Linked Annotation External Source PAT ID Label Synonyms Similar Term Definition Equivalent Term Annotation Term owl:Thing http://localhost/plosthes.2017-1#1628 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C129422 http://purl.jp/bio/4/id/200906074118403576 http://purl.obolibrary.org/obo/GO_0016570 http://purl.obolibrary.org/obo/VariO_0453 P00000069 Histone Modification Site Histone Modification Post-Translational Histone Modification modified histone modified histones [NCIt Definition]: Post-translational processing of amino acids within a histone protein. P00000069 http://purl.obolibrary.org/obo/GO_0016571 http://purl.obolibrary.org/obo/SO_0001701 P00000071 Histone Methylation Site Histone Glutamine Methylation histone methylation histone methylation site [SO Definition]: A histone modification site where the modification is the methylation of the residue. P00000071 http://localhost/plosthes.2017-1#9263 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20740 http://purl.obolibrary.org/obo/GO_0016573 http://www.bootstrep.eu/ontology/GRO#HistoneAcetylation P00000081 Histone Acetylation Site [NCIt Definition]: Histone Acetylation involves covalent linkage of acetyl groups to highly basic histone proteins associated with DNA, particularly in active chromatin, and may be involved in regulation of gene expression. P00000081 P00000090 Histone Butyrylation Site The modification of histones by addition of butyryl groups. P00000090 http://purl.obolibrary.org/obo/GO_0071110 P00000091 Histone Biotinylation Site [GO Definition]: The modification of a histone by the addition of a biotinyl group. [ http://www.ncbi.nlm.nih.gov/pubmed/19019041 http://www.ncbi.nlm.nih.gov/pubmed/14613969 GOC:rph ] P00000091 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501262/ P00000092 Histone Crotonylation Site The modification of a lysine residue on a histone by crotonylation. P00000092 http://purl.obolibrary.org/obo/GO_0036414 P00000093 Histone Citrullination Site histone deimination [GO Definition]: The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein. [ http://www.ncbi.nlm.nih.gov/pubmed/22853951 GOC:als http://www.ncbi.nlm.nih.gov/pubmed/23175390 ] P00000093 http://www.iiserpune.ac.in/~coee/histome/ptm.php?mod_type=lysine_ribosylation P00000094 Histone ADP-Ribosylation Site histone ADP ribosylation Histone proteins often undergo ribosylation (ar) i.e. the addition of poly (ADP-ribose) units specifically at the lysine residues. This modification is mediated by Poly [ADP-ribose] polymerase (PARP) enzymes. In this case, the NAD+ acts as the ADP-ribose donor. These are big units and each ADP-ribose moiety adds ~560 Da to the histone protein. ADP-ribosylation causes disruption of the nucleosome structure by loss of histone-DNA interaction on account of charge modification. ADP ribosylation plays an important role in DNA break repair mechanisms. P00000094 P00000095 Histone Glycosylation Site The modification of histones by addition of carbohydrate groups. P00000095 P00000096 Histone Malonylation Site The addition of a malonyl group to a histone lysine residue which serves a yet-to-be-determined function. P00000096 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176146/ P00000097 Histone O-GlcNAcylation Site O-GlcNAcylated histone histone O-GlcNAc glycosylation A histone modification site where the modification is the covalent linkage of N-acetylglucosamine (GlcNAc) to the histone residue. P00000097 https://www.ncbi.nlm.nih.gov/pubmed/14578449 P00000098 Histone Sumoylation Site The modification of histones by addition of small Ubiquitin-like Modifier (SUMO) groups. P00000098 P00000099 Histone Propionylation Site The modification of histones by addition of propionyl groups. P00000099 http://purl.obolibrary.org/obo/GO_0016572 P00000100 Histone Phosphorylation Site histone-serine phosphorylation histone-threonine phosphorylation histone-tyrosine phosphorylation [GO Definition]: The modification of histones by addition of phosphate groups. [ GOC:ai ] P00000100 http://purl.obolibrary.org/obo/GO_0016574 http://purl.obolibrary.org/obo/SO_0001716 P00000103 Histone Ubiquitination Site histone ubiquitination site histone ubiquitinylation histone ubiquitylation [GO Definition]: The modification of histones by addition of ubiquitin groups. [ GOC:ai ] P00000103 http://purl.obolibrary.org/obo/GO_0033522 P00000104 Histone H2A Ubiquitination Site [GO Definition]: The modification of histone H2A by addition of one or more ubiquitin groups. [ GOC:mah http://www.ncbi.nlm.nih.gov/pubmed/15509584 GOC:bf http://www.ncbi.nlm.nih.gov/pubmed/16473935 http://www.ncbi.nlm.nih.gov/pubmed/18430235 ] P00000104 P00000122 Epigenetic Enzyme P00000122 P00000123 Histone Modifying Enzyme P00000123 http://purl.bioontology.org/ontology/MESH/D051548 P00000124 Histone Acetyltransferase HAT HATs histone acetylase histone acetylases histone acetyltransferase histone acetyltransferases [MeSH Definition]: Enzymes that catalyze acyl group transfer from ACETYL-CoA to HISTONES forming CoA and acetyl-histones. P00000124 http://purl.obolibrary.org/obo/GO_0070775 P00000125 H3 Histone Acetyltransferase Complex H3 HAT complex H3 histone acetyltransferase complex [GO Definition]: A multisubunit complex that catalyzes the acetylation of histone H3. P00000125 http://purl.obolibrary.org/obo/GO_1902562 P00000126 H4 Histone Acetyltransferase Complex Hpa3 (homo-)dimer Hpa3 complex [GO Definition]: A protein complex which is capable of H4 histone acetyltransferase activity. An example of this is Hpa2 in yeast [Q06592] in PMID:23775086 [IDA]. P00000126 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16682 P00000127 Histone Deacetylase HDAC histone deacetylase [NCIt Definition]: Histone acetylation and deacetylation alternately exposes and occludes DNA to transcription factors. Histone deacetylation is catalyzed by the histone deacetylases. There are at least 2 classes of HDACs, class I consisting of proteins homologous to yeast Rpd3 (e.g., HDAC1, HDAC2, and HDAC3) and class II consisting of proteins homologous to yeast Hda1 (e.g., HDAC4 and HDAC6). (from OMIM) P00000127 P00000128 Histone Serine Kinase P00000128 http://purl.bioontology.org/ontology/MESH/C021362 P00000129 Histone Methyltransferase histone H3 methyltransferase histone methylase P00000129 http://purl.bioontology.org/ontology/SNOMEDCT/426752007 http://www.iiserpune.ac.in/~coee/histome/enzyme_sp.php?enzyme_sp=Histone-arginine%20methyltransferase%20CARM1 P00000130 Histone-Arginine N-Methyltransferase CARM1 Coactivator-associated arginine methyltransferase 1 Histone-arginine N-methyltransferase (substance) Histone-arginine methyltransferase CARM1 Protein arginine N-methyltransferase 4 Protein methylase I coactivator-associated arginine methyltransferase 1 P00000130 P00000131 Histone-Glutamine Methyltransferase P00000131 P00000132 Histone Demethylase P00000132 http://purl.obolibrary.org/obo/GO_0035097 P00000133 Histone Methyltransferase Complex [GO Definition]: A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins. P00000133 http://purl.obolibrary.org/obo/GO_0000118 P00000134 Histone Deacetylase Complex HDAC complex histone deacetylase complex [GO Definition]: A protein complex that possesses histone deacetylase activity. Note that this term represents a location, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone deacetylase activity ; GO:0004407'. P00000134 http://purl.bioontology.org/ontology/MESH/C449880 P00000135 O-GlcNAc Transferase [MeSH Definition]: catalyzes polypeptide glycosylation by the addition of N-acetylglucosamine to serine and theronine residues P00000135 P00000136 DNA Modifying Enzyme An enzyme that modifies DNA. P00000136 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16508 P00000137 DNA Methyltransferase DNA MTase DNA Methyltransferase DNA Modification Methylase DNA methylase DNA methyltransferase DNA-Methyltransferase Dnmt EC 2.1.1.113 Site-Specific DNA-methyltransferase [NCIt Definition]: DNA Methyltransferases are a subclass of transferase enzymes that catalyze the transfer of a methyl group from a donor compound to DNA. P00000137 https://www.sciencedirect.com/science/article/pii/S0092867400816566 P00000138 De Novo Methyltransferase de novo methyltransferases The establishment of DNA methylation patterns requires de novo methylation by de novo methyltransferases that occurs predominantly during early development and gametogenesis in mice (https://www.sciencedirect.com/science/article/pii/S0092867400816566) P00000138 http://localhost/plosthes.2017-1#1702 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13201 http://purl.bioontology.org/ontology/MESH/D002843 http://purl.bioontology.org/ontology/SNOMEDCT/60085001 http://purl.obolibrary.org/obo/GO_0000785 http://purl.org/sig/ont/fma/fma67526 http://www.bootstrep.eu/ontology/GRO#Chromatin P00000139 Chromatin Chromatin (substance) Karyoplas Nuclear sap chromosome scaffold [NCIt Definition]: The genetic material of the nucleus, consisting of deoxyribonucleoprotein, which occurs in two forms during the phase between mitotic divisions: 1) as heterochromatin, seen as condensed, readily stainable clumps; 2) as euchromatin, dispersed lightly staining or nonstaining material. During mitotic division the chromatin condenses into chromosomes. P00000139 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13241 http://purl.bioontology.org/ontology/MESH/D006570 http://purl.bioontology.org/ontology/SNOMEDCT/69307006 http://purl.obolibrary.org/obo/GO_0000792 P00000140 Heterochromatin [NCIt Definition]: A tightly packed area of chromatin that may function to protect chromosome integrity and regulate gene expression. P00000140 https://www.sciencedirect.com/science/article/pii/S1097276507006235) P00000141 Facultative Heterochromatin Facultative heterochromatin (fHC) designates genomic regions in the nucleus of a eukaryotic cell that have the opportunity to adopt open or compact conformations within temporal and spatial contexts. (https://www.sciencedirect.com/science/article/pii/S1097276507006235) P00000141 http://purl.obolibrary.org/obo/GO_0031933 P00000142 Telomeric Heterochromatin [GO Definition]: Heterochromatic regions of the chromosome found at the telomeres. P00000142 http://purl.obolibrary.org/obo/GO_0005721 P00000143 Centromeric Heterochromatin centric heterochromatin centromeric heterochromatin pericentric heterochromatin [GO Definition]: Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3. P00000143 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13289 P00000144 Euchromatin open chromatin [NCIt Definition]: The parts of chromosomes that, during interphase, are uncoiled dispersed threads and not stained by ordinary dyes; metabolically active, in contrast to the inert heterochromatin. P00000144 http://purl.obolibrary.org/obo/GO_0005677 P00000145 Chromatin Silencing Complex [GO Definition]: Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing. P00000145 http://purl.obolibrary.org/obo/GO_0030869 P00000146 RENT Complex [GO Definition]: A protein complex that mediates transcriptional silencing at the rDNA locus (the name derives from regulator of nucleolar silencing and telophase). In Saccharomyces the complex contains Net1p, Sir2p, Cdc14p, and at least one more subunit. P00000146 http://purl.obolibrary.org/obo/GO_0016585 P00000147 Chromatin Remodeling Complex Chromatin Modifying Complex Chromatin Modifying Complexes chromatin remodelling complex nucleosome remodeling complex [GO Definition]: Any complex that mediates dynamic changes in eukaryotic chromatin. P00000147 http://purl.obolibrary.org/obo/GO_0070209 P00000148 ASTRA Complex [GO Definition]: A protein complex that is part of the chromatin remodeling machinery; the acronym stands for ASsembly of Tel, Rvb and Atm-like kinase. In Saccharomyces cerevisiae this complex includes Rvb1p, Rvb2p, Tra1p, Tel2p, Asa1p, Ttilp and Tti2p. P00000148 http://purl.obolibrary.org/obo/GO_0008623 http://purl.obolibrary.org/obo/NCIT_C19805 P00000149 Chromatin Accessibility Complex CHRAC ISW2 complex [GO Definition]: A multisubunit complex that uses ATP to increase the general accessibility of DNA in chromatin. Unlike other known chromatin remodeling complexes, CHRAC can also function during chromatin assembly; it uses ATP to convert irregular chromatin into a regular array of nucleosomes with even spacing. P00000149 https://www.epicypher.com/histone-modification-binding-proteins/ P00000151 Histone Modification Binding Domain Protein motifs that facilitate recognition of histone modifications. P00000151 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13732 P00000152 Bromodomain [NCIt Definition]: A motif common in chromatin remodeling factors. It consists of approximately 110 amino acids in a left-handed up-and-down four helix bundle with a left handed twist. A hydrophobic pocket in the bromodomain creates an acetyl-lysine binding domain. Bromodomain-containing proteins may recruit remodeling complexes to acetylated chromatin regions. P00000152 (https://www.epibeat.com/epigenetics-glossary/#T) P00000153 Chromodomain a motif of 40-50 amino acids common to proteins that function in chromatin remodeling; may function in binding DNA, RNA, and protein; often binds methylated histones (https://www.epibeat.com/epigenetics-glossary/#T) P00000153 P00000154 Malignant Brain Tumor (MBT) Domain P00000154 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14098 P00000155 PHD Finger Domain C4HC3 Zinc Finger PHD Finger PHD Finger Motif PHD-Finger Plant Homeodomain (PHD) Type Zinc Finger [NCIt Definition]: A C4HC3 zinc-finger-like motif, the PHD finger is found in nuclear proteins thought involved in chromatin-mediated transcriptional regulation. Single or multiple fingers are found. A specific function is not yet known, but it could be involved in protein-protein interactions important for assembly/activity of multi-component transcriptional regulatory complexes. In CBP it is an integral part of the acetyltransferase enzymatic core domain and contributes to CBP transcriptional activity. PHD fingers fold into an interleaved Zn-finger chelating two Zn ions in an atypical cross-braced conformation also shared by the FYVE and RING fingers; the zinc sites are located at opposite ends of a beta-sheet. Surrounding loops vary significantly in length and sequence between these three domains. P00000155 http://purl.bioontology.org/ontology/MESH/D000071856 P00000156 Tudor Domain Motif, Tudor Motifs, Tudor Tudor Domains Tudor Motif Tudor Motifs [MeSH Definition]: A conserved, approximately 50 amino acid, protein sequence that adopts a characteristic strongly bent, five stranded anti-parallel beta-sheet barrel-like fold. The Tudor domain recognizes dimethylated ARGININE through its negatively-charged surface and occurs in many proteins that co-localize with RNA; RIBONUCLEOPROTEINS or SINGLE-STRANDED DNA complexes in the CELL NUCLEUS; MITOCHONDRIA; or KINETOCHORES P00000156 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14044 P00000157 PWWP Domain [NCIt Definition]: Around 70 amino acids and weakly conserved, the PWWP Domain is named after a conserved Pro-Trp-Trp-Pro motif often found as multiple copies in proteins that contain chromatin-association domains or in cell growth and differentiation transcription factors, such as WHSC1 (C-terminus) and ASH1/Trithorax Group proteins. Although its function is unknown, the amino acid composition suggests that it may be involved in protein-protein interactions. The domain N-terminal half resembles a barrel-like five-stranded structure; the C-terminal half contains a five-helix bundle. The halves form a module that exhibits positive electrostatic potential. Alone, the domain binds DNA in vitro, probably through its basic surface. P00000157 P00000158 Trithorax-Group Protein Trithorax-group protein Trithorax-group proteins trxG A family of proteins that remodel chromatin such that transcription factors can bind to promoter sequences in DNA, switching genes on. (https://www.