  can induce a conformational change in the structure of the protein via long-range  allostery  with other hydrophobic and hydrophilic residues in the protein.


The  kinases  Ipl1 (Sc) / AuroraB (Hs), RSK2,  MSK1 ,  ERK1 ,  p38 ,  Fyn ,  Chk1 , PRK1 are involved in the S10 phosphorylation. [ 11 ]


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. [ 12 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 13 ]  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. [ 14 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 15 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 16 ]  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. [ 17 ] [ 18 ]


A substantial number of phosphorylated histone residues are associated with gene expression. Interestingly, these are often related to regulation of proliferative genes. Phosphorylation of serines 10 and 28 of H3 and serine 32 of H2B has been associated with regulation of epidermal growth factor (EGF)-responsive gene transcription. H3S10ph and H2BS32ph have been linked to the expression of proto-oncogenes such as c-fos, c-jun and c-myc.50-52 Furthermore, targeting H3S28 phosphorylation to promoters of genes such as c-fos and α-globin was shown to control their activation.53 Notably, phosphorylation of H3S10 and H3S28 is not exclusive to EGF stimulation, but it also increases upon UVB radiation. Phosphorylation of H3 on T11 and T6 has also been implicated in transcription regulation in response to androgen stimulation,54,55 and to DNA-damage in mouse cells.56


Phosphorylation of H3S10, T11 and S28 has been clearly associated with H3 acetylation, strongly implicating these modifications in transcription activation. Independent studies show that these phosphorylation events are mechanistically linked to Gcn5-dependent H3 acetylation (Fig. 1).57-59 Indeed, in EGF-stimulated cells, phosphorylation of H3S10 is tightly coupled to H3 K9ac and K14ac, both marks of transcriptional activation.51,60,61 It has been shown that phosphorylation of H3S10 promotes acetylation of H3K14 by the Gcn5 acetyltransferase in vitro and allows Gcn5-regulated gene transcription in vivo.57 A similar link has been described in yeast where H3S10 phosphorylated by Snf1 acts in concert with Gcn5-dependent H3K14 acetylation to enhance transcription.62 This functional link between H3S10ph and Gcn5 is likely mediated by the direct interaction of the acetyltransferase with the phosphorylated H3S10 residue, which has been observed in vitro.57,60 However, analysis of the c-jun promoter activation showed that K14ac appears before S10ph and that inhibition of S10 phosphorylation has no effect on K14ac, suggesting that these two events can be uncoupled.61,63 Interestingly, phosphorylation of the H3 tail on T11 in addition to S10 was shown to enhance its interaction with Gcn5 at promoters of Gcn5-dependent genes such as the cell-cycle regulators cyclin B and cdk1, leading to increased H3K9 and K14 acetylation and stimulation of transcription.54,56,58 Likewise, phosphorylation of H3S28 was found to promote K9 acetylation.59 Altogether, these data suggest complex crosstalk between phosphorylation of H3S10, T11 and S28 in the control of Gcn5-dependent H3 acetylation, gene expression, and cell proliferation.


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 ]


H3S28P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation the 28th  serine  residue of the histone H3 protein.


Early  mitosis  phosphorylation patterns for  H3S10  and H3S28 are quite similar, starting at the initiation of chromosomal condensation during  prophase . Phosphorylation of H3S28 has  transcription  effects and  acetylates  other histones.


The name of this modification indicates the protein phosphorylation of serine 28 on histone H3 protein subunit:
 [ 1 ]


A substantial number of phosphorylated histone residues are associated with gene expression. Interestingly, these are often related to the regulation of proliferative genes. Phosphorylation of serines 10 and 28 of H3 and serine 32 of H2B has been associated with the regulation of epidermal growth factor (EGF)-responsive gene transcription. Depending on the environment in which it happens, the same phosphorylated residue might have drastically different consequences on chromatin structure. H3S10 and H3S28 phosphorylation is an excellent illustration of this duality: both phosphorylated residues are involved in chromatin compaction during mitosis and meiosis, as well as chromatin relaxation after transcription activation. [ 2 ]  Because of the diverse roles that these phosphorylation events play, individual residue phosphorylation can't be examined in isolation. The impact is determined by the cellular environment and interplay with other cis or trans changes. [ 2 ]


Early mitosis phosphorylation patterns for H3S10 and H3S28 are quite similar, starting at the initiation of chromosomal condensation during prophase. [ 3 ]   At gene promoters, H3S28 phosphorylation is expected to remove  Polycomb  restrictive complexes from chromatin, causing demethylation and acetylation of the nearby K27 residue, so activating transcription. This transition is mediated by the phosphorylation of H3S28 on a site next to  H3K27 . [ 3 ]  It was discovered that phosphorylating H3S28 in the promoters of genes like c-fos and -globin controlled their activation. [ 3 ]


In addition to H3K27ac, H3S28p plays a role in transcription activation. [ 3 ]    H3S28p prevents  H3K27me3  from accumulating, allowing H3K27 acetylation to occur. [ 4 ]   Similarly, it was discovered that phosphorylation of H3S28 promotes K9 acetylation. [ 3 ]


UVB radiation  phosphorylates H3S10 and H3S28, while H3S28 is additionally phosphorylated by the  kinases   MSK1 ,  ERK1 ,  p38 ,  FYN , MLTK,  ERK2 , and to a lesser extent  JNK1  and  JNK2 . [ 3 ]


Kinases  phosphorylate proteins and  phosphatases  dephosphorylate proteins. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a  conformational change  in the structure in many  enzymes  and  receptors , causing them to become activated or deactivated. Phosphorylation usually occurs on serine,  threonine ,  tyrosine  and  histidine  residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phosphorylation. [ 9 ]  In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or  arginine  or  lysine  residues. [ 9 ] [ 10 ]  The addition of a phosphate (PO 4 3- ) molecule to a non-polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of a molecule. In this way  protein dynamics  can induce a conformational change in the structure of the protein via long-range  allostery  with other hydrophobic and hydrophilic residues in the protein.


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. [ 11 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 12 ]  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. [ 13 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 14 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 15 ]  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. [ 16 ] [ 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 ]


H3T3P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation the 3rd  threonine  residue of the histone H3 protein.


Pre-existing vs newly generated H3 is distinguished by phosphorylation at threonine 3. H3T3P separates sister chromatids enriched with diverse pools of H3 in order to coordinate asymmetric segregation of "old" H3 into germ stem cells and that male germline activity requires tight regulation of H3T3 phosphorylation.


The name of this modification indicates the protein phosphorylation of threonine 3 on histone H3 protein subunit:
 [ 1 ]


How stem cells preserve their identity via numerous divisions is unknown.  Adult stem cells divide asymmetrically to produce a self-renewing stem cell and a daughter cell that will differentiate later.  Many human disorders, ranging from cancer to tissue dystrophy to infertility, are caused by a disruption in this balance.


