Pathway Human Homo sapiens

Chromatin modifying enzymes

R-HSA-3247509 in Reactome release 97: under Chromatin organization, with 272 genes placed in it by the mapping files and 5 child pathways in the hierarchy.

The same number in the other species

Reactome writes the mouse and rat events it infers from a human pathway under the human number with the species token. A door opens only where that species' own list in this release holds the id: R-MMU-3247509 (mouse), R-RNO-3247509 (rat). Whether the event was inferred from this one is what the record says.

The record
The genes
Parents and children

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This page reads the pathway's record from its source while you read the rest; with scripts off the card stays at its loading line. Reload with scripts on to see it, or open the source's own page from the link in the card.

01The record

Reactome's own record of this pathway

What this tells you

The pathway list, the hierarchy and the genes on this page are read from the files Reactome publishes for Reactome release 97, built into this site on 2026-09-09: the pathway list, the hierarchy relationship file and the two gene mapping files. The record card is the one live read, Reactome's own record of this pathway.

Reactome's download page describes the mapping files: Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. [R13] The gene list here is the all-levels mapping of NCBI Gene ids, filled from the all-levels mapping of Ensembl ids where the NCBI file has no row for a gene; each row names which file it came from by the shape of its source id. Each row carries the evidence codes the file writes for it, as written and unranked, and both where the file writes both; no page of Reactome's documentation the survey read defines the codes, so this page does not expand them. A gene id the identity files do not name is kept as the source's own id with no door rather than turned into a symbol.

On citing what a search finds, Reactome says: It should be remembered that while we strive to contain the most current and accurate data, Reactome should not be used in citations where other primary sources of information are available. [R12] The record card prints the literature Reactome attaches to a curated pathway for that reason. The data are public domain: All data in the Reactome database and files derived from that data are licensed under the Creative Commons Public Domain Dedication (CC0). User may copy, modify, and distribute these data, even for commercial purposes, without asking for permission. Attribution is encouraged but not required. [R10] The pathway illustrations are licensed apart, under CC BY 4.0, and none is shown here.

A gene on this list is one Reactome places in this pathway in this release, and that is all the row says: it does not say the gene is expressed in a tissue or associated with a disease, which are the other two explorers' questions, read from other sources. Reactome's papers of record are [R01] [R02].

[R01] Ragueneau E, Gong C, Sinquin P, Sevilla C, Beavers D, Grentner A, et al. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Research 54:D673-D681. PMID 41251150, doi 10.1093/nar/gkaf1223.
[R02] Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, et al. (2024). The Reactome Pathway Knowledgebase 2024. Nucleic Acids Research 52:D672-D678. PMID 37941124, doi 10.1093/nar/gkad1025.
[R10] Reactome, reactome.org. License Agreement. https://reactome.org/license, read 2026-09-09.
[R12] Reactome, reactome.org. Citing us. https://reactome.org/cite, read 2026-09-09.
[R13] Reactome, reactome.org. Download. https://reactome.org/download-data, read 2026-09-09.

Stable id: R-HSA-3247509.6
Class: Pathway
Species: Homo sapiens (human)
Inferred: no: a curated human pathway
Disease pathway: no
Released: 2013-12-04
Last updated: 2021-09-15
Events inside: 9, counted from the record

Eukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect it from damage. Access to DNA is achieved by highly regulated local chromatin decondensation.

The 'building block' of chromatin is the nucleosome. This contains ~150 bp of DNA wrapped around a histone octamer which consists of two each of the core histones H2A, H2B, H3 and H4 in a 1.65 left-handed superhelical turn (Luger et al. 1997, Andrews & Luger 2011).

Most organisms have multiple genes encoding the major histone proteins. The replication-dependent genes for the five histone proteins are clustered together in the genome in all metazoans. Human replication-dependent histones occur in a large cluster on chromosome 6 termed HIST1, a smaller cluster HIST2 on chromosome 1q21, and a third small cluster HIST3 on chromosome 1q42 (Marzluff et al. 2002). Histone genes are named systematically according to their cluster and location within the cluster.

The 'major' histone genes are expressed primarily during the S phase of the cell cycle and code for the bulk of cellular histones. Histone variants are usually present as single-copy genes that are not restricted in their expression to S phase, contain introns and are often polyadenylated (Old & Woodland 1984). Some variants have significant differences in primary sequence and distinct biophysical characteristics that are thought to alter the properties of nucleosomes. Others localize to specific regions of the genome. Some variants can exchange with pre-existing major histones during development and differentiation, referred to as replacement histones (Kamakaka & Biggins 2005). These variants can become the predominant species in differentiated cells (Pina & Suau 1987, Wunsch et al. 1991). Histone variants may have specialized functions in regulating chromatin dynamics.

The H2A histone family has the highest sequence divergence and largest number of variants. H2A.Z and H2A.XH2A are considered 'universal variants', found in almost all organisms (Talbert & Henikoff 2010). Variants differ mostly in the C-terminus, including the docking domain, implicated in interactions with the (H3-H4)x2 tetramer within the nucleosome, and in the L1 loop, which is the interaction interface of H2A-H2B dimers (Bonisch & Hake 2012). Canonical H2A proteins are expressed almost exclusively during S-phase. There are several nearly identical variants (Marzluff et al. 2002). No functional specialization of these canonical H2A isoforms has been demonstrated (Bonisch & Hake 2012). Reversible histone modifications such as acetylation and methylation regulate transcription from genomic DNA, defining the 'readability' of genes in specific tissues (Kouzarides 2007, Marmorstein & Trievel 2009, Butler et al. 2012).