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.091907) P00000158 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C118479 http://purl.bioontology.org/ontology/MESH/D063146 P00000159 Polycomb-Group Protein PRC1 Like Complex PRC1-Like Complex PcG PcG Complex Proteins Polycomb Polycomb Family Polycomb Family Protein Polycomb Group Polycomb Group (PcG) Multiprotein PRC1-Like Complex Polycomb Group Protein Polycomb Group Protein Complexes Polycomb Group Proteins Polycomb Repressive Complex Proteins Polycomb Response Element Polycomb-Group Polycomb-Group Protein Polycomb-Group Protein Complex Polycomb-Group Protein Complexes Polycomb-Group Proteins [NCIt Definition]: A family of chromatin remodeling factors that contribute to epigenetic silencing during embryonic development. P00000159 http://purl.obolibrary.org/obo/GO_0061638 P00000161 CENP-A Containing Chromatin centromeric core domain chromatin centromeric core region chromatin The specialized chromatin located the centromeric core region or the entire centromeric region in organisms with point centromeres, which is enriched for CENP-A-containing nucleosomes. This chromatin forms a 3-dimensional structure which provides a platform for kinetochore assembly and microtubule attachment. P00000161 centromeric core region chromatin http://purl.obolibrary.org/obo/GO_0061638 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13268 http://purl.obolibrary.org/obo/GO_0000786 P00000162 Nucleosome [NCIt Definition]: A DNA packaging complex comprised of approximately 200 base pairs of DNA wound around a protein core, which is formed by an octomer of histones. The histone octomer includes two dimers of histones H2A and H2B that surround a tetramer consisting of two molecules of histone H3 and two molecules of histone H4. P00000162 http://purl.obolibrary.org/obo/GO_0043505 P00000163 CENP-A Containing Nucleosome CENP-S-T-W-X centromere specific nucleosome centromere-specific nucleosome centromeric nucleosome [GO Definition]: A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3). P00000163 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16687 http://purl.obolibrary.org/obo/CHEBI_15358 P00000164 Histone histone histone protein histone proteins histones [NCIt Definition]: Major protein component of chromatin. Highly conserved basic proteins, originally classified into classes based on the relative amounts of arginine and lysine in each protein. The various classes are now termed H1, H2A, H2B, H3, and H4. In chromatin, they are found in an octamer, containing two each of H2A, H2B, H3, and H4, complexed with DNA in nucleosomes. The histones in the octamer complex are also known as the core histones. The H1 class of histones, termed the linker histones, is loosely associated with the nucleosome. P00000164 http://purl.org/sig/ont/fma/fma84133 P00000165 Histone Octamer P00000165 P00000167 Histone Tail P00000167 P00000168 Histone Variant P00000168 http://purl.jp/bio/4/id/200906094072199147 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433953/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004355/ P00000169 Histone Chaperone Histone Chaperones Histone chaperones are now broadly defined as a group of proteins that bind histones and regulate nucleosome assembly P00000169 P00000170 Histone Cell Cycle Regulator P00000170 P00000282 Epigenetically Modified DNA P00000282 P00000283 Modified DNA Base P00000283 P00000284 Modified Adenine P00000284 http://purl.obolibrary.org/obo/CHEBI_134104 http://purl.obolibrary.org/obo/SO_0001967 P00000285 8-Oxoadenine 6-amino-1,7-dihydro-8H-purin-8-one 7,8-Dihydro-8-oxoadenine 8 oxoadenine 8-oxo-7,8-dihydroadenine 8-oxoA Oxyadenine [SO Definition]: A modified DNA adenine base,at the 8 carbon, often the product of DNA damage. P00000285 http://purl.obolibrary.org/obo/SO_0000161 P00000286 Methylated Adenine methylated A methylated adenine methylated adenine base methylated adenine residue methylated_A [SO Definition]: A modified base in which adenine has been methylated. P00000286 http://purl.obolibrary.org/obo/CHEBI_25272 http://purl.obolibrary.org/obo/RNAO_1000024 http://purl.obolibrary.org/obo/SO_0001920 P00000287 N6-methyladenine 6-mA 6-methyladenine 6mA N6-methyladenine m-6A m6a [SO Definition]: An adenine methylated at the 6 nitrogen. P00000287 http://purl.obolibrary.org/obo/SO_0001963 P00000288 Modified Cytosine [SO Definition]: A modified cytosine DNA base feature. P00000288 http://purl.bioontology.org/ontology/MESH/C000618843 http://purl.obolibrary.org/obo/CHEBI_76793 http://purl.obolibrary.org/obo/SO_0001966 P00000289 5-Carboxycytosine 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid 4-amino-2-oxopyrimidine-5-carboxylic acid 5-caC 5-carboxycytosine 5-carboxylcytosine 5caC nucleoside Cytosine-5-carboxylic acid [SO Definition]: A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon. P00000289 http://purl.bioontology.org/ontology/MESH/C560973 http://purl.obolibrary.org/obo/CHEBI_76794 http://purl.obolibrary.org/obo/RNAO_1000125 http://purl.obolibrary.org/obo/SO_0001961 P00000290 5-Formylcytosine 4-amino-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde 4-amino-2-oxopyrimidine-5-carbaldehyde 5-fC 5-formylcytosine 5-formylcytosine nucleobase cytosine-5-carbaldehyde [SO Definition]: A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon. P00000290 http://purl.obolibrary.org/obo/CHEBI_134207 http://purl.obolibrary.org/obo/SO_0000114 P00000291 Methylated Cytosine methylated C methylated cytosine methylated cytosine base methylated cytosine residue methylated_C methylcytosine [SO Definition]: A methylated deoxy-cytosine. P00000291 http://purl.bioontology.org/ontology/MESH/C039052 http://purl.obolibrary.org/obo/SO_0001919 P00000292 N4-Methylcytosine 4-mC 4-methylcytosine N(4)-methylcytosine N4 methylcytosine N4-methylcytosine N4_methylcytosine m-4C m4c [SO Definition]: A cytosine methylated at the 4 nitrogen. P00000292 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C129008 http://purl.bioontology.org/ontology/CSP/2517-6208 http://purl.bioontology.org/ontology/MESH/D044503 http://purl.bioontology.org/ontology/NDFRT/N0000167184 http://purl.obolibrary.org/obo/CHEBI_27551 http://purl.obolibrary.org/obo/RNAO_1000068 http://purl.obolibrary.org/obo/SO_0001918 P00000293 5-Methylcytosine 4-Amino-5-methyl-2-pyrimidinol 4-amino-5-methyl-2(1H)-pyrimidinone 4-amino-5-methylpyrimidin-2(1H)-one 5 Methylcytosine 5 Methylcytosine Monohydrochloride 5 methylcytosine 5-Methylcytosine 5-Methylcytosine Monohydrochloride 5-mC 5-methylcytosine 5-methylcytosine nucleobase Monohydrochloride, 5-Methylcytosine m-5C m5c [SO Definition]: A cytosine methylated at the 5 carbon. P00000293 http://purl.bioontology.org/ontology/MESH/C011865 http://purl.obolibrary.org/obo/RNAO_1000157 http://purl.obolibrary.org/obo/SO_0001960 P00000294 5-Hydroxymethylcytosine 4-amino-5-(hydroxymethyl)-2(1H)-pyrimidinone 5-hmC 5-hydroxylmethylcytosine 5-hydroxymethylcytosine 5-hydroxymethylcytosine nucleobase [SO Definition]: A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon. P00000294 http://purl.obolibrary.org/obo/SO_0001964 P00000295 Modified Guanine [SO Definition]: A modified guanine DNA base feature. P00000295 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105826 http://purl.bioontology.org/ontology/MESH/C453560 http://purl.obolibrary.org/obo/CHEBI_44605 http://purl.obolibrary.org/obo/SO_0001965 P00000296 8-Oxoguanine 1H-Purine-6,8-Dione, 2-Amino- 1H-Purine-6,8-Dione, 2-Amino-7,9-Dihydro- 2-Amino-6,8-Dihydroxypurine 2-Amino-7,9-Dihydro-1H-Purine-6,8-Dione 2-Aminopurine-6,8-Diol 2-amino-1H-purine-6,8-dione 7,8-Dihydro-8-Oxoguanine 8-Hydroxyguanine 8-Oxo-7,8-Dihydroguanine 8-Oxo-Gua 8-Oxoguanine 8-oxoG 8-oxoG nucleobase 8-oxoguanine 8OG Purine-6,8(1H,9H)-Dione, 2-Amino- Purine-6,8-Diol, 2-Amino- [SO Definition]: A modified DNA guanine base,at the 8 carbon, often the product of DNA damage. P00000296 P00000297 Imprinted Gene imprinted genes Imprinted genes are genes whose expression is determined by the parent that contributed them. P00000297 P00000298 Maternally-Expressed Imprinted Gene maternally controlled imprinted genes maternally expressed genes maternally-expressed imprinted genes The variable phenotypic expression of a GENE of maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. P00000298 P00000299 Paternally-Expressed Imprinted Gene paternally expressed genes paternally-expressed imprinted genes The variable phenotypic expression of a GENE of paternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. P00000299 P00000300 Maternally Silenced Gene maternal gene silencing maternal silencing maternally silenced genes Maternally regulated interruption or suppression of the expression of a gene at transcriptional or translational levels. P00000300 P00000301 Paternally Silenced Gene paternal silencing paternally silenced genes Paternally regulated interruption or suppression of the expression of a gene at transcriptional or translational levels. P00000301 P00000302 Imprinted Cluster P00000302 P00000303 Imprinting Control Region P00000303 P00000304 Imprint Control Element P00000304 P00000305 Methylated Imprinted Control Element P00000305 P00000306 Unmethylated Imprinted Control Element P00000306 http://purl.obolibrary.org/obo/SO_0000897 P00000307 Allelically Excluded Gene allelically excluded genes [SO Definition]: A gene that is allelically excluded. P00000307 P00000308 CpG Site P00000308 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54668 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#CpG_Island http://purl.bioontology.org/ontology/CSP/4007-0032 http://purl.obolibrary.org/obo/OGI.owl#CpG_Island P00000309 CpG Island [NCIt Definition]: Short region of DNA in which the frequency of the CG sequence is higher than in other regions. P00000309 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889898/ P00000310 CpG Island Shore CpG Island Shores CpG island “shore” region of a comparatively low CpG density that is present near traditional CpG islands, typically within 2 kb [Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889898/] P00000310 http://purl.bioontology.org/ontology/MESH/D000070593 P00000311 Methyl CpG Binding Domain Methyl CpG DNA Binding Domain [MeSH Definition]: A protein domain of about 70 amino acids in length that folds into a sandwich structure consisting of a beta sheet, alpha helix, and C-terminal hairpin loop which forms a hydrophobic methylated-DNA binding patch. It binds to methylated CPG ISLANDS in eukaryotes and occurs with other DNA and CHROMATIN binding domains such as AT-HOOK MOTIFS in eukaryotic DNA BINDING PROTEINS. P00000311 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C67101 P00000312 CpG Dinucleotide CpG CpG Dinucleotide [NCIt Definition]: A dinucleotide consisting of cytosine followed by guanine. P00000312 P00000313 CpG Density P00000313 P00000314 Methylated DNA differentially methylation region P00000314 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C106057 P00000315 Methylome methylome methylomes [NCIt Definition]: The characterization of all of the nucleic acid methylation modifications in a particular cell or in the genome of an organism. P00000315 P00000316 Hemimethylated DNA hemi-methylated DNA hemimethylated DNA Hemimethylated DNA is when only one of two (complementary) strands is methylated. P00000316 P00000317 DNA Unmethylated Region P00000317 P00000318 Partially Methylated Domain partially methylated domain partially methylated domains P00000318 P00000319 Highly Methylated Domain HMD HMDs highly methylated domain highly methylated domains P00000319 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic P00000320 Methylation Outlier methylation outlier methylation outliers Methylation sites whose methylation level differed significantly in one sample (as compared with all of the other samples) -[Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic] P00000320 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic P00000321 Hypomethylated Outlier hypomethylated outlier hypomethylated outliers Methylation sites whose methylation level differed significantly in one sample (as compared with all of the other samples) -lower methylation [Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic] P00000321 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic P00000322 Hypermethylated Outlier hypermethylated outlier hypermethylated outliers Methylation sites whose methylation level differed significantly in one sample (as compared with all of the other samples)-higher methylation [Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586460/?report=classic] P00000322 http://gbol.life/0.1/ncRNA http://purl.obolibrary.org/obo/SO_0000655 http://www.bootstrep.eu/ontology/GRO#NcRNA P00000324 Noncoding RNA INSDC_qualifier:other known_ncrna ncRNA non-coding RNA noncoding RNA [SO Definition]: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. P00000324 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C97492 http://purl.bioontology.org/ontology/MESH/C077885 http://purl.bioontology.org/ontology/OMIM/314670 http://purl.obolibrary.org/obo/OGG_3000007503 P00000325 X-Inactive Specific Transcript (XIST) DXS1089 DXS399E LINC00001 NCRNA00001 Non-Protein Coding RNA 1 SXI1 X (Inactive)-Specific Transcript X (inactive)-Specific Imprint X (inactive)-specific transcript (XIST) X (inactive)-specific transcript (XIST), human X (inactive)-specific transcript (non-protein coding) RNA X (inactive)-specific transcript, mouse X INACTIVATION CENTER X INACTIVATION, FAMILIAL SKEWED, 1 XIC XIST XIST RNA, human XIST RNA, mouse XIST gene product, human XIST gene product, mouse XIST non-coding RNA ncRNA XIST swd66 [OGG Definition]: X inactive specific transcript (non-protein coding) P00000325 http://purl.bioontology.org/ontology/MESH/C465658 http://purl.bioontology.org/ontology/OMIM/300181 http://purl.obolibrary.org/obo/OGG_3000009383 P00000326 TSIX LINC00013 NCRNA00013 X (inactive)-specific transcript (TSIX) antisense, mouse XIST-ANTISENSE XIST-AS XIST-AS1 XISTAS [OGG Definition]: TSIX transcript, XIST antisense RNA P00000326 http://purl.obolibrary.org/obo/SO_0000646 http://regenbase.org/ontology#RB_0000129 http://www.bioassayontology.org/bao#BAO_0000324 http://www.bootstrep.eu/ontology/GRO#SmallInterferingRNA P00000327 Small Interfering RNA INSDC_feature:ncRNA INSDC_qualifier:siRNA ds-siRNA siRNA small interfering RNA small