Pre-existing vs newly generated H3 is distinguished by phosphorylation at threonine 3. [ 2 ]   H3T3P separates sister chromatids enriched with diverse pools of H3 in order to coordinate asymmetric segregation of "old" H3 into germ stem cells and that male germline activity requires tight regulation of H3T3 phosphorylation. [ 3 ]


Post-translational modification of histones such as histone phosphorylation has been shown to modify the chromatin structure by changing protein:DNA or protein:protein interactions. [ 4 ]  Histone post-translational modifications modify the chromatin structure. The most commonly associated histone phosphorylation occurs during cellular responses to DNA damage, when phosphorylated histone H2A separates large chromatin domains around the site of DNA breakage. [ 5 ]  Researchers investigated whether modifications of histones directly impact RNA polymerase II directed transcription. Researchers choose proteins that are known to modify histones to test their effects on transcription, and found that the  stress-induced kinase, MSK1, inhibits RNA synthesis. Inhibition of transcription by MSK1 was most sensitive when the template was in chromatin, since DNA templates not in chromatin were resistant to the effects of MSK1. It was shown that MSK1 phosphorylated histone H2A on serine 1, and mutation of serine 1 to alanine blocked the inhibition of transcription by MSK1. Thus results suggested that the acetylation of histones can stimulate transcription by suppressing an inhibitory phosphorylation by a kinase as MSK1. [ 6 ]


Phosphorylation introduces a charged and hydrophilic group in the side chain of amino acids, possibly changing a protein's structure by altering interactions with nearby amino acids. Some proteins such as  p53  contain multiple phosphorylation sites, facilitating complex, multi-level regulation. Because of the ease with which proteins can be phosphorylated and dephosphorylated, this type of modification is a flexible mechanism for cells to respond to external signals and environmental conditions. [ 7 ]


Kinases  phosphorylate proteins and  phosphatases  dephosphorylate proteins. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a  conformational change  in the structure in many  enzymes  and  receptors , causing them to become activated or deactivated. Phosphorylation usually occurs on serine,  threonine ,  tyrosine  and  histidine  residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phosphorylation. [ 8 ]  In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or  arginine  or  lysine  residues. [ 8 ] [ 9 ]  The addition of a phosphate (PO 4 3- ) molecule to a non-polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of a molecule. In this way  protein dynamics  can induce a conformational change in the structure of the protein via long-range  allostery  with other hydrophobic and hydrophilic residues in the protein.


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. [ 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 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. [ 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 ]  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. [ 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 ]


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 ]


H3T6P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation of the 6th  threonine  residue of the histone H3 protein.


H3S10P  and H3T6P levels are higher in  cervical cancer  cells and are responsible for cellular transformation.


The writing of H3T6P by androgen-dependent kinase signaling precludes the removal of active methyl tags from  H3K4  during AR-stimulated gene expression. H3T6P levels are positively correlated with high  Gleason scores  in  prostate carcinomas.


The name of this modification indicates the protein phosphorylation of threonine 6 on histone H3 protein subunit:
 [ 1 ]


H3S10P and H3T6P levels are higher in cervical cancer cells and are responsible for cellular transformation. [ 2 ]


The writing of H3T6P by androgen-dependent kinase signaling precludes the removal of active methyl tags from H3K4 during AR-stimulated gene expression.  PKCbeta (I) and H3T6P levels are positively correlated with high Gleason scores in prostate carcinomas. Inhibiting PKCbeta(I) reduces AR-induced tumor cell proliferation in vitro and cancer progression in vivo. [ 3 ]


H3T11P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation the 11th  threonine  residue of the histone H3 protein.


Histone H3 phosphorylation at threonine 11 establishes a unique chromatin mark for transcriptional control. The levels of phosphorylated H3T11 are higher in  prostate carcinomas  as measured by  Gleason scores .


H3T11P is a biomarker for aging and nutritional stress. Under stress, the Sch9 and CK2 kinases work together to regulate H3T11P. By changing dietary stress responses, H3pT11 mutants were able to extend their chronological longevity.


The name of this modification indicates the protein phosphorylation of threonine 11 on histone H3 protein subunit:
 [ 1 ]


Protein-kinase-C-related kinase 1 (PRK1) phosphorylates histone H3 at threonine 11 when ligand-dependent recruitment to androgen receptor target genes occurs. The levels of PRK1 and phosphorylated H3T11 are higher in prostate carcinomas as measured by Gleason scores. PRK1 inhibition inhibits AR-induced tumor cell proliferation, making it a potential therapeutic target. [ 2 ]   The androgen receptor functions as a transcription factor in the genesis and progression of prostate cancer. [ 3 ]


H3T11P is a biomarker for aging and nutritional stress. Under stress, the  Sch9  and  CK2 kinases  work together to regulate H3T11P. By changing dietary stress responses, H3T11P mutants were able to extend their chronological longevity. The phosphorylation of H3T11 by Sch9 and CK2 links a nutritional stress response to chromatin in the regulation of lifespan. Loss of H3T11P prolongs lifespan by altering the stress response at an early stage. [ 4 ]


H3T45P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation the 45th  threonine  residue of the histone H3 protein.


During  apoptosis , H3T45 phosphorylation is required for structural changes inside the nucleosome that enable DNA nicking and/or fragmentation.


The H3T45 residue appears to be a  nucleosome  gatekeeper, regulating DNA accessibility at transcription target sites. This could be a new regulatory network that coordinates gene expression to enable the necessary cell expansion that comes with cell proliferation. It could be a particularly distinctive target for cancer therapies and as a  biomarker .


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.


The name of this modification indicates the protein phosphorylation of  threonine  45 on histone H3 protein subunit:
 [ 1 ]


In vitro and in vivo, the kinase responsible for H3T45ph is  protein kinase C-delta . H3T45ph causes structural changes inside the nucleosome to promote DNA nicking and/or fragmentation due to its nucleosomal location. [ 2 ]


H3T45 is phosphorylated by a histone kinase complex that includes the conserved S-phase replication start enzyme Cdc7, its activating protein Dbf4, and a number of other components. [ 3 ]  The H3T45 residue appears to be a nucleosome gatekeeper, regulating DNA accessibility at transcription target sites. This could be a new regulatory network that coordinates gene expression to enable the necessary cell expansion that comes with cell proliferation. [ 3 ]


H3T45 phosphorylation promotes  H3K56  acetylation. [ 4 ]  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. [ 5 ]


Post-translational modification of histones such as histone phosphorylation has been shown to modify the chromatin structure by changing protein:DNA or protein:protein interactions. [ 6 ]  Histone post-translational modifications modify the chromatin structure. The most commonly associated histone phosphorylation occurs during cellular responses to DNA damage, when phosphorylated histone H2A separates large chromatin domains around the site of DNA breakage. [ 7 ]  Researchers investigated whether modifications of histones directly impact RNA polymerase II directed transcription. Researchers choose proteins that are known to modify histones to test their effects on transcription, and found that the  stress-induced kinase, MSK1, inhibits RNA synthesis. Inhibition of transcription by MSK1 was most sensitive when the template was in chromatin, since DNA templates not in chromatin were resistant to the effects of MSK1. It was shown that MSK1 phosphorylated histone H2A on serine 1, and mutation of serine 1 to alanine blocked the inhibition of transcription by MSK1. Thus results suggested that the acetylation of histones can stimulate transcription by suppressing an inhibitory phosphorylation by a kinase as MSK1. [ 8 ]


Phosphorylation introduces a charged and hydrophilic group in the side chain of amino acids, possibly changing a protein's structure by altering interactions with nearby amino acids. Some proteins such as  p53  contain multiple phosphorylation sites, facilitating complex, multi-level regulation. Because of the ease with which proteins can be phosphorylated and dephosphorylated, this type of modification is a flexible mechanism for cells to respond to external signals and environmental conditions. [ 9 ]


Kinases  phosphorylate proteins and  phosphatases  dephosphorylate proteins. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a  conformational change  in the structure in many  enzymes  and  receptors , causing them to become activated or deactivated. Phosphorylation usually occurs on serine,  threonine ,  tyrosine  and  histidine  residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phosphorylation. [ 10 ]  In prokaryotic proteins phosphorylation occurs on the serine, threonine, tyrosine, histidine or  arginine  or  lysine  residues. [ 10 ] [ 11 ]  The addition of a phosphate (PO 4 3- ) molecule to a non-polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of a molecule. In this way  protein dynamics  can induce a conformational change in the structure of the protein via long-range  allostery  with other hydrophobic and hydrophilic residues in the protein.