interfering ribonucleic acid [SO Definition]: A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. P00000327 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C95953 http://purl.obolibrary.org/obo/SO_0001035 P00000328 Piwi-Associated RNA (piRNA) INSDC_feature:ncRNA INSDC_qualifier:piRNA Piwi-Interacting RNA piRNA piwi-associated RNA [NCIt Definition]: Single-stranded RNA molecules that are expressed in animal cells and form complexes with Piwi proteins. They are involved in transcriptional gene silencing. P00000328 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25966 http://purl.bioontology.org/ontology/CSP/5005-0015 http://purl.obolibrary.org/obo/MI_2204 http://purl.obolibrary.org/obo/SBO_0000316 http://purl.obolibrary.org/obo/SO_0000276 http://www.bioassayontology.org/bao#BAO_0000322 http://www.bootstrep.eu/ontology/GRO#MicroRNA P00000329 MicroRNA INSDC_feature:ncRNA INSDC_qualifier:miRNA MIR MIRN Micro RNA MicroRNA Small Temporal RNA miRNA micro RNA micro-RNA micro-rna microRNA mirna small temporal RNA stRNA [NCIt Definition]: A sequence of single-stranded RNA, that is 20-25 nucleotides in length, which is transcribed from DNA but is not translated into a protein. This nucleic acid may regulate the transcription or translation of other genes. P00000329 P00000330 Promoter-Associated RNA P00000330 http://purl.obolibrary.org/obo/SO_0001870 P00000331 Enhancer RNA eRNA [SO Definition]: A short ncRNA that is transcribed from an enhancer. May have a regulatory function. P00000331 http://purl.bioontology.org/ontology/MESH/D062085 http://purl.obolibrary.org/obo/MI_2190 http://purl.obolibrary.org/obo/SO_0001877 P00000332 Long ncRNA INSDC_feature:ncRNA INSDC_qualifier:lncRNA Large Non-Coding RNA Long Non Coding RNA Long Non Protein Coding RNA Long Non-Coding RNA Long Non-Protein-Coding RNA Long Non-Translated RNA Long Noncoding RNA Long Untranslated RNA Long ncRNA Long ncRNAs Non-Coding RNA, Long Non-Protein-Coding RNA, Long Non-Translated RNA, Long Noncoding RNA, Long RNA, Long Non Translated RNA, Long Non-Coding RNA, Long Non-Protein-Coding RNA, Long Non-Translated RNA, Long Untranslated Untranslated RNA, Long lncRNA lncRNA_transcript lncrna long non coding RNA long non coding ribonucleic acid long non-coding RNA ncRNA, Long ncRNAs, Long [MeSH Definition]: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin. P00000332 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C88924 http://purl.obolibrary.org/obo/SO_0001463 P00000333 LincRNA Imprinted lincRNA LINC RNA Large Intervening Non-Coding RNA LincRNA LincRNAs Long Intergenic Non-Coding RNA Long Intergenic Noncoding RNA large intervening non-coding RNA lincRNA long intergenic non-coding RNA long intervening non-coding RNA [NCIt Definition]: A molecule of RNA 200-17000 nucleotides in length that is transcribed by non-protein coding areas of DNA. These ribonucleotides may play a role in a variety of biological processes. P00000333 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16683 http://purl.obolibrary.org/obo/HINO_0008401 http://purl.obolibrary.org/obo/PR_000038372 http://purl.org/sig/ont/fma/fma84118 P00000346 Histone H1 Histone 1 Histone H1 linker histone [NCIt Definition]: Linker Histone H1 interacts with DNA between nucleosome units in mediating chromatin compaction into higher order structures. Histones are basic nuclear proteins responsible for the nucleosome structure of eukaryotic chromatin. Repeating nucleosome units contain two molecules each of core Histones H2A, H2B, H3, and H4 that form an octamer complex around which approximately 146 base pairs of DNA is wrapped. P00000346 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114866 P00000347 Histone H2 Histone 2 Histone H2 [NCIt Definition]: Proteins in the core histone families, histone H2A and histone H2B represent 2 of the 4 families of histones found in the core of nucleosomes. Histones in the H2A family dimerize with those in the H2B family, then two H2A/H2B dimers can associate with a tetramer containing 2 proteins from the histone H3 family and 2 proteins from the histone H4 family to form the octameric nucleosome core. The octameric complex is the basic unit for eukaryotic DNA packaging. P00000347 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16685 http://purl.obolibrary.org/obo/PR_000027594 http://purl.org/sig/ont/fma/fma84131 P00000348 Histone H3 Histone 3 Histone H3 [NCIt Definition]: Histone H3 is a core subunit of the eukaryotic nucleosome complex. Histones are basic nuclear proteins responsible for the nucleosome structure of chromatin. Repeating nucleosome units contain two molecules each of Histones H2A, H2B, H3, and H4 that form an octamer complex around which approximately 146 base pairs of DNA is wrapped. Linker Histone H1 interacts with DNA between nucleosome units in mediating chromatin compaction into higher order structures. P00000348 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16686 http://purl.obolibrary.org/obo/PR_000008603 http://purl.org/sig/ont/fma/fma84132 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H4 P00000349 Histone H4 HIST1H4 HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H4A HIST2H4B HIST4H4 Histone 1, H4 Histone H4 histone cluster 1, H4a histone cluster 1, H4b histone cluster 1, H4c histone cluster 1, H4d histone cluster 1, H4e histone cluster 1, H4f histone cluster 1, H4h histone cluster 1, H4i histone cluster 1, H4j histone cluster 1, H4k histone cluster 1, H4l histone cluster 2, H4a histone cluster 2, H4b histone cluster 4, H4 [NCIt Definition]: Histone H4 (103 aa, ~11 kDa) is encoded by the human HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 genes. This protein plays a role in nucleating the formation of high order chromatin structures as a part of nucleosomes. P00000349 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C126425 http://purl.bioontology.org/ontology/MESH/C569262 http://purl.obolibrary.org/obo/PR_000008574 P00000350 Histone H1.1 H1 VAR.3 H1F1 H1a HIST1H1A Histone H1.1 Histone H1a [NCIt Definition]: Histone H1.1 (215 aa, ~22 kDa) is encoded by the human HIST1H1A gene. This protein is involved in both DNA binding and chromatin compaction into higher order structures. P00000350 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C115355 http://purl.obolibrary.org/obo/PR_000008578 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1.4 P00000351 Histone H1.4 H1 VAR.2 H1F4 H1e HIST1H1E Histone H1.4 Histone H1b Histone H1s-4 histone H1b histone cluster 1, H1e [NCIt Definition]: Histone H1.4 (219 aa, ~22 kDa) is encoded by the human HIST1H1E gene. This protein is involved in chromosome compaction. P00000351 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16684 http://purl.obolibrary.org/obo/PR_000027547 http://purl.org/sig/ont/fma/fma84129 P00000352 Histone H2A H2A HIST1H2A Histone 2A Histone H2A [NCIt Definition]: Slightly lysine rich histone. One of four histones assembled into a nucleosomal core octamer. Various posttranslationally modified forms and variants exist. Combines with histone H2B in a heterodimer; two H2A/H2B dimers are incorporated in the nucleosomal octamer. P00000352 ]http://purl.org/sig/ont/fma/fma84130 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17460 http://purl.obolibrary.org/obo/PR_000036509 P00000353 Histone H2B H2B [NCIt Definition]: Histone H2B is a core subunit of the eukaryotic nucleosome complex. Histones are basic nuclear proteins responsible for the nucleosome structure of chromatin. Repeating nucleosome units contain two molecules each of Histones H2A, H2B, H3, and H4 that form an octamer complex around which approximately 146 base pairs of DNA is wrapped. Linker Histone H1 interacts with DNA between nucleosome units in mediating chromatin compaction into higher order structures. P00000353 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C95407 http://purl.obolibrary.org/obo/PR_000008419 P00000354 Core Histone Macro-H2A Core Histone Macro-H2A Histone MacroH2A MacroH2A mH2A [NCIt Definition]: A histone protein that is comprised of a histone H2A domain, which allows interaction with the nucleosome, and a macro domain, which may bind to ADP-ribose. This protein can substitute for histone H2A in the nucleosomal complex and plays a role in transcriptional repression and X chromosome inactivation. P00000354 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C113624 http://purl.obolibrary.org/obo/PR_000008419 P00000355 Core Histone Macro-H2A.1 Core Histone Macro-H2A.1 H2A.y H2A/y H2A1.1 H2AFY Histone H2A.Y Histone MacroH2A1 Histone MacroH2A1.1 Histone MacroH2A1.2 MACROH2A1 MACROH2A1.1 Medulloblastoma Antigen MU-MB-50.205 histone H2A.y histone macroH2A1 mH2A1 medulloblastoma antigen MU-MB-50.205 [NCIt Definition]: Core histone macro-H2A.1 (372 aa, ~40 kDa) is encoded by the human H2AFY gene. This protein plays a role in chromatin modification. P00000355 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154659 http://purl.obolibrary.org/obo/PR_000008420 P00000356 Core Histone Macro-H2A.2 Core Histone Macro-H2A.2 Core Histone MacroH2A2.2 H2A2.2 H2AFY2 H2afy3 Histone MacroH2A2 MACROH2A2 histone macroH2A2 mH2A2 [NCIt Definition]: Core histone macro-H2A.2 (372 aa, ~40 kDa) is encoded by the human H2AFY2 gene. This protein plays a role in nucleosome formation and transcriptional repression. P00000356 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154613 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.B/#msa_div_browse P00000357 Histone H2A-Bbd H2A Barr Body Deficient H2A Barr Body-Deficient H2A.B H2A.Bbd H2A.Lap1 Histone H2A-Bbd [NCIt Definition]: A variant form of histone H2A found in chromatin structures that are transcriptionally active. P00000357 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154651 http://purl.obolibrary.org/obo/PR_000008414 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A-Bbd_type_1 P00000358 Histone H2A-Bbd Type 1 H2A histone family, member B1 H2AFB1 Histone H2A-Bbd Type 1 [NCIt Definition]: Histone H2A-Bbd type 1 (115 aa, ~13 kDa) is encoded by the human H2AFB1 gene. This protein plays a role in chromatin structures that are associated with active gene expression. P00000358 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154656 http://purl.obolibrary.org/obo/PR_000008415 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A-Bbd_type_2/3 P00000359 Histone H2A-Bbd Type 2/3 H2A histone family, member B2 H2A histone family, member B3 H2AFB2 H2AFB3 H2AFB[2/3] [NCIt Definition]: Histone H2A-Bbd type 2/3 (115 aa, ~13 kDa) is encoded by the human H2AFB2 and H2AFB3 genes. This protein plays a role in the promotion of gene expression. P00000359 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C126766 http://purl.bioontology.org/ontology/MESH/C000611883 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.Z/#msa_div_browse P00000360 Histone H2A.Z H2A histone family, member Z, mouse H2A.V H2A.Z H2A.Z-1 H2A.Z-2 H2A.Zc H2A/z H2AZ Histone H2AZ.1 protein, mouse H2Av H2AvD Histone H2A.Z Htz1p hv1 member Z [NCIt Definition]: Histone H2A.Z (128 aa, ~14 kDa) is encoded by the human H2AFZ gene. This protein is involved in nucleosome and heterochromatin formation. P00000360 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C19432 http://purl.jp/bio/4/id/200906074937138288 P00000361 Histone H2A.X H2A Histone Family, Member X H2A.X H2A/X H2AFX H2AX H2AX Histone Histone H2A.X Histone H2AX [NCIt Definition]: Histone H2AX (143 aa, ~15 kDa) is encoded by the human H2AFX gene. This protein plays a role in nucleosome formation and V(D)J recombination. P00000361 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C116688 http://purl.obolibrary.org/obo/PR_000008588 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-D P00000362 Histone H2B Type 1-D H2B/b H2BFB HIRA-Interacting Protein 2 HIRA-interacting protein 2 HIRIP2 HIST1H2BD Histone H2B Type 1-D Histone H2B.1 B Histone H2B.b Histone H2B.b (H2B/b) histone H2B.1 B histone H2B.b histone cluster 1, H2bd [NCIt Definition]: Histone H2B type 1-D (126 aa, ~14 kDa) is encoded by the human HIST1H2BD gene. This protein plays a role in the structure of nucleosomes. P00000362 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101734 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H3.1 P00000363 Histone H3.1 HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Histone H3.1 Histone H3/a Histone H3/b Histone H3/c Histone H3/d Histone H3/f Histone H3/h Histone H3/i Histone H3/j Histone H3/k Histone H3/l histone cluster 1, H3a histone cluster 1, H3b histone cluster 1, H3c histone cluster 1, H3d histone cluster 1, H3e histone cluster 1, H3f histone cluster 1, H3g histone cluster 1, H3h histone cluster 1, H3i histone cluster 1, H3j [NCIt Definition]: Histone H3.1 (136 aa, ~15 kDa) is encoded by the human HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I and HIST1H3J genes. This protein plays a role in the formation of chromatin structures. P00000363 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154671 http://purl.obolibrary.org/obo/PR_000008602 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/TS_H3.4/#msa_div_browse P00000364 Histone H3.1t H3.4 H3/g H3/t H3FT H3t HIST3H3 Histone H3.1t Histone H3.4 TS H3.4 [NCIt Definition]: Histone H3.1t (136 aa, ~16 kDa) is encoded by the human HIST3H3 gene. This protein is involved in formation of higher order chromatin structures. P00000364 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C148067 http://purl.obolibrary.org/obo/PR_000036794 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H3.2 P00000365 Histone H3.2 HIST2H3A HIST2H3C HIST2H3D Histone H3.2 Histone H3/m Histone H3/o histone cluster 2, H3a histone cluster 2, H3c histone cluster 2, H3d [NCIt Definition]: Histone H3.2 (136 aa, ~15 kDa) is encoded by the human HIST2H3A, HIST2H3C, and HIST2H3D genes. This protein plays a role in nucleosome remodeling and chromosomal structure. P00000365 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101445 http://purl.obolibrary.org/obo/PR_000008425 http://www.bioassayontology.org/bao#BAO_0030000 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/H3.3/#msa_div_browse P00000366 Histone H3.3 H3.3 H3.3B H3F3B hv2 soH3-1 soH3-2 [NCIt Definition]: Histone H3.3 (136 aa, ~15 kDa) is encoded by both the human H3F3A and H3F3B genes. This protein plays a role in chromosomal structure. P00000366 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C154668 http://purl.obolibrary.org/obo/PR_000029532 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H3.3C P00000367 Histone H3.3C H3 histone, family 3C H3.3C H3.5 H3F3C Histone H3.3C Histone H3.5 [NCIt Definition]: Histone H3.3C (135 aa, ~15 kDa) is encoded by the human H3F3C gene. This protein is involved in the modulation of DNA accessibility to the transcriptional machinery. P00000367 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C155738 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/H3.Y/#msa_div_browse P00000368 Histone H3.Y H3.X H3.Y H3.Y.1 Histone H3.Y Histone H3.y [NCIt Definition]: Histone H3.Y (136 aa, ~15 kDa) is encoded by the human H3.Y gene. This protein may be involved in both transcriptional regulation and the formation of higher order chromatin structures. P00000368 http://purl.obolibrary.org/obo/GO_0043968 http://purl.obolibrary.org/obo/SO_0002142 P00000372 Histone H2A Acetylation Site H2A Acetylation H2Aac histone 2A acetylation site [GO Definition]: The modification of histone H2A by the addition of an acetyl group. P00000372 http://purl.obolibrary.org/obo/GO_0043969 http://purl.obolibrary.org/obo/SO_0002143 P00000373 Histone H2B Acetylation Site H2Bac histone 2B acetylation site [SO Definition]: A histone 2B modification where the modification is the acetylation of the residue. P00000373 http://purl.obolibrary.org/obo/GO_0043966 http://purl.obolibrary.org/obo/SO_0001973 P00000374 Histone H3 Acetylation Site AcH3 H3ac histone 3 acetylation site [SO Definition]: A histone 3 modification where the modification is the acetylation of the residue. P00000374 http://purl.obolibrary.org/obo/GO_0043967 http://purl.obolibrary.org/obo/SO_0001972 P00000375 Histone H4 Acetylation Site H4ac histone 4 acetylation site [SO Definition]: A histone 4 modification where the modification is the acetylation of the residue. P00000375 http://purl.obolibrary.org/obo/GO_0043977 http://purl.obolibrary.org/obo/SO_0001938 P00000377 H2AK5 Acetylation Site H2AK5 acetylation site H2AK5ac histone H2A acetylation at K5 histone H2A-K5 acetylation [GO Definition]: The modification of histone H2A by the addition of an acetyl group to a lysine residue at position 5 of the histone. Source: GOC:jl P00000377 http://purl.obolibrary.org/obo/GO_0043978 http://purl.obolibrary.org/obo/SO_0001944 P00000378 H2AK9 Acetylation Site H2AK9 acetylation site H2AK9ac histone H2A acetylation at K9 histone H2A-K9 acetylation [GO Definition]: The modification of histone H2A by the addition of an acetyl group to a lysine residue at position 9 of the histone. [ GOC:jl ] P00000378 P00000379 Histone H2A.X Acetylation Site H2A.Xac H2AXac Histone H2A.X acetylation histone 2AX acetylation site A histone 2AX modification where the modification is the acetylation of the residue. P00000379 http://purl.obolibrary.org/obo/SO_0002144 P00000380 Histone H2A.Z Acetylation Site H2A.Zac H2AZac histone 2AZ acetylation site [SO Definition]: A histone 2AZ modification where the modification is the acetylation of the residue. P00000380 P00000381 H2A.XK5 Acetylation Site H2A.XK5ac H2AXK5 acetylation site H2AXK5ac histone H2A.X acetylation at K5 histone H2A.X-K5 acetylation histone H2AX acetylation at K5 histone H2AX-K5 acetylation A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2AX histone protein is acetylated. P00000381 http://purl.obolibrary.org/obo/SO_0002145 P00000382 H2A.ZK4 Acetylation Site H2A.ZK4ac H2AZK4 acetylation site H2AZK4ac [SO Definition]: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated. P00000382 http://purl.obolibrary.org/obo/SO_0002146 P00000383 H2A.ZK7 Acetylation Site H2A.ZK7ac H2AZK7 acetylation site H2AZK7ac [SO Definition]: A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated. P00000383 http://purl.obolibrary.org/obo/SO_0002147 P00000384 H2A.ZK11 Acetylation Site H2A.ZK11ac H2AZK11 acetylation site H2AZK11ac histone H2AZ acetylation at K11 histone H2AZ-K11 acetylation [SO Definition]: A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated. P00000384 http://purl.obolibrary.org/obo/SO_0002148 P00000385 H2A.ZK13 Acetylation Site H2A.ZK13ac H2AZK13 acetylation site H2AZK13ac [SO Definition]: A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated. P00000385 http://purl.obolibrary.org/obo/SO_0002149 P00000386 H2A.ZK15 Acetylation Site H2A.ZK15ac H2AZK15 acetylation site H2AZK15ac [SO Definition]: A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated. P00000386 http://purl.obolibrary.org/obo/GO_0043979 http://purl.obolibrary.org/obo/SO_0002164 P00000387 H2BK5 Acetylation Site H2BK5 acetylation site H2BK5ac histone H2B acetylation at K5 histone H2B-K5 acetylation [SO Definition]: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated. P00000387 http://purl.obolibrary.org/obo/GO_0043980 http://purl.obolibrary.org/obo/SO_0001937 P00000388 H2BK12 Acetylation Site H2BK12 acetylation site H2BK12ac histone H2B acetylation at K12 histone H2B-K12 acetylation [SO Definition]: A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated. P00000388 http://purl.obolibrary.org/obo/SO_0001946 P00000389 H2BK15 Acetylation Site H2BK15 acetylation site H2BK15ac [SO Definition]: A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated. P00000389 http://purl.obolibrary.org/obo/SO_0001942 P00000390 H2BK20 Acetylation Site H2BK20 acetylation site H2BK20ac A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated. P00000390 http://purl.obolibrary.org/obo/SO_0001940 P00000391 H2BK120 Acetylation Site H2BK120 acetylation site H2BK120ac [SO Definition]: A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated. P00000391 http://purl.obolibrary.org/obo/GO_0043973 http://purl.obolibrary.org/obo/SO_0001943 P00000392 H3K4 Acetylation Site H3K4 acetylation site H3K4ac histone H3 acetylation at K4 histone H3-K4 acetylation histone H3K4 acetylation [SO Definition]: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000392 http://purl.obolibrary.org/obo/GO_0043970 http://purl.obolibrary.org/obo/SO_0001703 P00000393 H3K9 Acetylation Site H3K9 acetylation site H3K9ac histone H3 acetylation at K9 histone H3-K9 acetylation histone H3K9 acetylation [SO Definition]: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000393 http://purl.obolibrary.org/obo/GO_0044154 http://purl.obolibrary.org/obo/SO_0001704 P00000394 H3K14 Acetylation Site H3K14 acetylation site H3K14ac histone H3 acetylation at K14 histone H3-K14 acetylation histone H3K14 acetylation [SO Definition]: A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000394 http://purl.obolibrary.org/obo/GO_0043971 http://purl.obolibrary.org/obo/SO_0001718 P00000395 H3K18 Acetylation Site H3K18 acetylation site H3K18ac histone H3 acetylation at K18 histone H3-K18 acetylation histone H3K18 acetylation [SO Definition]: A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000395 http://purl.obolibrary.org/obo/GO_0043972 http://purl.obolibrary.org/obo/SO_0001719 P00000396 H3K23 Acetylation Site H3K23 acetylation site H3K23ac histone H3 acetylation at K23 histone H3-K23 acetylation histone H3K23 acetylation [SO Definition]: A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated. P00000396 http://purl.obolibrary.org/obo/GO_0043974 http://purl.obolibrary.org/obo/SO_0002049 P00000397 H3K27 Acetylation Site H3K27 acetylation site H3K27ac histone H3 acetylation at K27 histone H3-K27 acetylation histone H3K27 acetylation [SO Definition]: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000397 http://purl.obolibrary.org/obo/GO_0043975 http://purl.obolibrary.org/obo/SO_0001936 P00000398 H3K36 Acetylation Site H3K36 acetylation site H3K36ac histone H3 acetylation at K36 histone H3-K36 acetylation histone H3K36 acetylation [SO Definition]: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000398 http://purl.obolibrary.org/obo/GO_0097043 http://purl.obolibrary.org/obo/SO_0001945 P00000399 H3K56 Acetylation Site H3K56 acetylation site H3K56ac histone H3 acetylation at K56 histone H3-K56 acetylation histone H3K56 acetylation [SO Definition]: A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated. P00000399 P00000400 H3K72 Acetylation Site H3K72 acetylation site H3K72ac histone H3 acetylation at K72 histone H3-K72 acetylation histone H3K72 acetylation A kind of histone modification site, whereby the 72nd residue (a lysine), from the start of the H3 histone protein is acetylated. P00000400 http://purl.obolibrary.org/obo/GO_0043976 P00000401 H3K79 Acetylation Site histone H3 acetylation at K79 histone H3-K79 acetylation histone H3K79 acetylation [GO Definition]: The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 79 of the histone. [ GOC:jl ] P00000401 P00000402 H3R18 Acetylation Site H3R18 acetylation site H3R18ac histone H3 acetylation at R18 histone H3-R18 acetylation histone H3R18 acetylation A kind of histone modification site, whereby the 18th residue (an arginine), from the start of the H3 histone protein is acetylated." P00000402 http://purl.obolibrary.org/obo/GO_0043981 http://purl.obolibrary.org/obo/SO_0001730 P00000403 H4K5 Acetylation Site H4K5 acetylation site H4K5ac histone H4 acetylation at K5 histone H4-K5 acetylation [SO Definition]: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated. P00000403 http://purl.obolibrary.org/obo/GO_0043982 http://purl.obolibrary.org/obo/SO_0001731 P00000404 H4K8 Acetylation Site H4K8 acetylation site H4K8ac histone H4 acetylation at K8 histone H4-K8 acetylation [SO Definition]: A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated. P00000404 http://purl.obolibrary.org/obo/GO_0043983 http://purl.obolibrary.org/obo/SO_0001939 P00000405 H4K12 Acetylation Site H4K12 acetylation site H4K12ac histone H4 acetylation at K12 histone H4-K12 acetylation [SO Definition]: A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated. P00000405 http://purl.obolibrary.org/obo/GO_0043984 http://purl.obolibrary.org/obo/SO_0001729 P00000406 H4K16 Acetylation Site H4K16 acetylation site H4K16ac histone H4 acetylation at K16 histone H4-K16 acetylation [SO Definition]: A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated. P00000406 P00000407 H4K20 Acetylation Site H4K20 acetylation site H4K20ac histone H4 acetylation at K20 histone H4-K20 acetylation A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4 histone protein is acetylated. P00000407 http://purl.obolibrary.org/obo/SO_0001941 P00000408 H4K91 Acetylation Site H4K91 acetylation site H4K91ac [SO Definition]: A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated. P00000408 P00000409 Histone H2A ADP-Ribosylation Site A histone H2A modification where the modification is the ADP-ribosylation of the residue. P00000409 P00000410 Histone H2B ADP-Ribosylation Site A histone H2B modification where the modification is the ADP-ribosylation of the residue. P00000410 P00000411 Histone H3 ADP-Ribosylation Site A histone H3 modification where the modification is the ADP-ribosylation of the residue. P00000411 P00000412 Histone H4 ADP-Ribosylation Site A histone H4 modification where the modification is the ADP-ribosylation of the residue. P00000412 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK13ar P00000413 H2AK13 ADP-Ribosylation Site H2AK13ar PARP1 is shown to mediate H2A K13 ADP-ribosylation in in vitro conditions. This site is also confirmed by mass spectrometry (PMID: 20525793). P00000413 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2BK30ar P00000414 H2BK30 ADP-Ribosylation Site H2BK30ar PARP1 is shown to mediate H2B K30 ADP-ribosylation in in vitro conditions. This site is also confirmed by mass spectrometry (PMID: 20525793). P00000414 P00000415 H3K27 ADP-Ribosylation Site H3K27ar A kind of histone modification, whereby the 27th residue (a lysine), from the start of the H3 histone protein is ADP-ribosylated. P00000415 P00000416 H3K37 ADP-Ribosylation Site K3H37ar A kind of histone modification, whereby the 37th residue (a lysine), from the start of the H3 histone protein is ADP-ribosylated. P00000416 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4K16ar P00000417 H4K16 ADP-Ribosylation Site H4K16ar Different acetylation patterns on histone H4 are subjected to binding of different number of ADP-ribosyl units. Poly ADP ribosylation of histone H4 plays an important role during chromatin replication (PMID: 2387872). Important in shuttling of histones in and out of DNA (PMID: 1326536). It s also implicated in DNA excision repair (PMID: 1429884). P00000417 P00000418 Histone H2A Biotinylation Site The modification of histone H2A by the addition of a biotinyl group. P00000418 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK9bio P00000419 H2AK9 Biotinylation Site H2AK9bio Biotinidase is shown to mediate H2A K9 biotinylation in in vitro conditions. This site is also confirmed by mass spectrometry (PMID: 16772434). P00000419 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK13bio P00000420 H2AK13 Biotinylation Site H2AK13bio Biotinidase is shown to mediate H2A K13 biotinylation in in vitro conditions. This site is also confirmed by mass spectrometry (PMID: 16772434). P00000420 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK125bio P00000421 H2AK125 Biotinylation Site H2AK125bio Substitution of neighbouring lysines eg: K127 and K129 causes a considerable decrease in the biotinylation at K125 (PMID: 16109483). Site also confirmed by Mass Spectrometry (PMID: 16772434). P00000421 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK127bio P00000422 H2AK127 Biotinylation Site H2AK127bio Substitution of neighbouring lysines eg: K125 and K129 causes a considerable decrease in the biotinylation at K127 (PMID: 16109483). Site also confirmed by Mass Spectrometry (PMID: 16772434). P00000422 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK129bio P00000423 H2AK129 Biotinylation Site H2AK129bio K129 is a sturdy site for biotinylation since substitution of neighbouring lysines e.g. K125 and K127 did not significantly affect biotinylation at his site (PMID: 16109483). Site also confirmed by Mass Spectrometry (PMID: 16772434). P00000423 P00000424 Histone H3 Biotinylation Site The modification of histone H3 by the addition of a biotinyl group. P00000424 P00000425 H3K4 Biotinylation Site H3K4bio The modification of histone H3 by the addition of an biotinyl group to a lysine residue at position 4 of the histone. P00000425 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3K9bio P00000426 H3K9 Biotinylation Site H3K9bio Holocarboxylase synthetase (HCS) catalyses the biotinylation of H3K9 (PMID: 20688500). P00000426 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3K18bio P00000427 H3K18 Biotinylation Site H3K18bio Holocarboxylase synthetase (HCS) catalyses the biotinylation of H3K18 (PMID: 20688500). P00000427 P00000428 H3K23 Biotinylation Site H3K23bio The modification of histone H3 by the addition of an biotinyl group to a lysine residue at position 23 of the histone. P00000428 P00000429 Histone H4 Biotinylation Site The modification of histone H4 by the addition of a biotinyl group. P00000429 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4K8bio P00000430 H4K8 Biotinylation Site H4K8bio H4K8 is a preferred site for biotinylation (PMID: 15153116). Biotinylated histone H4 is enriched in pericentromeric heterochromatin and it participates in gene silencing, mitotic condensation of chromatin, and the cellular response to DNA damage(PMID: 16772434). P00000430 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4K12bio P00000431 H4K12 Biotinylation Site H4K12bio H4K12 is a preferred site for biotinylation (PMID: 15153116). Biotinylated histone H4 is enriched in pericentromeric heterochromatin, and that biotinylation of histone H4 participates in gene silencing, mitotic condensation of chromatin, and the cellular response to DNA damage(PMID: 16772434). P00000431 P00000432 Histone H2A Citrullination Site The modification of histone H2A by the hydrolysis of peptidyl-arginine to form peptidyl-citrulline. P00000432 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AR3ci P00000433 H2AR3 Citrullination Site H2AR3ci The modification of histone H2A by the hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 3 of the histone. P00000433 P00000434 Histone H3 Citrullination Site The modification of histone H3 by the hydrolysis of peptidyl-arginine to form peptidyl-citrulline. P00000434 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R2ci P00000435 H3R2 Citrullination Site H3R2ci PADI4 catalyses deimination at R2 position on H3. This activity inhibits the methylation of these residues by CARM1 thus causing transcriptional repression of target genes (PMID: 15339660). P00000435 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R8ci P00000436 H3R8 Citrullination Site H3R8ci H3 arginine 8 citrullination by PADI4 helps in reversing the transcriptional activation brought about by the combined efforts of nuclear hormone receptor coactivators, histone arginine methyltransferases and histone deacetylases (PMID: 15345777). H3 deimination increases rapidly in response to neutrophile activation stimuli like LPS, TNF, lipoteichoic acid, f-MLP, or hydrogen peroxide and is released to the extracellular space as part of the neutrophil response to infections (PMID: 18209087). R8 deimination prevents methylation by CARM1 thus causing transcriptional repression of target genes (PMID: 15339660). P00000436 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R17ci P00000437 H3R17 Citrullination Site H3R17ci H3 arginine 17 citrullination by PADI4 helps in reversing the transcriptional activation brought about by nuclear hormone receptor coactivators and histone arginine methyltransferases and histone deacetylases.