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 ]


H3Y41P  is an  epigenetic  modification to the DNA packaging protein  histone H3 . It is a mark that indicates the phosphorylation the 41st  tyrosine  residue of the histone H3 protein.


To impose cell cycle-dependent regulation of constitutive heterochromatin, H3Y41p collaborates with other regulatory mechanisms.


In activated B-cell–like  diffuse large B-cell lymphoma ,  JAK1  mediates autocrine  IL-6  and  IL-10  cytokine activation via a noncanonical epigenetic regulation mechanism involving phosphorylation of histone H3 on tyrosine 41. [ 1 ]


The name of this modification indicates the protein phosphorylation of tyrosine 41 on histone H3 protein subunit:
 [ 2 ]


In activated B-cell–like (ABC)  diffuse large B-cell lymphoma ,  JAK1  mediates autocrine  IL-6  and  IL-10  cytokine activation via a noncanonical epigenetic regulation mechanism involving phosphorylation of histone H3 on tyrosine 41. [ 1 ]


On histone H3, JAK2 phosphorylates Y41. Heterochromatin protein 1 alpha (HP1) binds to this region of H3, and JAK2 activation of H3Y41 hinders this binding. Inhibition of JAK2 activity lowers both the expression of the hematopoietic oncogene  LMO2  and the phosphorylation of H3Y41 at its promoter in leukemic cells while enhancing HP1 binding at the same location. [ 3 ]


The ability to be transcribed is directly influenced by the degree of chromatin compaction at distinct chromosomal locations.  Euchromatin , which is generally open and found in most coding sequences, and  heterochromatin , which is more compacted and found in highly repetitive sections, are the two types of chromatin.  Heterochromatin is further separated into facultative and constitutive heterochromatin, the former of which is found in DNA sequences that code for developmental proteins. Non-coding repetitive DNA associated with specific chromosomal locations, such as centromeres and telomeres, is referred to as constitutive heterochromatin.  To impose cell cycle-dependent regulation of constitutive heterochromatin, H3Y41p collaborates with other regulatory mechanisms.  H3Y41p is closely controlled throughout the cell cycle, with phosphorylation occurring in M-phase and lasting until mid-S-phase; this happens before the septation index peaks, and its presence coincides with Swi6 displacement from centromeric heterochromatin. [ 4 ]  H3Y41p causes a transition in CD proteins, with Swi6/HP1 being displaced to provide  RNA polymerase II  access to the DNA and Chp1, a RITS component, being recruited for the RNAi-mediated formation of heterochromatin. [ 4 ]


H4K5ac  is an  epigenetic  modification to the DNA packaging protein  histone H4 . It is a mark that indicates the  acetylation  at the 5th  lysine  residue of the histone H4 protein. H4K5 is the closest lysine residue to the N-terminal tail of histone H4. [ 1 ]  It is enriched at the  transcription start site  (TSS) and along gene bodies. [ 2 ]   Acetylation of histone H4K5 and  H4K12ac  is enriched at centromeres. [ 3 ]


H4K5ac indicates acetylation of  lysine  5 on histone H4 protein subunit:
 [ 4 ]


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 . [ 5 ] [ 6 ]


H4 modifications are not as well known as H3's and H4 has fewer variations which might explain their important function.  [ 1 ]


H4K5 is acetylated by  TIP60  and  CBP/p300  proteins. [ 1 ]   CAP/p300 open transcriptional start site chromatin by acetylating histones. [ 1 ]   H4K5ac has also been implicated in  epigenetic bookmarking  which allows gene expression patterns to be faithfully passed to daughter cells through mitosis. [ 1 ]   Important cell-type specific genes are marked in some way that prevents them from being compacted during mitosis and ensures their rapid transcription. [ 1 ]   H4K5ac appears to prime activity-dependent genes expressed during learning. [ 1 ]


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. [ 7 ]


The regulation of transcription factors, effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism [ 8 ]  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 this post-translational modification may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 9 ] [ 10 ] [ 11 ]


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. [ 12 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 13 ]  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. [ 14 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 15 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 16 ]


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. [ 17 ]


H4K5ac is implicated in  inflammatory bowel disease  and  Crohn's disease . [ 2 ]


H4K8ac , representing an  epigenetic  modification to the DNA packaging protein  histone H4 , is a mark indicating the  acetylation  at the 8th  lysine  residue of the histone H4 protein. It has been implicated in the prevalence of  malaria .


H4K8ac indicates acetylation of  lysine  8 on histone H4 protein subunit:
 [ 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 : 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 . [ 2 ] [ 3 ]


H4 modifications are not as well known as H3's and H4 have fewer variations which might explain their important function. [ 4 ]


H4K8ac is part of 17 modifications of a group of active promoters. H4K8ac is found more often in active promoters and transcribed regions than other marks. [ 4 ]   H4K8ac is modified by a different group of enzymes than other H4 lysines. [ 4 ]


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. [ 5 ]


The regulation of transcription factors, effector proteins,  molecular chaperones , and cytoskeletal proteins by acetylation and deacetylation is a significant post-translational regulatory mechanism [ 6 ]  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 this post-translational modification may also crosstalk with  phosphorylation ,  methylation ,  ubiquitination , sumoylation, and others for dynamic control of cellular signaling. [ 7 ] [ 8 ] [ 9 ]


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. [ 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 ]


This mark has been implicated in the prevalence of  malaria . [ 21 ]


H4K12ac  is an  epigenetic  modification to the DNA packaging protein  histone H4 . It is a mark that indicates the  acetylation  at the 12th  lysine  residue of the histone H4 protein. H4K12ac is involved in learning and memory. It is possible that restoring this modification could reduce age-related decline in memory.


H4K12ac indicates acetylation of  lysine  12 on histone H4 protein subunit:
 [ 1 ]


Acetylation of histone H4K5 and H4K12 is enriched at  centromeres . [ 4 ] [ 4 ]   H4K8ac and H4K12ac are associated with active promoters to form a backbone. [ 4 ]   H4 localizes more to gene bodies promoters than other acetylations so H4K8ac facilitates  transcriptional elongation . [ 4 ]


H4K12ac is involved in learning and memory so it could help with reducing age-related decline in memory. [ 4 ]  It has also been implicated in enabling developmental plasticity. [ 5 ]  High levels early in development are thought to provide transcriptional flexibility, while lower levels are thought to contribute to repressed transcription. In this way, H4K12 acetylation and deacetylation could open and close "critical windows" of environmental sensitivity. [ 6 ]


H4K16ac  is an  epigenetic  modification to the  DNA  packaging protein  Histone H4 . It is a mark that indicates the  acetylation  at the 16th  lysine  residue of the histone H4 protein.


H4K16ac is unusual in that it has both  transcriptional activation  AND  repression  activities.


The loss of  H4K20me3  along with a reduction of H4K16ac is a strong indicator of 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 ]


H4K16ac indicates acetylation of  lysine  16 on histone H4 protein subunit:
 [ 6 ]


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 ]


Secondly, it can block the function of chromatin remodelers. [ 15 ]  Thirdly, it neutralizes the positive charge on lysines. [ 15 ]  Acetylation of histone H4 on lysine 16 (H4K16Ac) is especially important for chromatin structure and function in a variety of eukaryotes and is catalyzed by specific histone lysine acetyltransferases (HATs). H4K16 is particularly interesting because this is the only acetylatable site of the H4 N-terminal tail, and can influence the formation of a compact higher-order chromatin structure. [ 15 ]   Hypoacetylation of H4K16 appears to cause delayed recruitment of  DNA repair  proteins to sites of  DNA damage  in a mouse model of the premature aging, such as   Hutchinson–Gilford progeria syndrome . [ 16 ]   H4K16Ac also has roles in transcriptional activation and the maintenance of  euchromatin . [ 17 ]


H4K16ac is unusual in that it is associated with both transcriptional activation and repression. The  bromodomain  of TIP5, part of NoRC, binds to H4K16ac and then the NoRC complex silences rDNA with HATs and DNMTs. [ 18 ]


There is also a reduction in the levels of  H3K56ac  during aging and an increase in the levels of H4K16ac. [ 19 ]  Increased H4K16ac in old yeast cells is associated with the decline in levels of the  HDAC  Sir2, which can increase the life span when overexpressed. [ 19 ]


The loss of the repressive H4K20me3 mark defines cancer along with a reduction of activating H4K16ac mark. It is not clear how the loss of a repressive and an activating mark is an indicator of cancer. [ 20 ]   It is not clear exactly how but this reduction happens at repetitive sequences along with general reduced DNA methylation. [ 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. [ 21 ]


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. [ 22 ]


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. [ 23 ] [ 24 ] [ 25 ]


H4K20me  is an  epigenetic  modification to the DNA packaging protein  Histone H4 . It is a mark that indicates the  methylation  at the 20th  lysine  residue of the histone H4 protein. This mark can be  mono-, di-, or tri-methylated.  It is critical for genome integrity including DNA damage repair, DNA replication and chromatin compaction.


H4K20me2 is the most common methylation state on histone H4 and was one of the earliest modified histone residues to be identified back in pea and calf extracts in 1969. It is one of only two identified methylated lysine residues on the H4 histone, the other being monomethylated H4K12. [ 1 ] [ 2 ]


Each degree of methylation at H4K20 has a very different cellular process. The loss of H4K20me3 along with a reduction of  H4K16ac  is a strong indicator of cancer.


H4K20me indicates  monomethylation  of  lysine  20 on histone H4 protein subunit: [ 3 ]


This diagram shows the progressive methylation of a lysine residue. The mono-methylation (second from left) denotes the methylation present in H4K20me. [ 4 ]


H4K20me exists in three distinct states as mono-, di- and trimethylation. [ 4 ]


H4K20me1 is associated with transcriptional activation. [ 5 ]


H4K20me2 is similar to H4K20me1 but has a different distribution and this dimethylation controls the cell cycle and DNA damage response. [ 5 ] [ 6 ]


H4K20me3 is very different. H4K20me3 represses transcription when present at promoters.  H4K20me3 also silences repetitive DNA and transposons. The loss of H4K20me3 defines cancer along with a reduction of H4K16ac. [ 5 ] [ 7 ]


H4K20me3  is involved in  Hutchinson-Gilford Progeria syndrome  where patients have premature and very rapid aging caused by de novo mutations that occurs in a gene that encodes  lamin A . Lamin A is made but isn't processed properly. This poor processing creates a really abnormal nuclear morphology and disorganized  heterochromatin . Patients also don't have appropriate DNA repair, and they also have increased genomic instability. [ 8 ]


The loss of the repressive H4K20me3 mark defines cancer along with a reduction of activating H4K16ac mark. It is not clear how the loss of a repressive and an activating mark is an indicator of cancer. [ 7 ]   It is not clear exactly how but this reduction happens at repetitive sequences along with general reduced DNA methylation. [ 9 ]


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 . [ 10 ] [ 11 ]


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. [ 12 ]  The current understanding and interpretation of histones comes from two large scale projects:  ENCODE  and the Epigenomic roadmap. [ 13 ]  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. [ 14 ]  Different developmental stages were profiled in Drosophila as well, an emphasis was placed on histone modification relevance. [ 15 ]  A look in to the data obtained led to the definition of chromatin states based on histone modifications. [ 16 ]


H4K20 was one of the earliest modified histone residues to be identified back in pea and calf extracts in 1969. [ 1 ]


H4K20me is important for DNA damage repair, DNA replication and chromatin compaction. [ 4 ]


There are a set of H4K20-specific histone methyltransferases (SET8/PR-Set7, SUV4-20H1 and SUV4-20H2). Without these enzymes there is a disruption of genomic instability. [ 4 ]


The histone mark H4K20me can be detected in a variety of ways:


H4K91ac  is an  epigenetic  modification to the DNA packaging protein  histone H4 . It is a mark that indicates the  acetylation  at the 91st  lysine  residue of the histone H4 protein. No known diseases are attributed to this mark but it might be implicated in  melanoma .


H4K91ac indicates acetylation of  lysine  91 on histone H4 protein subunit:
 [ 1 ]


As December 15, 2019, no diseases are attributed to this mark [ 5 ]  although  Pleckstrin homology domain 's (PHIP) targetable bromodomain specifically binds H4K91ac which could implicate PHIP in the progression of melanoma. [ 6 ]  It is found at the  transcription start site  (TSS) of active and poised genes. [ 5 ]


Histone acetyltransferase  KAT2A  is the specific reader. [ 5 ]


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. [ 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 ]


H4R3me2  is an  epigenetic  modification to the DNA packaging protein  histone H4 . It is a mark that indicates the di- methylation  at the 3rd  arginine  residue of the histone H4 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 3 on histone H4 protein subunit:
 [ 2 ]


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.


JMJD6 , a  Jumonji  domain-containing protein, was reported to demethylate H4R3me2.
 [ 4 ]   H4R3me2 is a major mark deposited by  Prmt5 . [ 4 ]   H4R8me2s  is linked to transcriptional repression and is tightly linked with H4R3me2s methylation. [ 4 ]


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 ] [ 11 ]


There is evidence of crosstalk between H4R3me2 and  H3K9ac  and  H3K14ac  in cell differentiation and the response to  cocaine . [ 1 ]


Hard inheritance  was a model of  heredity  that explicitly excludes any acquired characteristics, such as of  Lamarckism . It is the exact opposite of  soft inheritance , coined by  Ernst Mayr  to contrast ideas about  inheritance .