(PMID: 15345777). H3 deimination increases rapidly in response to neutrophile acivation stimuli like LPS, TNF, lipoteichoic acid, f-MLP, or hydrogen peroxide and is released to the extracellular space as part of the neutrophil response to infections. (PMID: 18209087) . R17 deimination prevents methylation by CARM1 thus causing transcriptional repression of target genes (PMID: 15339660). P00000437 http://purl.obolibrary.org/obo/GO_0036413 P00000438 H3R26 Citrullination Site H3R26ci histone H3 arginine 26 citrullination histone H3-R26 citrullination [GO Definition]: The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3. [ GOC:als http://www.ncbi.nlm.nih.gov/pubmed/22853951 ] P00000438 P00000439 Histone H4 Citrullination Site The modification of histone H4 by the hydrolysis of peptidyl-arginine to form peptidyl-citrulline. P00000439 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4R3ci P00000440 H4R3 Citrullination Site H4R3ci H4R3 methylation is converted to citrulline by PADI4 (PMID: 15345777). P00000440 http://purl.obolibrary.org/obo/GO_0000412 P00000442 Histone Peptidyl-Prolyl Isomerization Site histone proline isomerization [GO Definition]: The modification of a histone by cis-trans isomerization of a proline residue. [ GOC:krc ] P00000442 P00000443 Histone 3 Peptidyl-Prolyl Isomerization Site The modification of a histone H3 by cis-trans isomerization of a proline residue. P00000443 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764789/ P00000444 H3P30 Peptidyl-Prolyl Isomerization Site The modification of a histone H3 by cis-trans isomerization of a proline residue at position 30. P00000444 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764789/ P00000445 H3P38 Peptidyl-Prolyl Isomerization Site The modification of a histone H3 by cis-trans isomerization of a proline residue at position 38. P00000445 P00000446 Histone H1 Methylation Site The modification of histone H1 by the addition of methyl groups. P00000446 P00000447 Histone H2A Methylation Site The modification of histone H2A by the addition of methyl groups. P00000447 P00000448 Histone H2B Methylation Site The modification of histone H2B by the addition of methyl groups. P00000448 P00000449 Histone H3 Methylation Site The modification of histone H3 by the addition of methyl groups. P00000449 P00000450 Histone H4 Methylation Site The modification of histone H4 by the addition of methyl groups. P00000450 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1K25me1 P00000451 H1K26 Methylation Site H1K25 Methylation H1K25me H1K25me1 H1K26me H1K26me1 H1.4 K25 (reported as H1K26) methylation is mediated by Ezh2 of the Polycomb repressive complex (PRC2) which is associated with transcriptional repression and might play a role in the formation of chromatin fibre (PMID: 15099518). H1.4K26 is specifically required for the binding of Heterochromatin protein 1 (HP1), whereas simultaneous phosphorylation at S27 blocks HP1 binding (PMID: 16127177). P00000451 http://purl.obolibrary.org/obo/GO_0070612 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AR3me2 P00000452 H2AR3 Methylation Site histone methylase activity (H2A-R3 specific) histone methyltransferase activity (H2A-R3 specific) histone-arginine N-methyltransferase activity (H2A-R3 specific) H2AR3 is a preferred site for PRMT methylation activity (PMID: 18079182). P00000452 P00000453 H2AR11 Methylation Site The modification of histone H2A by addition of one or more methyl groups to arginine at position 11 of the histone. P00000453 P00000454 H2AR29 Methylation Site The modification of histone H2A by addition of one or more methyl groups to arginine at position 29 of the histone. P00000454 http://purl.obolibrary.org/obo/SO_0001714 P00000455 H2BK5 Monomethylation Site H2BK5 mono-methylation site H2BK5 monomethylation site [SO Definition]: A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. P00000455 http://purl.obolibrary.org/obo/GO_0051568 http://purl.obolibrary.org/obo/SO_0001734 P00000456 H3K4 Methylation Site H3K4 methylation site histone H3 K4 methylation histone H3-K4 methylation histone H3K4me histone lysine H3 K4 methylation [SO Definition]: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. P00000456 http://purl.obolibrary.org/obo/GO_0097692 http://purl.obolibrary.org/obo/SO_0001705 P00000457 H3K4 Monomethylation Site H3K4 mono-methylation site H3K4me1 histone H3-K4 monomethylation [SO Definition]: A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. P00000457 http://purl.obolibrary.org/obo/GO_0044648 http://purl.obolibrary.org/obo/SO_0001725 P00000458 H3K4 Dimethylation Site H3K4 di-methylation site H3K4Me2 histone H3-K4 dimethylation [SO Definition]: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. P00000458 http://purl.obolibrary.org/obo/GO_0080182 http://purl.obolibrary.org/obo/SO_0001706 P00000459 H3K4 Trimethylation Site H3K4 tri-methylation H3K4me3 histone H3-K4 trimethylation [SO Definition]: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. P00000459 http://purl.obolibrary.org/obo/GO_0051567 http://purl.obolibrary.org/obo/SO_0001736 P00000460 H3K9 Methylation Site H3K9 methylation site histone H3 K9 methylation histone H3-K9 methylation histone H3K9me histone lysine H3 K9 methylation [SO Definition]: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. P00000460 http://purl.obolibrary.org/obo/SO_0001727 P00000461 H3K9 Monomethylation Site H3K9 mono-methylation site H3K9Me1 [SO Definition]: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. P00000461 http://purl.obolibrary.org/obo/GO_0036123 http://purl.obolibrary.org/obo/SO_0001728 P00000462 H3K9 Dimethylation Site H3K9 di-methylation site H3K9Me2 histone H3 K9 dimethylation histone H3-K9 dimethylation histone lysine H3 K9 dimethylation [SO Definition]: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. P00000462 http://purl.obolibrary.org/obo/GO_0036124 http://purl.obolibrary.org/obo/SO_0001707 P00000463 H3K9 Trimethylation Site H3K9 tri-methylation site H3K9Me3 histone H3-K9 trimethylation [SO Definition]: A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. P00000463 P00000464 H3K20 Methylation Site The modification of histone H3 by addition of one or more methyl groups to lysine at position 20 of the histone. P00000464 http://purl.obolibrary.org/obo/SO_0001935 P00000465 H3K20 Trimethylation Site H3K20 trimethylation site [SO Definition]: A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated. P00000465 P00000466 H3K23 Methylation Site The modification of histone H3 by addition of one or more methyl groups to lysine at position 23 of the histone. P00000466 http://purl.obolibrary.org/obo/SO_0001951 P00000467 H3K23 Dimethylation Site H3K23 dimethylation site H3K23me2 [SO Definition]: A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated. P00000467 http://purl.obolibrary.org/obo/GO_0070734 http://purl.obolibrary.org/obo/SO_0001732 P00000468 H3K27 Methylation Site H3K27 methylation site histone H3 K27 methylation histone H3-K27 methylation histone H3K27me histone lysine H3 K27 methylation [GO Definition]: The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone. [ GOC:pr GOC:mah ] P00000468 http://purl.obolibrary.org/obo/SO_0001708 P00000469 H3K27 Monomethylation Site H2K27 mono-methylation site H2K27 monomethylation site H2K27Me1 [SO Definition]: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. P00000469 http://purl.obolibrary.org/obo/SO_0001726 P00000470 H3K27 Dimethylation Site H3K27 di-methylation site H3K27 dimethylation site H3K27Me2 [SO Definition]: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. P00000470 http://purl.obolibrary.org/obo/GO_0098532 http://purl.obolibrary.org/obo/SO_0001709 P00000471 H3K27 Trimethylation Site H3K27 tri-methylation site H3K27 trimethylation site H3K27Me3 histone H3 lysine 27 trimethylation histone H3-K27 trimethylation [SO Definition]: A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. P00000471 http://purl.obolibrary.org/obo/GO_0010452 http://purl.obolibrary.org/obo/SO_0001733 P00000472 H3K36 Methylation Site H3K36 methylation site histone H3 K36 methylation histone H3K36me histone lysine H3 K36 methylation [SO Definition]: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. P00000472 http://purl.obolibrary.org/obo/SO_0001722 P00000473 H3K36 Monomethylation Site H3K36 mono-methylation site H3K36 monomethylation site H3K36<Me1 [SO Definition]: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. P00000473 http://purl.obolibrary.org/obo/GO_0097676 http://purl.obolibrary.org/obo/SO_0001723 P00000474 H3K36 Dimethylation Site H3K36 di-methylation site H3K36Me2 histone H3-K36 dimethylation [SO Definition]: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. P00000474 http://purl.obolibrary.org/obo/GO_0097198 http://purl.obolibrary.org/obo/SO_0001724 P00000475 H3K36 Trimethylation Site H3K36 tri-methylation site H3K36Me3 histone H3-K36 trimethylation [SO Definition]: A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. P00000475 http://purl.obolibrary.org/obo/GO_0034729 http://purl.obolibrary.org/obo/SO_0001735 P00000476 H3K79 Methylation Site H3K79 methylation site histone H3 K79 methylation histone H3-K79 methylation histone H3K79me histone lysine H3 K79 methylation [SO Definition]: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. P00000476 http://purl.obolibrary.org/obo/SO_0001710 P00000477 H3K79 Monomethylation Site H3K79 mono-methylation site H3K79 monomethylation site H3K79me1 [SO Definition]: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. P00000477 http://purl.obolibrary.org/obo/GO_0097725 http://purl.obolibrary.org/obo/SO_0001711 P00000478 H3K79 Dimethylation Site H3K79 di-methylation site H3K79 dimethylation site H3K79Me2 histone H3 K79 dimethylation histone H3-K79 dimethylation histone lysine H3 K79 dimethylation [SO Definition]: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. P00000478 http://purl.obolibrary.org/obo/SO_0001712 P00000479 H3K79 Trimethylation Site H3K79 tri-methylation site H3K79 trimethylation site H3K79Me3 [SO Definition]: A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. P00000479 http://purl.obolibrary.org/obo/GO_0034970 P00000480 H3R2 Methylation Site histone H3 R2 methylation histone H3-R2 methylation histone H3R2me histone lysine H3 R2 methylation [GO Definition]: The modification of histone H3 by addition of a methyl group to arginine at position 2 of the histone. [ GOC:mah ] P00000480 http://purl.obolibrary.org/obo/SO_0001947 P00000481 H3R2 Monomethylation Site H3R2 monomethylation site H3R2me1 [SO Definition]: A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated. P00000481 http://purl.obolibrary.org/obo/SO_0001948 P00000482 H3R2 Dimethylation Site H3R2 dimethylation site H3R2me2 [SO Definition]: A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated. P00000482 P00000484 H3R8 Methylation Site The modification of histone H3 by addition of a methyl group to arginine at position 8 of the histone. P00000484 http://purl.obolibrary.org/obo/GO_0034971 P00000485 H3R17 Methylation Site histone H3 R17 methylation histone H3-R17 methylation histone H3R17me histone lysine H3 R17 methylation [GO Definition]: The modification of histone H3 by addition of a methyl group to arginine at position 17 of the histone. [ GOC:mah ] P00000485 http://purl.obolibrary.org/obo/GO_0034972 P00000486 H3R26 Methylation Site H3R26me1 histone H3 R26 methylation histone H3-R26 methylation histone H3R26me histone lysine H3 R26 methylation [GO Definition]: The modification of histone H3 by addition of a methyl group to arginine at position 26 of the histone. [ GOC:mah ] P00000486 P00000487 H4K4 Methylation Site The modification of histone H4 by addition of one or more methyl groups to lysine at position 4 of the histone. P00000487 http://purl.obolibrary.org/obo/SO_0001950 P00000488 H4K4 Trimethylation Site H4K4 trimethylation site H4K4me3 [SO Definition]: A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated. P00000488 http://purl.obolibrary.org/obo/GO_0034770 P00000489 H4K20 Methylation Site histone H4 K20 methylation histone H4-K20 methylation histone H4K20me histone lysine H4 K20 methylation [GO Definition]: The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone. [ GOC:mah ] P00000489 http://purl.obolibrary.org/obo/GO_0034771 http://purl.obolibrary.org/obo/SO_0001713 P00000490 H4K20 Monomethylation Site H4K20 mono-methylation site H4K20Me1 histone H4 K20 monomethylation histone H4-K20 monomethylation histone lysine H4 K20 monomethylation [SO Definition]: A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated. P00000490 P00000492 H4K59 Methylation Site The modification of histone H4 by addition of one or more methyl groups to lysine at position 59 of the histone. P00000492 http://purl.obolibrary.org/obo/GO_0043985 P00000493 H4R3 Methylation Site histone H4 R3 methylation histone H4 methylation at R3 histone H4-R3 methylation histone H4R3me [GO Definition]: The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone. [ GOC:mah ] P00000493 http://purl.obolibrary.org/obo/SO_0001949 P00000494 H4R3 Dimethylation Site H4R3 dimethylation site H4R3me2 [SO Definition]: A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated. P00000494 P00000495 Histone Palmitoylation Site The modification of histones by O-palmitoylation. P00000495 https://www.ncbi.nlm.nih.gov/pubmed/21685381 P00000496 Histone H4 Palmitoylation Site The modification of histone H4 by O-palmitoylation. P00000496 https://www.ncbi.nlm.nih.gov/pubmed/21685381 P00000497 H4S47 Palmitoylation Site The modification of