Hard inheritance states that characteristics of an organism's offspring (passed on through  DNA ) will not be affected by the actions that the  parental   organism  performs during its lifetime. For example: a medieval  blacksmith  who uses only his right arm to  forge   steel  will not sire a son with a stronger right arm than left because the blacksmith's actions do not alter his genetic code. Inheritance due to usage and non-usage is excluded. Inheritance works as described in the  modern synthesis of evolutionary biology . [ 1 ]


The existence of inherited  epigenetic variants  has led to renewed interest in soft inheritance. [ 2 ]


Edith Heard  (born 1965) [ 1 ]   FRS   MAE [ 2 ]  is a British-French researcher in  epigenetics  who has been serving as the Director General of the  European Molecular Biology Laboratory  (EMBL) since January 2019. [ 3 ] [ 4 ]  She is also Professor at the  Collège de France , holding the Chair of Epigenetics and Cellular Memory. In 2025 she will become CEO of the Francis Crick Institute in London, U.K.


From 2010 to 2018, Heard was the Director of the Genetics and Developmental Biology department at the  Curie Institute (Paris) , France. Heard is noted for her studies of  X-chromosome - inactivation . [ 5 ] [ 6 ] [ 7 ] [ 8 ] [ 9 ] [ 10 ]


Heard graduated with a  Bachelor of Arts  degree in  Natural Sciences (Genetics)  from the  University of Cambridge  as a student of  Emmanuel College, Cambridge , graduating in 1986. She was awarded a  PhD  from  Imperial College London [ 11 ]  for research investigating  gene amplification  in rat cells in 1990 while working at the  Imperial Cancer Research Fund  Laboratory in London, UK. [ 1 ]


Heard's main areas of research include genetics,  epigenetics  and developmental biology, [ 3 ] [ 12 ]  in particular focussing on  X-chromosome inactivation , which occurs when one of the two copies of the X chromosomes in female mammals is inactivated. Her work on this process started in the 1990’s during her post-doc in the laboratory of Philip Avner at the Pasteur Institute. After joining the CNRS, she continued to work on X inactivation, performing functional studies on the X-inactivation centre locus that regulates the initiation of X inactivation. [ 13 ] [ 14 ]  In 2000, Heard spent a year as a visiting scientist in David Spector’s group at  Cold Spring Harbor Laboratory [ 15 ]  where she discovered some of the early chromatin changes in the X-inactivation process. [ 10 ]


Heard set up her own laboratory at the Institut Curie in 2001. Amongst her contributions, her group showed that X-chromosome inactivation happens not once, but twice, during development: first in all cells designated to building the  placenta , then again in some cells sent off to build the embryo. [ 16 ] [ 17 ] [ 18 ]


Heard developed powerful single-cell techniques enabling the analysis of fixed and living embryos and embryonic stem cells. These led to one of her major discoveries, showing that X-inactivation is a highly dynamic process during early  embryogenesis  and revealing major differences in X-inactivation strategies in different mammals, from mouse to man. Heard has also performed pioneering work revealing that in addition to epigenetic modifications,  chromosome  organization and nuclear compartmentalization are important players in the initiation and maintenance of X inactivation. [ 2 ] [ 19 ]  Thanks to their studies on the X-inactivation centre, the Heard group also revealed the existence of Topologically Associating Domains (TADs) in collaboration with Job Dekker. [ 20 ]


Heard has been a professor at the  Collège de France , holding the Chair of Epigenetics and Cellular Memory, and from 2010 to 2018 she was director of the Genetics and Developmental Biology department at the  Institut Curie  in Paris. [ 21 ]  She and her laboratory moved to EMBL in 2019. In 2016, Heard was involved in establishing a  Government of France  programme to support scientists displaced by war or conflict – the Programme d'aide à l'accueil en urgence des scientifiques en exil (PAUSE). [ 22 ]


In June 2017, Heard's appointment as the fifth Director General of the  European Molecular Biology Laboratory  was announced, and she took office in January 2019. [ 5 ]  She has served as a member of the science council of the   World Health Organization  (WHO) since 2021. [ 23 ]


Heard is a member of the Scientific Advisory Board of the  French National Centre for Scientific Research , [ 24 ]  the Biotech Research & Innovation Centre (Copenhagen, Denmark), [ 25 ]  the Institute of Molecular Biology and Biotechnology (Crete, Greece) [ 26 ]  and the  Francis Crick Institute . [ 27 ]


In 2023, Heard chaired the selection committee that chose  Yasmine Belkaid  to succeed  Stewart Cole  as director of the Institut Pasteur. [ 28 ]


In 2017, Heard was awarded the  Inserm  Grand Prix for her work on epigenetics. [ 29 ]  In 2013, she was elected a  Fellow of the Royal Society  (FRS) in recognition for her discoveries in epigenetics. [ 2 ]   Her nomination reads:


Heard has made several groundbreaking discoveries in  epigenetics , through her studies on X-chromosome inactivation, the process of dosage compensation in mammals. Heard developed powerful single-cell techniques enabling the analysis of fixed and living embryos and embryonic stem cells. These led to one of her major discoveries, showing that X-inactivation is a highly dynamic process during early  embryogenesis  and revealing major differences in X-inactivation strategies in different mammals, from mouse to man. Heard has also performed pioneering work revealing that in addition to epigenetic modifications,  chromosome  organization and nuclear compartmentalization are important players in the initiation and maintenance of X inactivation. [ 2 ]


In 2011, Heard received the Grand Prix de la  Fondation pour la recherche médicale . In 2009, she received the Prix  Jean Hamburger . In 2005, Heard was a laureate of the  FSER  award. [ 30 ]  Heard has been an  EMBO Member  since 2005 and won the  Suffrage Science award  in 2012. [ 31 ]  She received the European Society for Human Genetics Award in 2017  [ 32 ]  and the Hansen Family Award in 2019. [ 33 ]


In 2020, she was awarded the  L'Oréal-UNESCO For Women in Science Awards [ 34 ]  and in April 2021 was appointed a member of the  World Health Organization  Science Council, [ 35 ]  and also elected as a foreign  Member of the National Academy of Sciences . [ 36 ]  In 2021 she was elected to the  German National Academy of Sciences Leopoldina . [ 37 ]  In October 2021, she was elected as an International Member of the  National Academy of Medicine . [ 38 ]  In May 2022, she was appointed a Member of the  Royal Danish Academy of Science and Letters . [ 39 ]  In July 2022, the  Pontifical Academy of Sciences  announced Heard's appointment as a member. [ 40 ]  In December 2022, Heard was  elected to the  French Academy of Sciences  under the section ‘Human Biology and Medical Sciences’ for her work on epigenetics, particularly in deciphering the process of X-chromosome inactivation.  [ 41 ]  On December 12, 2024 she received the  CNRS Gold Medal . [ 42 ]


Heard has been chosen as the 2025 recipient of The Croonian Medal and Lecture for being a leading figure in X-chromosome biology. [ 43 ]


Heard is married to French molecular biologist Vincent Colot. They have two children. [ 44 ]