histone H4 by O-palmitoylation at position 47 of the histone. P00000497 P00000498 Histone H1 Phosphorylation Site H1 Phosphorlyation Histone 1 Phosphorylation The modification of histone H1 by addition of phosphate groups. P00000498 http://purl.obolibrary.org/obo/GO_1990164 P00000499 Histone H2A Phosphorylation Site h2a phosphorylation histone 2a phosphorylation [GO Definition]: The modification of histone H2A by the addition of a phosphate group. [ http://www.ncbi.nlm.nih.gov/pubmed/23080121 GOC:mah ] P00000499 P00000500 Histone H2B Phosphorylation Site The modification of histone H2B by the addition of a phosphate group. P00000500 P00000501 Histone H3 Phosphorylation Site The modification of histone H3 by the addition of a phosphate group. P00000501 P00000502 Histone H4 Phosphorylation Site The modification of histone H4 by the addition of a phosphate group. P00000502 P00000503 H1S27 Phosphorylation Site H1S27p histone H1 phosphorylation at S27 histone H1-S27 phosphorylation histone H1S27 phosphorylation The modification of histone H1 by the addition of an phosphate group to a serine residue at position 27 of the histone. P00000503 http://purl.obolibrary.org/obo/GO_0043990 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AS1ph P00000504 H2AS1 Phosphorylation Site H2AS1p H2AS1ph histone H2A phosphorylation at S1 histone H2A-S1 phosphorylation histone H2AS1 phosphorylation [GO Definition]: The modification of histone H2A by the addition of an phosphate group to a serine residue at position 1 of the histone. [ GOC:jl ] P00000504 http://purl.obolibrary.org/obo/GO_0072370 P00000505 H2AS121 Phosphorylation Site histone H2A phosphorylation at S121 histone H2A-S121 phosphorylation histone H2AS121 phosphorylation [GO Definition]: The modification of histone H2A by the addition of an phosphate group to a serine residue at position 121 of the histone. [ GOC:mah http://www.ncbi.nlm.nih.gov/pubmed/19965387 ] P00000505 P00000506 H2AS122 Phosphorylation Site histone H2A phosphorylation at S122 histone H2A-S122 phosphorylation histone H2AS122 phosphorylation The modification of histone H2A by the addition of an phosphate group to a serine residue at position 122 of the histone. P00000506 http://purl.obolibrary.org/obo/GO_0035978 P00000507 H2AS139 Phosphorylation Site H2AS139p H2AS139ph [GO Definition]: The modification of histone H2A by the addition of an phosphate group to a serine residue at position 139 of the histone. [ GOC:yaf http://www.ncbi.nlm.nih.gov/pubmed/16061642 ] P00000507 http://purl.obolibrary.org/obo/GO_1990245 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AT120ph P00000508 H2AT120 Phosphorylation Site H2AT120p H2AT120ph histone H2A phosphorylation at T120 histone H2A-T120 phosphorylation histone H2AT120 phosphorylation [GO Definition]: The modification of histone H2A by the addition of a phosphate group to a threonine residue at position 120 of the histone. [ http://www.ncbi.nlm.nih.gov/pubmed/24140421 ] P00000508 P00000509 Histone H2A.X Phosphorylation Site The modification of histone H2A.X by the addition of a phosphate group. P00000509 P00000510 H2A.XS139 Phosphorylation Site H2AXS139p" H2AXS139ph histone H2AX phosphorylation at S139 histone H2AX-S139 phosphorylation histone H2AXS139 phosphorylation The modification of histone H2A.X by the addition of an phosphate group to a serine residue at position 139 of the histone. P00000510 P00000511 H2A.XY142 Phosphorylation Site H2AXY142p H2AXY142ph histone H2AX phosphorylation at Y142 histone H2AX-Y142 phosphorylation histone H2AXY142 phosphorylation The modification of histone H2A.X by the addition of an phosphate group to a tyrosine residue at position 142 of the histone. P00000511 http://purl.obolibrary.org/obo/GO_0034772 P00000526 H4K20 Dimethylation Site histone H4 K20 dimethylation histone H4-K20 dimethylation histone lysine H4 K20 dimethylation [GO Definition]: The modification of histone H4 by addition of two methyl groups to lysine at position 20 of the histone. [ GOC:mah ] P00000526 http://purl.obolibrary.org/obo/GO_0034773 P00000527 H4K20 Trimethylation Site histone H4 K20 trimethylation histone H4-K20 trimethylation histone lysine H4 K20 trimethylation [GO Definition]: The modification of histone H4 by addition of three methyl groups to lysine at position 20 of the histone. [ GOC:mah ] P00000527 P00000528 H2BK14 Phosphorylation Site H2BK14p H2BK14ph histone H2B phosphorylation at K14 histone H2B-K14 phosphorylation histone H2BK14 phosphorylation The modification of histone H2B by the addition of an phosphate group to a lysine residue at position 14 of the histone. P00000528 http://purl.obolibrary.org/obo/GO_0043991 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2BS14ph P00000529 H2BS14 Phosphorylation Site h2bs14p h2bs14ph histone H2B phosphorylation at S14 histone H2B-S14 phosphorylation histone H2BS14 phosphorylation [GO Definition]: The modification of histone H2B by the addition of an phosphate group to a serine residue at position 14 of the histone. [ GOC:jl ] P00000529 http://purl.obolibrary.org/obo/GO_0043987 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3S10ph P00000530 H3S10 Phosphorylation Site H3S10p H3S10ph histone H3 phosphorylation at S10 histone H3-S10 phosphorylation histone H3S10 phosphorylation [GO Definition]: The modification of histone H3 by the addition of an phosphate group to a serine residue at position 10 of the histone. [ GOC:jl ] P00000530 http://purl.obolibrary.org/obo/GO_0043988 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3S28ph P00000531 H3S28 Phosphorylation Site H3S28p H3S28ph histone H3 phosphorylation at S28 histone H3-S28 phosphorylation histone H3S28 phosphorylation [GO Definition]: The modification of histone H3 by the addition of an phosphate group to a serine residue at position 28 of the histone. [ GOC:jl ] P00000531 http://purl.obolibrary.org/obo/GO_0072355 P00000532 H3T3 Phosphorylation Site H3T3p H3T3ph [GO Definition]: The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 3 of the histone. [ GOC:mah ] P00000532 http://purl.obolibrary.org/obo/GO_0035408 P00000533 H3T6 Phosphorylation Site H3T6p H3T6ph [GO Definition]: The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 6 of the histone. [ GOC:bf ] P00000533 http://purl.obolibrary.org/obo/GO_0035407 P00000534 H3T11 Phosphorylation Site H3T11p H3T11ph [GO Definition]: The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 11 of the histone. [ GOC:bf ] P00000534 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3T45ph P00000535 H3T45 Phosphorylation Site H3T45p H3T45ph H3T45 phosphorylation induces structural change within the nucleosome to facilitate DNA nicking and/or fragmentation linking its role to apoptosis (PMID: 19363025). P00000535 http://purl.obolibrary.org/obo/GO_0035409 P00000536 H3Y41 Phosphorylation Site H3Y41p H3Y41ph [GO Definition]: The modification of histone H3 by the addition of a phosphate group to a tyrosine residue at position 41 of the histone. [ GOC:bf ] P00000536 http://purl.obolibrary.org/obo/GO_0043989 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4S1ph P00000537 H4S1 Phosphorylation Site H4S1p H4S1ph histone H4 phosphorylation at S1 histone H4-S1 phosphorylation histone H4S1 phosphorylation [GO Definition]: The modification of histone H4 by the addition of an phosphate group to a serine residue at position 1 of the histone. [ GOC:jl ] P00000537 http://purl.obolibrary.org/obo/GO_0036351 P00000538 H2AK13 Ubiquitination Site histone H2A ubiquitination (H2A-K13) histone H2A-K13 ubiquitination [GO Definition]: The modification of histone H2A by addition of ubiquitin group at lysine 13 (H2A-K13) in metazoans, and at the equivalent residue in other organisms. Monoubiquitin is first attached to H2A-K13 and K63-linked ubiquitin chains are then extended from this monoubiquitin. [ http://www.ncbi.nlm.nih.gov/pubmed/22713238 http://www.ncbi.nlm.nih.gov/pubmed/22980979 GOC:sp ] P00000538 http://purl.obolibrary.org/obo/GO_0036352 P00000539 H2AK15 Ubiquitination Site histone H2A ubiquitination (H2A-K15) histone H2A-K15 ubiquitination [GO Definition]: The modification of histone H2A by addition of ubiquitin group at lysine 15 (H2A-K15) in metazoans, and at the equivalent residue in other organisms. Monoubiquitin is first attached to H2A-K15 and K63-linked ubiquitin chains are then extended from this monoubiquitin. [ GOC:sp http://www.ncbi.nlm.nih.gov/pubmed/22713238 http://www.ncbi.nlm.nih.gov/pubmed/22980979 ] P00000539 http://purl.obolibrary.org/obo/GO_0070535 P00000540 H2AK63-Linked Ubiquitination Site histone H2A K63-linked ubiquitination [GO Definition]: A histone ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a lysine residue in histone H2A or the variant H2AX. [ GOC:mah http://www.ncbi.nlm.nih.gov/pubmed/18430235 ] P00000540 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK119ub P00000541 H2AK119 Ubiquitination Site H2AK119ub H2AK119 ubiquitination is linked to Polycomb mediated gene silencing (PMID: 15386022). P00000541 P00000542 H2A.X Ubiquitination Site The modification of histone H2A.X by addition of one or more ubiquitin groups. P00000542 http://purl.obolibrary.org/obo/GO_0036353 P00000543 H2AK119 Monoubiquitination Site histone H2A monoubiquitination (H2A-K119) histone H2A-K119 monoubiquitination [GO Definition]: The modification of histone H2A by addition of a single ubiquitin group to lysine-119 (H2A- K119) in metazoans, and at the equivalent residue in other organisms. [ http://www.ncbi.nlm.nih.gov/pubmed/15386022 GOC:sp ] P00000543 P00000544 H2A.XK119 Ubiquitination Site H2A.XK119ub H2AXK119 Ubiquitination The modification of histone H2A.X by addition of ubiquitin group at lysine 119. P00000544 http://purl.obolibrary.org/obo/GO_0033523 http://purl.obolibrary.org/obo/SO_0001717 P00000545 Histone H2B Ubiquitination Site H2B ubiquitination site H2BUbiq [GO Definition]: The modification of histone H2B by addition of ubiquitin groups. [ GOC:mah ] P00000545 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2BK120ub P00000546 H2BK120 Ubiquitination Site H2BK120ub H2B-K120 monoubiquitination is essential for subsequent H3-K4 and H3-K79 methylation and these modifications are marks for active gene transcription (PMID: 16307923). H2BK120ub1 stimulates elongation by RNA polymerase II through chromatin (PMID: 16713563). H2B specific ubiquitin ligase RNF20/hBRE1 which mediates H2BK120ub acts as a putative tumour suppressor through selective regulation of gene expression (PMID: 18832071). CDK9 is reported to regulate gene expression by controlling H2BK120ub1 mark at a global level (PMID: 19575011). P00000546 P00000547 Histone H4 Ubiquitination Site The modification of histone H2B by addition of ubiquitin groups. P00000547 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4K91ub P00000548 H4K91 Ubiquitination Site H4K91ub H4K91 monoubiquitination is essential for protection against DNA damage. Mutation at the H4K91 residue exhibits defective chromatin assembly and increased sensitivity to DNA-damaging agents (PMID: 19818714). P00000548 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1.0 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/H1.0/ P00000549 Histone H1.0 H1° H1δ H5 Histone H1' Histone H1(0) RI H1 H1.0 is a replication independent linker histone found in animals expressed in terminally differentiated cells. Has a common monophyletic origin that can be traced back before the differentiation between protostomes and deuterostomes, very early in metazoan evolution. P00000549 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1oo https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/OO_H1.8/#msa_div_browse P00000550 Histone H1oo H1 histone family, member O, oocyte-specific H1FOO H1oo OO Histone H1.8 Oocyte-specific histone H1 Oocyte-specific linker histone H1 (osH1) H1oo gene is located on chromosome number 3. This variant is expressed specifically in oocytes and its mRNA is polyadenylated (PMID: 12711322). Human oocytes are reported to express H1oo starting from primordial follicle stage to early embryogenesis. Its incorporation into the sperm chromatin is supposed to affect the fertilization process (PMID: 19147139). P00000550 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/scH1/#msa_div_browse P00000551 Histone scH1 A special variant of H1 found in Saccharomyces and probably other yeast species that has two globular domains. Saccharomyces cerevisiae has only one gene that encodes H1 histone (HHO1). P00000551 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1t https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/TS_H1.6/#msa_div_browse P00000552 Histone H1t H1t HIST1H1T TS H1.6 Testicular H1 histone histone cluster 1, H1t A testis specific variant of H1 common in mammals. P00000552 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/TS_H1.7/ P00000553 Testis-specific Histone H1 H1 histone family, member N, testis-specific H1FNT H1T2 Haploid germ cell-specific nuclear protein 1 Histone H1t2 TS H1.7 A testis specific variant of H1 common in mammals. P00000553 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H1/variant/TS_H1.9/#msa_div_browse P00000554 Histone TS H1.9 Hils1 (TS) H1.9 is a testis specific variant of H1 common in mammals. P00000554 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.1/#msa_div_browse P00000555 Histone H2A.1 HIST1H2AG HIST1H2AI HIST1H2AK HIST1H2AL HIST1H2AM Histone H2A type 1 Histone H2A/p TH2A TS H2A.1 histone cluster 1, H2ag histone cluster 1, H2ai histone cluster 1, H2ak histone cluster 1, H2al histone cluster 1, H2am H2A.1 is a mammalian testis, oocyte and zygote specific variant. It can preferentially dimerize with H2B.1. So far characterized only in mouse, but a similar gene in human is available. The gene is located at the end of the largest histone gene cluster. P00000555 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.L/#msa_div_browse P00000556 Histone H2A.L H2A.Lap2 H2A.Lap3 H2A.Lap4 H2AL H2AL1 H2AL2 H2A.L is involved in pericentric chromatin organization in spermatids and spermiogenesis. It is a rapildy evolving variant and can form subnucleosmal particles with H2B.1. H2A.L has a shorter C-terminal tail and docking domain. P00000556 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.P/#msa_div_browse P00000557 Histone H2A.P CXorf27 HIP17 HYPM Huntingtin-interacting protein M H2A.P is a putative variant closely related to H2A.B and H2A.L, but forming a distinct clade. It is likely restricted to placental mammals. P00000557 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2A/variant/H2A.W/#msa_div_browse P00000558 Histone H2A.W H2A with SPKK motifs H2A.W is a plant specific variant, that has SPKK motifs at the C-terminus, which have putative minor-groove-binding activity. P00000558 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2B/variant/H2B.1/#msa_div_browse P00000559 Histone H2B.1 H2B.1 TH2B TS H2B.1 hTSH2B H2B.1 is a mammalian testis, oocyte and zygote specific variant that forms subnucleosomal particles in spermatids. It can preferentially dimerize with H2A.L and H2A.1. The gene is located at the end of the largest histone gene cluster. P00000559 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2B/variant/H2B.Z/#msa_div_browse P00000561 Histone H2B.Z H2Bv H2B.Z in an apicomplexan specific variant that is known to interact with H2A.Z. P00000561 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2B/variant/sperm_H2B/#msa_div_browse P00000562 Sperm Histone H2B cleavage H2B early H2B sperm H2B Putative histone variant class containing sperm H2B histones from sea and sand urchins. P00000562 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2B/variant/subH2B/#msa_div_browse P00000563 Histone subH2B H2BL1 subH2B subH2Bv subH2B is involved in spermiogenesis and is found in subacrosomes of spermatozoa. It has a bipartite nuclear localization signal. This variant is present outside of nucleus in acrosomal space of spermatozoa, extent of its involvement in nucleosome formation is unclear P00000563 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H3-like_centromeric_protein_A https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/cenH3/#msa_div_browse P00000564 Histone cenH3 CENP-A CNA1 CNP1 Centromere autoantigen A Centromere protein A (CENP-A) Cse4 HCP-3 HTR12 Histone H3-like centromeric protein A centromere protein A cid cenH3 is a centromere-specific histone variant, which replaces canonical H3 in centromeric nucleosomes. It is required for kinetochore formation, mitotic progression and chromosome segregation. cenH3 has an extended L1-loop and its N-terminal tail is very different from other H3 variants. cenH3s have an extended L1-loop and usually replace Phe84 in canonical H3 with Trp, and Thr 107 with Ala, Cys, or Ser. cenH3s ususally lack a conserved glutamine in the alpha1 helix of the histone fold. cenH3s typically have only about 50-60% amino acid identity to canonical H3 in the histone fold domain and no conservation of the N-terminus. [Source: https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/cenH3/#msa_div_browse] P00000564 https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H3/variant/H3.5/#msa_div_browse P00000565 Histone H3.5 A hominid specific variant expressed in seminiferous tubules of human testis. P00000565 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1.2 P00000566 Histone H1.2 HIST1H1C Histone H1d histone cluster 1, H1c H1.2 expression is replication dependent. Its gene is present in cluster 1 on chromosome number 6 and its mRNA is not polyadenylated (PMID: 19587527). H1.2 has another function apart from acting as a linker histone. It interacts directly with p53 and forms a repressor complex that represses transcription via multiple ways (PMID: 18258596). H1.2 is also shown to translocate inside mitochondria after sensing apoptotic signals (PMID: 17879944). Shown to be expressed at a higher level in many cell lines compared to other H1 variants (PMID: 9324306). H1.2 shows a dynamic exchange between chromatin and cytoplasm at different stages of mitotic phase (PMID: 20104577). A recent report classifies it as a weak condenser of chromatin (PMID: 19794910). P00000566 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1.3 P00000567 Histone H1.3 HIST1H1D Histone H1c histone cluster 1, H1d H1.3 expression is replication dependent. Its gene is present in cluster 1 on chromosome number 6 and its mRNA is not polyadenylated (PMID: 19587527). HL-60 and its differentiated cell types are shown to differ significantly in the presence of H1.3 variant (PMID: 11478838). H1.3 is detected in chromatin throughout the cell cycle whereas other varaints partition between chromatin and cytoplasm in a phase dependent manner (PMID: 20104577). Recent report classifies it as an intermediate condensor of chromatin (PMID: 19794910). P00000567 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1.5 P00000568 Histone H1.5 HIST1H1B Histone H1a histone cluster 1, H1b H1.5 exhibits a replication dependent expression. Its gene is present in cluster 1 on chromosome number 6 and the mRNA is not polyadenylated (PMID: 19587527). Histone H1.5 expression is increased during early apoptosis (PMID: 9882631). H1.5 shows the maximum fold change in expression during S phase compared to other H1 variants (PMID: 9324306). H1.5 shows a dynamic exchange between chromatin and cytoplasm at different stages of mitosis (PMID: 20104577). A recent report classifies it as a strong condensor of chromatin (PMID: 19794910). P00000568 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H1x P00000569 Histone H1x H1 histone family, member X H1FX H1x exhibits a replication independent expression. Expression levels remain unaltered throughout cell cycle. Gene is present on chromosome number 3 and mRNA is polyadenylated (PMID: 19587527). Highly expressed in neuroendocrine tumors (PMID: 19108733). Recent report classifies it as a strong condensor of chromatin (PMID: 19794910). P00000569 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-A P00000570 Histone H2A Type 1-A HIST1H2AA Histone H2A/r histone cluster 1, H2aa P00000570 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-B/E P00000571 Histone H2A Type 1-B/E HIST1H2AB HIST1H2AE Histone H2A.2 Histone H2A/a Histone H2A/m histone cluster 1, H2ab histone cluster 1, H2ae P00000571 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-C P00000572 Histone H2A Type 1-C HIST1H2AC Histone H2A/l histone cluster 1, H2ac P00000572 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-D P00000573 Histone H2A Type 1-D HIST1H2AD Histone H2A.3 Histone H2A/g histone cluster 1, H2ad P00000573 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-H P00000574 Histone H2A Type 1-H HIST1H2AH Histone H2A/s histone cluster 1, H2ah P00000574 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_1-J P00000575 Histone H2A Type 1-J HIST1H2AJ Histone H2A/e histone cluster 1, H2aj P00000575 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_2-A P00000576 Histone H2A Type 2-A HIST2H2AA3 HIST2H2AA4 Histone H2A.2 Histone H2A/o histone cluster 2, H2aa3 histone cluster 2, H2aa4 P00000576 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_2-B P00000577 Histone H2A Type 2-B HIST2H2AB histone cluster 2, H2ab P00000577 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A_type_2-C P00000578 Histone H2A Type 2-C HIST2H2AC Histone H2A-GL101 Histone H2A/q histone cluster 2, H2ac P00000578 P00000579 Histone H2A Type 3 HIST3H2A histone cluster 3, H2a P00000579 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A.J P00000580 Histone H2A.J H2A histone family, member J H2AFJ H2a/j P00000580 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2A.V P00000581 Histone H2A.V H2A histone family, member V H2A.F/Z H2AFV P00000581 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-A P00000582 Histone H2B Type 1-A HIST1H2BA Histone H2B, testis Testis-specific histone H2B histone cluster 1, H2ba P00000582 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-B P00000583 Histone H2B Type 1-B HIST1H2BB Histone H2B.1 Histone H2B.f (H2B/f) histone cluster 1, H2bb P00000583 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-C/E/F/G/I P00000584 Histone H2B Type 1-C/E/F/G/I HIST1H2BC HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BI Histone H2B.1 A Histone H2B.a (H2B/a) Histone H2B.g (H2B/g) Histone H2B.h (H2B/h) Histone H2B.k (H2B/k) Histone H2B.l (H2B/l) histone cluster 1, H2bc histone cluster 1, H2be histone cluster 1, H2bf histone cluster 1, H2bg histone cluster 1, H2bi P00000584 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-H P00000585 Histone H2B Type 1-H HIST1H2BH Histone H2B.j (H2B/j) histone cluster 1, H2bh P00000585 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-J P00000586 Histone H2B Type 1-J HIST1H2BJ Histone H2B.1 Histone H2B.r (H2B/r) histone cluster 1, H2bj P00000586 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-K P00000587 Histone H2B Type 1-K HIRA-interacting protein 1 HIST1H2BK histone cluster 1, H2bk P00000587 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-L P00000588 Histone H2B Type 1-L HIST1H2BL Histone H2B.c (H2B/c) histone cluster 1, H2bl P00000588 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-M P00000589 Histone H2B Type 1-M HIST1H2BM Histone H2B.e (H2B/e) histone cluster 1, H2bm P00000589 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-N P00000590 Histone H2B Type 1-N HIST1H2BN Histone H2B.d (H2B/d) histone cluster 1, H2bn P00000590 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_1-O P00000591 Histone H2B Type 1-O HIST1H2BO Histone H2B.2 Histone H2B.n (H2B/n) histone cluster 1, H2bo P00000591 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_2-E P00000592 Histone H2B Type 2-E HIST2H2BE Histone H2B-GL105 Histone H2B.q (H2B/q) histone cluster 2, H2be P00000592 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_2-F P00000593 Histone H2B Type 2-F HIST2H2BF histone cluster 2, H2bf P00000593 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_3-B P00000594 Histone H2B Type 3-B H2B type 12 HIST3H2BB histone cluster 3, H2bb P00000594 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_F-M P00000595 Histone H2B Type F-M H2B histone family, member M H2BFM Histone H2B.s (H2B/s) P00000595 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_F-S P00000596 Histone H2B Type F-S H2B histone family, member S H2BFS Histone H2B.s (H2B/s) P00000596 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Histone_H2B_type_W-T https://www.ncbi.nlm.nih.gov/research/HistoneDB2.0/index.fcgi/type/H2B/variant/H2B.W/#msa_div_browse P00000597 Histone H2B Type W-T H2B histone family member W testis-specific H2B histone family, member W, testis-specific H2BFWT Histone H2B.W member W type W-T H2B.W is involved in spermiogenesis and telomere associated functions in sperm and is found in spermatogenic cells. It has an extended N-terminal tail. P00000597 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Putative_histone_H2B_type_2-C P00000598 Putative Histone H2B Type 2-C HIST2H2BC Histone H2B.t (H2B/t) histone cluster 2, H2bc P00000598 http://www.iiserpune.ac.in/~coee/histome/variants.php?variant=Putative_histone_H2B_type_2-D P00000599 Putative Histone H2B Type 2-D HIST2H2BD histone cluster 2, H2bd P00000599 P00000600 Protein-arginine Deiminase P00000600 P00000602 H2AR3 Dimethylation Site H2AR3me2 The modification of histone H2A by addition of three methyl groups to arginine at position 3 of the histone. P00000602 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R17me1 P00000603 H3R17 Monomethylation Site H3R17me1 Methylation of H3R17 is catalysed by CARM1 and this in turn coactivates nuclear hormone receptor-mediated transcription suggesting that the H3R17 methylation may be involved in transcriptional activation (PMID: 15186775). P00000603 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R17me2 P00000604 H3R17 Dimethylation Site H3R17me2 CARM1 dependent methylation of H3R17 leads to the activation of E2F1 promoter indicating its role in gene activation (PMID: 18172323). H3R17me2 is important for transcriptional activation of MHC II HLA-DRA genes (PMID: 17478518). P00000604 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3R8me2 P00000605 H3R8 Dimethylation Site H3R8me2 PRMT5-dependent dimethylation of H3R8 plays a role in regulating rRNA promoter activity (PMID: 19998411). P00000605 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H4R3me1 P00000606 H4R3 Monomethylation Site H3R4me1 H4 R3 methylation plays a major role in transcriptional activation by nuclear hormone receptors. Methylation of arginine 3 by PRMT1 facilitates subsequent acetylation of H4 tails by p300 (PMID: 11387442). H4R3 methylation stimulates subsequent acetylation of H3 and H4 resulting in gene activation (PMID: 16103216). P00000606 http://www.iiserpune.ac.in/~coee/histome/enzyme_sp.php?enzyme_sp=Bifunctional%20arginine%20demethylase%20and%20lysyl-hydroxylase%20JMJD6 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Arginine_demethylases P00000611 Histone Argnine Demethylase Histone arginine demethylase JMJD6 JMJD6 JmjC domain-containing protein 6 Jumonji domain-containing protein 6 Lysyl-hydroxylase JMJD6 Peptide-lysine 5-dioxygenase JMJD6 Phosphatidylserine receptor (Protein PTDSR) jumonji domain containing 6 Only one enzyme is known to show histone arginine demethylation activity in humans. It belongs to 2-oxoglutarate (2-OG)-dependent oxygenases. The mechanism involves hydroxylation of methyl group followed by deformylation. [Source: http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Arginine_demethylases] P00000611 P00000612 Histone H1 Acetylation Site H1 Acetylation H1ac The modification of histone H1 by the addition of an acetyl group. P00000612 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1K25ac P00000613 H1K25 Acetylation Site H1K25ac histone H1 acetylation at K25 histone H1-K25 acetylation Deacetylation of H1 K25 (reported as H1K26) by SirT1 is involved in formation of repressive heterochromatin (PMID: 15469825). P00000613 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2BK16ac P00000614 H2BK16 Acetylation Site H2BK16ac H2BK16 acetylation is found at differentially methylated regions of imprinted genes (PMID: 20693536). P00000614 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2BK46ac P00000615 H2BK46 Acetylation Site H2BK46ac H2BK46 acetylation is found at differentially methylated regions of imprinted genes (PMID: 20693536). P00000615 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_biotinases P00000616 Histone Lysine Biotinase Biotin apo-protein ligase HLCS holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase) There is only a single biotinase known in humans. Its activity is cell cycle dependent. It binds to biotin and catalyses the reaction in 2 steps. First step: activation of biotin by addition of AMP to give biotinyl-5'-AMP. This step utilizes ATP as a donor. Second step: transfer to histones via removal of AMP. Deficiency of this enzymes leads to an autosomal recessive disorder called multiple carboxylase deficiency (MCD). P00000616 P00000617 Histone-Lysine N-Methyltransferase P00000617 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1K186me1 P00000619 H1K187 Methylation Site H1k186me1 Histone H1.2 K186 methylation (reported as H1K187) is cell cycle-independent (PMID: 20334638). P00000619 P00000621 H2A.Z Ubiquitination Site The modification of histone H2A.Z by addition of one or more ubiquitin groups. P00000621 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AK121ub P00000622 H2A.ZK121 Ubiquitination Site K2AK121ub Monoubiquitylated H2A.Z is enriched on the inactive X chromosome in females. H2A.Z preferentially associates with H3K4me2 and H3K4me3 in the nucleosome context. H2A.Z is associated with facultative heterochromatin, and this modification marks the fraction of H2A.Z associated with gene silencing.