“All text published under the heading 'Biography' on Fellow profile pages is available under  Creative Commons Attribution 4.0 International License .” -- "Royal Society Terms, conditions and policies" . Archived from the original on 25 September 2015 . Retrieved  9 March  2016 . {{ cite web }} :  CS1 maint: bot: original URL status unknown ( link )


The family of  heterochromatin protein 1  ( HP1 )  ("Chromobox Homolog", CBX) consists of highly conserved  proteins , which have important functions in the  cell nucleus . These functions include  gene repression  by  heterochromatin  formation,  transcriptional  activation, regulation of binding of cohesion complexes to centromeres, sequestration of genes to the nuclear periphery, transcriptional arrest,  maintenance of heterochromatin integrity, gene repression at the single nucleosome level, gene repression by heterochromatization of  euchromatin , and  DNA repair . HP1  proteins  are fundamental units of  heterochromatin  packaging that are enriched at the  centromeres  and  telomeres  of nearly all  eukaryotic   chromosomes  with the notable exception of  budding yeast , in which a yeast-specific silencing complex of SIR (silent information regulatory) proteins serve a similar function. Members of the HP1 family are characterized by an N-terminal  chromodomain  and a C-terminal  chromoshadow  domain, separated by a hinge region. HP1 is also found at some euchromatic sites, where its binding can correlate with either  gene repression  or gene activation. HP1 was originally discovered by Tharappel C James and  Sarah Elgin  in 1986 as a factor in the phenomenon known as  position effect variegation  in  Drosophila melanogaster . [ 1 ] [ 2 ]


Three different  paralogs  of HP1 are found in Drosophila melanogaster, HP1a, HP1b and HP1c. Subsequently  orthologs  of HP1 were also discovered in  S. pombe  (Swi6),  Xenopus  (Xhp1α and Xhp1γ),  Chicken  (CHCB1, CHCB2 and CHCB3),  Tetrahymena  (Pdd1p) and many other metazoans. In mammals, [ 3 ]  there are three  paralogs :  HP1α ,  HP1β  and  HP1γ . In  Arabidopsis thaliana  (a plant), there is one structural homolog: Like Heterochromatin Protein 1 (LHP1), also known as Terminal Flower 2 (TFL2). [ 4 ]


HP1β interacts with the  histone methyltransferase  (HMTase) Suv(3-9)h1 and is a component of both pericentric and telomeric  heterochromatin . [ 5 ] [ 6 ] [ 7 ]  HP1β is a dosage-dependent modifier of pericentric heterochromatin-induced silencing [ 8 ]  and silencing is thought to involve a dynamic association of the HP1β  chromodomain  with the tri-methylated  histone H3  K9me3. The binding of the K9me3-modified H3 N-terminal tail by the chromodomain is a defining feature of HP1 proteins.


HP1 interacts with numerous other proteins/molecules (in addition to H3K9me3) with different cellular functions in different organisms.  Some of these HP1 interacting partners are:  histone H1 ,  histone H3 ,  histone H4 ,  histone methyltransferase ,  DNA methyltransferase ,  methyl CpG binding protein MeCP2 , and the  origin recognition complex  protein ORC2. [ 9 ] [ 10 ] [ 11 ]


HP1 has a versatile structure with three main components; a chromodomain, a chromoshadow domain, and a hinge domain. [ 12 ]  The chromodomain is responsible for the specific binding affinity of HP1 to histone H3 when tri-methylated at the 9th lysine residue. [ 13 ]  HP1 binding affinity to nucleosomes containing histone H3 methylated at lysine K9 is significantly higher than to those with unmethylated lysine K9. HP1 binds  nucleosomes  as a dimer and in principle can form multimeric complexes. Some studies have interpreted HP1 binding in terms of nearest-neighbor  cooperative binding . However, the analysis of available data on HP1 binding to nucleosomal arrays  in vitro  shows that experimental HP1 binding isotherms can be explained by a simple model without cooperative interactions between neighboring HP1 dimers. [ 14 ]  Nevertheless, favorable interactions between nearest neighbors of HP1 lead to limited spreading of HP1 and its marks along the nucleosome chain  in vivo . [ 15 ] [ 16 ]


The binding affinity of the HP1 chromodomain has also been implicated in regulation of  alternative splicing . [ 17 ]  HP1 can act as both an enhancer and silencer of splicing alternative exons. The exact role it plays in regulation varies by gene and is dependent on the methylation patterns within the gene body. [ 17 ]  In humans, the role of HP1 on splicing has been characterized for alternative splicing of the EDA exon from the  fibronectin  gene. In this pathway HP1 acts as a mediator protein for repression of alternative splicing of the EDA exon. [ 18 ]  When the chromatin within the gene body is not methylated, HP1 does not bind and the EDA exon is transcribed. When the chromatin is methylated, HP1 binds the chromatin and recruits the  splicing factor   SRSF3  which binds HP1 and splices the EDA exon from the mature transcript. [ 17 ] [ 18 ]  In this mechanism HP1 recognizes the H3K9me3 methylated chromatin and recruits a splicing factor to alternatively splice the mRNA, thereby excluding the EDA exon from the mature transcript.


All HP1 isoforms (HP1-alpha, HP1-beta, and HP1-gamma) are recruited to DNA at sites of UV-induced damages, at oxidative damages and at DNA breaks. [ 19 ]   The HP1 protein isoforms are required for  DNA repair  of these damages. [ 20 ]   The presence of the HP1 protein isoforms at DNA damages assists with the recruitment of other proteins involved in subsequent DNA repair pathways. [ 20 ]   The recruitment of the HP1 isoforms to DNA damage is rapid, with half maximum recruitment (t 1/2 ) by 180 seconds in response to UV damage, and a t 1/2  of 85 seconds in response to double-strand breaks. [ 21 ]   This is a bit slower than the recruitment  of the very earliest proteins recruited to sites of DNA damage, though HP1 recruitment is still one of the very early steps in DNA repair.  Other earlier proteins may be recruited with a t 1/2  of 40 seconds for UV damage and a t 1/2  of about 1 second in response to double-strand breaks (see  DNA damage response ). [ citation needed ]


HIstome  is a database that provides information about human  histone proteins , their sites of modifications, variants and modifying enzymes, and diseases linked to histone modifications. [ 1 ]


HISTome2 is an updated version of the HIstome database released in 2020. [ 2 ]


In  biology ,  histones  are highly  basic   proteins  abundant in  lysine  and  arginine  residues that are found in  eukaryotic   cell nuclei  and in most  Archaeal   phyla . They act as spools around which  DNA  winds to create structural units called  nucleosomes . [ 1 ] [ 2 ]  Nucleosomes in turn are wrapped into 30- nanometer  fibers that form tightly packed  chromatin . Histones prevent DNA from becoming tangled and protect it from  DNA damage .  In addition, histones play important roles in  gene regulation  and  DNA replication . Without histones, unwound DNA in  chromosomes  would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 9 micrometers (0.09 mm) of 30 nm diameter chromatin fibers. [ 3 ]


There are five families of histones, which are designated H1/H5 (linker histones), H2, H3, and H4 (core histones). The nucleosome core is formed of two H2A-H2B  dimers  and a H3-H4  tetramer . The tight wrapping of DNA around histones, is to a large degree, a result of  electrostatic  attraction between the positively charged histones and negatively charged phosphate backbone of DNA.