(PMID: 17636032). P00000622 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S171ph P00000623 H1S171 Phosphorylation Site H1S171p H1S171ph histone H1 phosphorylation at S171 histone H1S-171 phosphorylation histone H1S171 phosphorylation Phosphorylated on H1.4 during interphase and mitosis (PMID: 20439994). P00000623 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S172ph P00000624 H1S17 Phosphorylation Site H1S17p H1S17ph histone H1 phosphorylation at S17 histone H1S-17 phosphorylation" histone H1S17 phosphorylation Interphase specific phosphorylation in H1.5 (PMID: 16377619, PMID: 16083285). P00000624 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S186ph P00000625 H1S186 Phosphorylation Site H1S186p H1S186ph H1.4 serine 186 (reported as H1S187) phosphorylation is preferentially associated with active rDNA promoters and enriched at hormone response element (PMID: 20439994). P00000625 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S188ph P00000626 H1S188 Phosphorylation Site H1S188p H1S188ph Interphase specific phosphorylation in H1.5 (PMID: 16377619). P00000626 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S26ph P00000627 H1S26 Phosphorylation Site H1S26p H1S26ph Histone H1.4 serine 26 (reported as H1S27) is phosphorylated exclusively during mitosis (PMID: 20439994). Inhibits the binding of Heterochromatin protein 1 (HP1) (PMID: 16127177). P00000627 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T10ph P00000628 H1T10 Phosphorylation Site H1T10p H1T10ph Mitosis-specific phosphorylation in H1.5 (PMID: 16377619, PMID: 19136008). P00000628 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T137ph P00000629 H1T137 Phosphorylation Site H1T137p H1T137ph Mitosis-specific phosphorylation in H1.5 (PMID: 16377619, PMID: 19007248). P00000629 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T145ph P00000630 H1T145 Phosphorylation Site H1T145p H1T145ph Histone H1 T145 (reported as H1T146) is phosphorylated exclusively during mitosis (PMID: 20439994). P00000630 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T153ph P00000631 H1T153 Phosphorylation Site H1T153p H1T153ph This site is phosphorylated exclusively during mitosis (PMID: 20439994). P00000631 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T154ph P00000632 H1T154 Phosphorylation Site H1T154p H1T154ph Mitosis-specific phosphorylation in H1.5 (PMID: 16377619). P00000632 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T17ph P00000633 H1T17 Phosphorylation Site H1T17p H1T17ph This site is phosphorylated exclusively during mitosis (PMID: 20439994). P00000633 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1T30ph P00000634 H1T30 Phosphorylation Site H1T30p H1T30ph This site is phosphorylated exclusively during mitosis (PMID: 20439994). P00000634 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H1S172ph P00000635 H1S172 Phosphorylation Site H1S172p H1S172ph Phosphorylated on H1.2 during interphase and mitosis (PMID: 20439994). Exclusively phosphorylated on H1.5 during interphase (PMID: 16377619). P00000635 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AS137ph P00000636 H2AS137 Phosphorylation Site H2AS137p H2AS137ph Macro H2A is found to be enriched on inactive X chromosome but its phosphorylation at S137 leads to the exclusion of this variant from the heterochromatic region, suggesting its unique role in chromatin regulation beyond X inactivation. S137 phosphorylation is enriched during mitosis phase. Thus suggesting its role in normal cell cycle progression (PMID: 18227505). P00000636 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H2AY142ph P00000637 H2AY142 Phosphorylation Site H2AY142p H2AY142ph Tyrosine 142 phosphorylation is mediated by WSTF tyrosine kinase which has no homology to any known kinase fold. This represents a separate mechanism for DNA damage response other than S139 phosphorylation of H2A.X.(PMID: 19092802). P00000637 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3S31ph P00000638 H3S31 Phosphorylation Site H3S31p H3S31ph H3.3 S31 phosphorylation is observed only in late prometaphase and metaphase and is absent in anaphase. H3.3 S31ph is localized in distinct chromosomal regions immediately adjacent to centromeres (PMID: 15851689). P00000638 http://www.iiserpune.ac.in/~coee/histome/ptm_sp.php?ptm_sp=H3S6ph P00000639 H3S6 Phosphorylation Site H3S6p H3S6ph CENP-A Serine 6 mutant cells show delay in cytokinesis. CENP-A is an essential histone H3-like kinetochore protein incorporated specifically at active centromeres. Thus phosphorylated S6 in kinetochore plays an important role in regulation of cytokinesis (PMID: 11756469). The initial phosphorylation of CENP-A on Ser-6 during prophase is mediated by Aurora-A, but the maintenance of this residue in the phosphorylated state during prometaphase is dependent on Aurora-B and seems to require prior phosphorylation of CENP-A by Aurora-A (PMID: 14667408). P00000639 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Arginine_deiminases P00000640 Histone Arginine Deiminase Enzymes in this category include protein arginine deiminases (PADs). Protein arginine deiminases catalyse the hydrolysis of guanidinium side chains of arginine residues to form citrulline and ammonia. Five types of PADs are found in humans; namely PAD1, PAD2, PAD3, PAD4 and PAD6. Out of these PAD4 has been implicated in histone arginine deimination. P00000640 P00000641 Histone Arginine Methyltransferase P00000641 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_methyltransferases P00000642 Histone Lysine Methyltransferase Lysine methyltransferases are the most widely studied and classified writers. All of these enzymes contain the evolutionarily conserved catalytic SET [Su(var)3-9, Enhancer-of-zeste, Trithorax] domain. They catalyse the transfer of methyl groups from S-Adenosyl methionine (SAM) to e-amino group of target lysine residues by an SN-2 mechanism. There are mainly 7 important families of methyltransferases known till date. These include EZ, SET1, SET2, SMYD, SUV39, SUV4-20, RIZ as main families and SET8/PR-SET7 and SET7/9 as other families. Each family has a characteristic domain associated with SET. It could be Pre-Set, Post-set, PHD, Tudor etc. We found 30 unique SET domain containing proteins belonging to the above mentioned families and capable of histone methylation through literature. Histone marks created by these enzymes can either activate transcription (H3K4me) or repress transcription (H3K27me, H2K9me). Hence the activity of these enzymes together helps in creation of bivalent chromatin marks in order to keep genes in a poised state (activation/repression). They play important role in many cellular processes like DNA replication, cell cycle progression, cytokinesis, transcriptional regulation of Hox genes and tumour suppressor genes, DNA damage response, replication stress response, X chromosome inactivation, and energy homeostasis. Another significant contribution is the regulation of master regulators like p53 and components of NF-kB pathway. They are also involved in maintenance of chromatin structure by creating marks that recruit heterochromatin protein (HP1) in order to initiate the process of heterochromatinisation. A large amount of literature supports the role of lysine methyltransferases in cancers. Either the expression of these proteins is altered or they undergo mutations. For example MLLs and NSDs have been heavily implicated in multiple cancers like breast, lung, colorectal, different types of blood and prostate cancers. These proteins are also involved in Sotos syndrome, Huntingtons disease, Wolf-Hirschhorn syndrome and Weaver syndrome. P00000642 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_ribosylases P00000643 Histone Ribosylase Histone Lysine Ribosylase Poly (ADP-ribose) Polymerase (PARP) is a class of enzyme that catalyse the poly ADP-ribosylation of various nuclear proteins. Histones are one of the targets of these enzymes and PARP1 catalyses the transfer of ADP-ribose group from Nicotinamide adenine dinucleotide (NAD) (donor) to the lysine residue of histones or to an already exhisting poly(ADP-ribose) chain. Poly ADP-ribosylation of histones leads to change in the chromatin structure and has been shown to affect transcription regulation. P00000643 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_ubiquitinases P00000644 Histone Ubiquitinase Lysine ubiquitination is carried out by Ubiquitin ligases. The whole process requires the interplay of 3 enzymes. E1 enzyme required for activation of ubiquitin, E2 ubiquitin-conjugating enzyme for binding to ubiquitin and E3 ligase for transfer of ubiquitin from E2 to the target protein. E3 recognise the target substrate and simultaneously bind to E2 followed by the transfer of ubiquitin from E2 to substrate. E3 are classified into 2 subclasses on the basis of the domain they harbour: HECT (Homologous to E6-AP Carboxy Terminus) domain ubiquitinases that form an intermediate thioester bond with ubiquitin, hence participate in catalysis, and... RING (Really Interesting New Gene) finger domain ubiquitinases that do not take part in the catalysis but only act as a scaffold to bring E2 and target substrate in close proximity. We found, in all, 12 E3 ubiquitin ligases through literature of which except E3 ubiquitin-protein ligase HUWE1 (HECT E3) rest all are RING finger E3 ligases. Ubiquitination machinery generally targets proteins for proteosomal degradation. However, ubiquitin marks are also shown to convey specific signals and recruit other factors. E3 ubiquitin ligases are also involved in cell cycle control, DNA damage response, base excision repair mechanisms, regulation of Hox genes, heterochromatinisation, maintainance of genome integrity and as diverse functions as VDJ recombination. P00000644 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Serine/threonine/tyrosine_kinases P00000645 Histone Kinase Histone serine kinase histone threonine kinase histone tyrosine kinase Protein phosphorylation is the function of members of protein kinase superfamily. They harbour a characteristic kinase domain. This kinase domain catalyses the transfer of gamma-phosphate group from a donor like ATP/GTP, specifically to the serine, threonine or tyrosine residues of the protein substrates. There are a large number of protein kinases and their classification is difficult. P00000645 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_demethylases P00000646 Histone Lysine Demethylase Histone demethylases have important role in various cellular processes like cell cycle progression, transcriptional regulation of hox genes, nuclear hormone mediated and NF-kB signalling, p53 regulation, unperturbed mitosis, fetoplacental development, regulation of DNA replication, control of rRNA expression, DNA repair processes etc. They are also implicated in the development of various diseases and cancers like X linked mental retardation, human papilloma virus (HPV)-associated cancers, renal cancers, breast cancers, prostate cancers, blood cancers, colon cancers, brain cancers. [Source: http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_demethylases] P00000646 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_deacetylases P00000647 Histone Lysine Deacetylase Histone acetylation marks are removed by the class of enzymes named 'histone deacetylases' (HDACs). They contain a 'histone deacetylase' catalytic domain that mediates this function. They often exist as a part of multi-subunit complexes. Eighteen deacetylases are known in humans that are classified into 4 classes based on homology: Class I: HDAC 1, 2, 3 and 8 Class IIa: HDAC 4, 5, 7 and 9 Class IIb: HDAC 6 and 10 Class III: NAD-dependent deacetylase Sirtuin 1 to 7 Class IV: HDAC 11 The mechanism of catalysis is same for Class I, II and IV wherein a metal ion (Zn/Fe) present at the active site makes a coordinate bond with the oxygen of the carbonyl group and activates a water molecule with the help of nearby histidine/aspartic acid for nucleophilic attack that further causes removal of the acetyl group. Sirtuins have a rather different mechanism wherein they first bind the acetylated substrate followed by NAD+. NAD+ is converted to nicotinamide after attack of carbonyl oxygen. The intermediate formed is alpha-1'-O-alkylamidate that finally deacetylates lysine and gives 2'-O-acetyl-ADP-ribose as the product. Apart from histones, HDACs have several non-histone targets as well. Histone deacetylation is generally linked to transcriptional repression. Other functions include control of cell motility by modifying tubulin, making critical decisions during immune responses, regulation of organismal aging, DNA damage repair, synaptic plasticity. Sirt1 is an important master molecule that regulates multiple and diverse cellular functions. It also regulates p53 which itself is a master regulator. They are also suggested as biomarkers for benign teratomas. HDACs are implicated in many cancers like human pancreatic adenocarcinoma tissues, hepatocellular carnicomas, blood cancers, gastric cancers and other diseases like Werner syndrome. P00000647 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_deribosylase P00000648 Histone Deribosylase histone lysine deribosylase Poly (ADP-ribose) glycohydrolase is the only enzyme known to deribosylate histones in humans. [Source: http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_deribosylase] P00000648 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Lysine_deubiquitinases P00000649 Histone Deubiquitinase Histone Lysine deubiquitinases Ubiquitin moieties attached to the core histones are cleaved using a group of proteases called 'deubiquitinases'. These are divided into 5 major classes: Class I: Ubiquitin carboxy-terminal hydrolases (UCHs), Class II: Ubiquitin-specific proteases (USPs)/ubiquitin-specific processing proteases, Class III: Ovarian tumour proteases, Class IV: Josephin or Machado-Joseph disease protein domain proteases, and Class V: Jab1/MPN domain-associated metalloisopeptidase domain proteins. Class I to IV are cysteine peptidases and V is a zinc metalloisopeptidase. We found 5 different deubiquitinases reported to be present in humans that recognise histones as substrates. While MYSM1 and BRCC36 belong to Class V, all other members belong to Class II deubiquitinases. Deubiquitinases significantly affect transcriptional regulation, DNA damage response, cytokinesis, telomere maintainance. USP22 is an important enzyme as it has been designated as the signature molecule of Cancer stem cells. It is also known to regulate myc protein that is heavily involved in oncogenesis. P00000649 http://www.iiserpune.ac.in/~coee/histome/enzymes.php?enzyme=Serine/threonine/tyrosine_phosphatases P00000650 Histone Phosphatase Histone Serine phosphatase Histone threonine phosphatase Histone tyrosine phosphatase Proteins that catalyse the removal of phosphate groups from the target proteins are called phosphatases. They are functionally of 2 types: one that dephosphorylate serine/threonine residues; others that dephosphorylate tyrosine residues. P00000650 P00000721 Histone H2A O-GlcNAcylation Site A histone modification site where the modification is the covalent linkage of N-acetylglucosamine (GlcNAc) to a residue on histone H2A. P00000721 https://www.ncbi.nlm.nih.gov/pubmed/27615797 P00000722 H2AS40 O-GlcNAcylation Site A histone modification site where the modification is the covalent linkage of N-acetylglucosamine (GlcNAc) to a serine 40 on histone H2A. H2A-S40Gc H2AS40 O-GlcNAcylation H2AS40Gc O-linked-N-acetylglucosamine (O-GlcNAc) modification of histone H2A at Ser(40) P00000722 Sub Class Of