Histones may be chemically modified through the action of enzymes to regulate gene transcription. The most common modifications are the  methylation  of arginine or lysine residues or the  acetylation  of lysine. Methylation can affect how other proteins such as  transcription factors  interact with the nucleosomes. Lysine acetylation eliminates a positive charge on lysine thereby weakening the electrostatic attraction between histone and DNA, resulting in partial unwinding of the DNA, making it more accessible for gene expression.


Five major families of histone proteins exist:  H1/H5 ,  H2A ,  H2B ,  H3 , and  H4 . [ 2 ] [ 4 ] [ 5 ] [ 6 ]  Histones H2A, H2B, H3 and H4 are known as the core or nucleosomal histones, while histones H1/H5 are known as the linker histones.


The core histones all exist as  dimers , which are similar in that they all possess the histone fold domain: three alpha helices linked by two loops. It is this helical structure that allows for interaction between distinct dimers, particularly in a head-tail fashion (also called the handshake motif). [ 7 ]  The resulting four distinct dimers then come together to form one octameric  nucleosome  core, approximately 63 Angstroms in diameter (a  solenoid (DNA) -like particle). Around 146  base pairs  (bp) of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across. [ 8 ]   The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place [ 9 ]  and allowing the formation of higher order structure.  The most basic such formation is the 10 nm fiber or beads on a string conformation.  This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of  DNA  separating each pair of  nucleosomes  (also referred to as linker  DNA ). Higher-order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed  chromosomes  are assembled through interactions between nucleosomes and other regulatory proteins.


Histones are subdivided into canonical replication-dependent histones, whose genes are expressed during the  S-phase  of the  cell cycle  and replication-independent  histone variants , expressed during the whole cell cycle. In mammals, genes encoding canonical histones are typically clustered along chromosomes in 4 different highly- conserved  loci, lack  introns  and use a stem loop structure at the  3' end  instead of a  polyA tail . Genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails. [ 10 ]  Complex multicellular organisms typically have a higher number of histone variants providing a variety of different functions. Recent data are accumulating about the roles of diverse histone variants highlighting the functional links between variants and the delicate regulation of organism development. [ 11 ]  Histone variants proteins from different organisms, their classification and variant specific features can be found in  "HistoneDB 2.0 - Variants"  database. [ 12 ] [ 13 ]  Several  pseudogenes  have also been discovered and identified in very close sequences of their respective functional ortholog genes. [ 14 ] [ 15 ]


The following is a list of human histone proteins, genes and pseudogenes: [ 10 ]


The  nucleosome  core is formed of two H2A-H2B  dimers  and a H3-H4 tetramer, forming two nearly  symmetrical  halves by  tertiary structure  ( C2  symmetry; one  macromolecule  is the mirror image of the other). [ 8 ]  The H2A-H2B dimers and H3-H4 tetramer also show pseudodyad symmetry. The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through  evolution , all featuring a ' helix turn helix  turn helix' motif (DNA-binding protein motif that recognize specific DNA sequence).  They also share the feature of long 'tails' on one end of the  amino acid  structure - this being the location of post-translational modification (see below). [ 16 ]


Archaeal histone only contains a H3-H4 like dimeric structure made out of a single type of unit. Such dimeric structures can stack into a tall superhelix ("hypernucleosome") onto which DNA coils in a manner similar to nucleosome spools. [ 17 ]  Only some archaeal histones have tails. [ 18 ]


The distance between the spools around which eukaryotic cells wind their DNA has been determined to range from 59 to 70 Å. [ 19 ]


In all, histones make five types of interactions with DNA:


The highly basic nature of histones, aside from facilitating DNA-histone interactions, contributes to their water solubility.


Histones are subject to post translational modification by enzymes primarily on their N-terminal tails, but also in their globular domains. [ 20 ] [ 21 ]  Such modifications include  methylation ,  citrullination ,  acetylation ,  phosphorylation ,  SUMOylation ,  ubiquitination , and  ADP-ribosylation . This affects their function of gene regulation.


In general,  genes  that are active have less bound histone, while inactive genes are highly associated with histones during  interphase . [ 22 ]   It also appears that the structure of histones has been  evolutionarily  conserved, as any deleterious  mutations  would be severely maladaptive. All histones have a highly positively charged N-terminus with many  lysine  and  arginine  residues.


Core histones are found in the  nuclei  of  eukaryotic   cells  and in most  Archaeal  phyla, but not in  bacteria . [ 18 ]  The unicellular algae known as  dinoflagellates  were previously thought to be the only eukaryotes that completely lack histones, [ 23 ]  but later studies showed that their DNA still encodes histone genes. [ 24 ]  Unlike the core histones, homologs of the lysine-rich linker histone (H1) proteins are found in bacteria, otherwise known as nucleoprotein HC1/HC2. [ 25 ]


It has been proposed that core histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, and to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their topology, these three folds share a homologous helix-strand-helix (HSH) motif. [ 16 ]  It's also proposed that they may have evolved from ribosomal proteins ( RPS6 / RPS15 ), both being short and basic proteins. [ 26 ]


Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones. [ 18 ]  Histone proteins are among the most highly conserved proteins in eukaryotes, emphasizing their important role in the biology of the nucleus. [ 2 ] : 939   In contrast mature sperm cells largely use  protamines  to package their genomic DNA, most likely because this allows them to achieve an even higher packaging ratio. [ 27 ]


There are some  variant  forms in some of the major classes. They share amino acid sequence homology and core structural similarity to a specific class of major histones but also have their own feature that is distinct from the major histones. These  minor histones  usually carry out specific functions of the chromatin metabolism. For example, histone H3-like  CENPA  is associated with only the  centromere  region of the chromosome. Histone H2A variant H2A.Z is associated with the promoters of actively transcribed genes and also involved in the prevention of the spread of silent  heterochromatin . [ 28 ]  Furthermore, H2A.Z has roles in chromatin for genome stability. [ 29 ]  Another H2A variant H2A.X is phosphorylated at S139 in regions around  double-strand breaks  and marks the region undergoing  DNA repair . [ 30 ]  Histone H3.3 is associated with the body of actively transcribed genes. [ 31 ]


Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large  genomes  of eukaryotes inside cell nuclei: the compacted molecule is 40,000 times shorter than an unpacked molecule.


Histones undergo  posttranslational modifications  that alter their interaction with  DNA  and nuclear proteins. The H3 and H4 histones have long tails protruding from the  nucleosome , which can be  covalently  modified at several places. Modifications of the tail include  methylation ,  acetylation ,  phosphorylation ,  ubiquitination ,  SUMOylation ,  citrullination , and ADP-ribosylation. The core of the histones H2A and H2B can also be modified. Combinations of modifications, known as  histone marks , are thought to constitute a code, the so-called " histone code ". [ 32 ] [ 33 ]  Histone modifications act in diverse biological processes such as  gene regulation ,  DNA repair , chromosome condensation ( mitosis ) and  spermatogenesis  ( meiosis ). [ 34 ]


The common nomenclature of histone modifications is:


So  H3K4me1  denotes the monomethylation of the 4th residue (a lysine) from the start (i.e., the  N-terminal ) of the H3 protein.


A huge catalogue of histone modifications have been described, but a functional understanding of most is still lacking. Collectively, it is thought that histone modifications may underlie a  histone code , whereby combinations of histone modifications have specific meanings. However, most functional data concerns individual prominent histone modifications that are biochemically amenable to detailed study.


The addition of one, two, or many methyl groups to lysine has little effect on the chemistry of the histone; methylation leaves the charge of the lysine intact and adds a minimal number of atoms so steric interactions are mostly unaffected. However, proteins containing Tudor, chromo or PHD domains, amongst others, can recognise lysine methylation with exquisite sensitivity and differentiate mono, di and tri-methyl lysine, to the extent that, for some lysines (e.g.: H4K20) mono, di and tri-methylation appear to have different meanings. Because of this, lysine methylation tends to be a very informative mark and dominates the known histone modification functions.


Recently it has been shown, that the addition of a  serotonin  group to the position 5 glutamine of H3, happens in serotonergic cells such as neurons. This is part of the differentiation of the serotonergic cells. This post-translational modification happens in conjunction with the H3K4me3 modification. The serotonylation potentiates the binding of the general transcription factor  TFIID  to the  TATA box . [ 43 ]


What was said above of the chemistry of lysine methylation also applies to arginine methylation, and some protein domains—e.g., Tudor domains—can be specific for methyl arginine instead of methyl lysine. Arginine is known to be mono- or di-methylated, and methylation can be symmetric or asymmetric, potentially with different meanings.


Enzymes called  peptidylarginine deiminases  (PADs) hydrolyze the imine group of arginines and attach a keto group, so that there is one less positive charge on the amino acid residue. This process has been involved in the activation of gene expression by making the modified histones less tightly bound to DNA and thus making the chromatin more accessible. [ 44 ]  PADs can also produce the opposite effect by removing or inhibiting mono-methylation of arginine residues on histones and thus antagonizing the positive effect arginine methylation has on transcriptional activity. [ 45 ]


Addition of an acetyl group has a major chemical effect on lysine as it neutralises the positive charge. This reduces electrostatic attraction between the histone and the negatively charged DNA backbone, loosening the chromatin structure; highly acetylated histones form more accessible chromatin and tend to be associated with active transcription. Lysine acetylation appears to be less precise in meaning than methylation, in that histone acetyltransferases tend to act on more than one lysine; presumably this reflects the need to alter multiple lysines to have a significant effect on chromatin structure. The modification includes  H3K27ac .


Addition of a negatively charged phosphate group can lead to major changes in protein structure, leading to the well-characterised role of  phosphorylation  in controlling protein function. It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification, and binding domains such as BRCT have been characterised.


Most well-studied histone modifications are involved in control of transcription.


Two histone modifications are particularly associated with active transcription:


Three histone modifications are particularly associated with repressed genes:


Analysis of histone modifications in embryonic stem cells (and other stem cells) revealed many gene promoters carrying both  H3K4Me3  and  H3K27Me3 , in other words these promoters display both activating and repressing marks simultaneously. This peculiar combination of modifications marks genes that are poised for transcription; they are not required in stem cells, but are rapidly required after differentiation into some lineages. Once the cell starts to differentiate, these bivalent promoters are resolved to either active or repressive states depending on the chosen lineage. [ 75 ]


Marking sites of DNA damage is an important function for histone modifications. Without a repair marker, DNA would get destroyed by damage accumulated from sources such as the  ultraviolet radiation  of the sun.


Epigenetic modifications of histone tails in specific regions of the brain are of central importance in addictions. [ 97 ] [ 98 ] [ 99 ]   Once particular epigenetic alterations occur, they appear to be long lasting "molecular scars" that may account for the persistence of addictions. [ 97 ]


Cigarette  smokers (about 15% of the US population) are usually addicted to  nicotine . [ 100 ]   After 7 days of nicotine treatment of mice, acetylation of both histone H3 and histone H4 was increased at the FosB promoter in the  nucleus accumbens  of the brain, causing 61% increase in FosB expression. [ 101 ]   This would also increase expression of the  splice variant   Delta FosB .  In the  nucleus accumbens  of the brain,  Delta FosB  functions as a "sustained molecular switch" and "master control protein" in the development of an  addiction . [ 102 ] [ 103 ]


About 7% of the US population is addicted to  alcohol .  In rats exposed to alcohol for up to 5 days, there was an increase in histone 3 lysine 9 acetylation in the pronociceptin promoter in the brain  amygdala  complex.  This acetylation is an activating mark for pronociceptin.  The nociceptin/nociceptin opioid receptor system is involved in the reinforcing or conditioning effects of alcohol. [ 104 ]


Methamphetamine  addiction occurs in about 0.2% of the US population. [ 105 ]   Chronic methamphetamine use causes  methylation of the lysine  in position 4 of histone 3 located at the  promoters  of the  c-fos  and the  C-C chemokine receptor 2  (ccr2)  genes, activating those genes in the nucleus accumbens (NAc). [ 106 ]   c-fos is well known to be important in  addiction . [ 107 ]   The  ccr2  gene is also important in addiction, since mutational inactivation of this gene impairs addiction. [ 106 ]


The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins are synthesized during S phase of the cell cycle. There are different mechanisms which contribute to the increase of histone synthesis.


Yeast carry one or two copies of each histone gene, which are not clustered but rather scattered throughout chromosomes. Histone gene transcription is controlled by multiple gene regulatory proteins such as transcription factors which bind to histone promoter regions. In budding yeast, the candidate gene for activation of histone gene expression is SBF. SBF is a transcription factor that is activated in late G1 phase, when it dissociates from its repressor  Whi5 . This occurs when  Whi5  is phosphorylated by Cdc8 which is a G1/S Cdk. [ 108 ]    Suppression of histone gene expression outside of S phases is dependent on Hir proteins which form inactive chromatin structure at the locus of histone genes, causing transcriptional activators to be blocked. [ 109 ] [ 110 ]


In  metazoans  the increase in the rate of histone synthesis is due to the increase in processing of pre-mRNA to its mature form as well as decrease in mRNA degradation; this results in an increase of active mRNA for translation of histone proteins. The mechanism for mRNA activation has been found to be the removal of a segment of the 3' end of the mRNA strand, and is dependent on association with stem-loop binding protein ( SLBP ). [ 111 ]  SLBP also stabilizes histone mRNAs during S phase by blocking degradation by the 3'hExo nuclease. [ 112 ]  SLBP levels are controlled by cell-cycle proteins, causing SLBP to accumulate as cells enter S phase and degrade as cells leave S phase. SLBP are marked for degradation by phosphorylation at two threonine residues by cyclin dependent kinases, possibly cyclin A/ cdk2, at the end of S phase. [ 113 ]   Metazoans also have multiple copies of histone genes clustered on chromosomes which are localized in structures called Cajal bodies as determined by genome-wide chromosome conformation capture analysis (4C-Seq). [ 114 ]


Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a transcription factor which activates histone gene transcription on chromosomes 1 and 6 of human cells. NPAT is also a substrate of cyclin E-Cdk2, which is required for the transition between G1 phase and S phase. NPAT activates histone gene expression only after it has been phosphorylated by the G1/S-Cdk cyclin E-Cdk2 in early S phase. [ 115 ]  This shows an important regulatory link between cell-cycle control and histone synthesis.