N.B. The coordinates of post-translational modifications represented here follow Reactome standardized naming, which includes the UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed; therefore the coordinates of post-translated histone residues described here are frequently +1 when compared with the literature. For more information on Reactome's standards for naming pathway events, the molecules that participate in them and representation of post-translational modifications, please refer to Naming Conventions on the Reactome Wiki or Jupe et al. 2014.

Literature Reactome attaches

Reactome's record attaches no literature to this pathway.

Reactome's record lists 14 orthologous events, R-RNO-3247509 (Rattus norvegicus), R-MMU-3247509 (Mus musculus) among the species this site serves, and 12 in species this site opens no page for.

Reactome ContentService, this pathway's record · Reactome v97 · read 2026-10-02 ET · Reactome pathway browser"Chromatin modifying enzymes". Reactome, release 97, https://reactome.org/PathwayBrowser/#/R-HSA-3247509 with StableID: R-HSA-3247509.6 (accessed 2026-10-02 ET). Reactome version 97 (CC0).

Reading this pathway's record from Reactome (the pathway record).Still reading. A first read of a pathway can take a while; this page waits up to 35 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.

02The genes

Genes Reactome places in this human pathway

The mapping files place 272 genes in this human pathway; showing 101 to 200, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 2 of 3
Gene	Authority id	Mapping file id	Evidence codes
GeneH3C4	AuthorityHGNC:4767	Mapping file id8351 NCBI file	EvidenceIEA, TAS
GeneH3C6	AuthorityHGNC:4769	Mapping file id8353 NCBI file	EvidenceIEA, TAS
GeneH3C7	AuthorityHGNC:4773	Mapping file id8968 NCBI file	EvidenceIEA, TAS
GeneH3C8	AuthorityHGNC:4772	Mapping file id8355 NCBI file	EvidenceIEA, TAS
GeneH4C1	AuthorityHGNC:4781	Mapping file id8359 NCBI file	EvidenceIEA, TAS
GeneH4C11	AuthorityHGNC:4785	Mapping file id8363 NCBI file	EvidenceIEA, TAS
GeneH4C12	AuthorityHGNC:4784	Mapping file id8362 NCBI file	EvidenceIEA, TAS
GeneH4C13	AuthorityHGNC:4791	Mapping file id8368 NCBI file	EvidenceIEA, TAS
GeneH4C14	AuthorityHGNC:4794	Mapping file id8370 NCBI file	EvidenceIEA, TAS
GeneH4C15	AuthorityHGNC:29607	Mapping file id554313 NCBI file	EvidenceIEA, TAS
GeneH4C16	AuthorityHGNC:20510	Mapping file id121504 NCBI file	EvidenceIEA, TAS
GeneH4C2	AuthorityHGNC:4789	Mapping file id8366 NCBI file	EvidenceIEA, TAS
GeneH4C3	AuthorityHGNC:4787	Mapping file id8364 NCBI file	EvidenceIEA, TAS
GeneH4C4	AuthorityHGNC:4782	Mapping file id8360 NCBI file	EvidenceIEA, TAS
GeneH4C5	AuthorityHGNC:4790	Mapping file id8367 NCBI file	EvidenceIEA, TAS
GeneH4C6	AuthorityHGNC:4783	Mapping file id8361 NCBI file	EvidenceIEA, TAS
GeneH4C8	AuthorityHGNC:4788	Mapping file id8365 NCBI file	EvidenceIEA, TAS
GeneH4C9	AuthorityHGNC:4793	Mapping file id8294 NCBI file	EvidenceIEA, TAS
GeneHAT1	AuthorityHGNC:4821	Mapping file id8520 NCBI file	EvidenceTAS
GeneHCFC1	AuthorityHGNC:4839	Mapping file id3054 NCBI file	EvidenceTAS
GeneHDAC1	AuthorityHGNC:4852	Mapping file id3065 NCBI file	EvidenceTAS
GeneHDAC10	AuthorityHGNC:18128	Mapping file id83933 NCBI file	EvidenceTAS
GeneHDAC2	AuthorityHGNC:4853	Mapping file id3066 NCBI file	EvidenceTAS
GeneHDAC3	AuthorityHGNC:4854	Mapping file id8841 NCBI file	EvidenceTAS
GeneHDAC8	AuthorityHGNC:13315	Mapping file id55869 NCBI file	EvidenceTAS
GeneHMG20B	AuthorityHGNC:5002	Mapping file id10362 NCBI file	EvidenceTAS
GeneING3	AuthorityHGNC:14587	Mapping file id54556 NCBI file	EvidenceIEA
GeneING4	AuthorityHGNC:19423	Mapping file id51147 NCBI file	EvidenceTAS
GeneING5	AuthorityHGNC:19421	Mapping file id84289 NCBI file	EvidenceTAS
GeneJADE1	AuthorityHGNC:30027	Mapping file id79960 NCBI file	EvidenceTAS
GeneJADE2	AuthorityHGNC:22984	Mapping file id23338 NCBI file	EvidenceTAS
GeneJADE3	AuthorityHGNC:22982	Mapping file id9767 NCBI file	EvidenceTAS
GeneJAK2	AuthorityHGNC:6192	Mapping file id3717 NCBI file	EvidenceTAS
GeneJMJD6	AuthorityHGNC:19355	Mapping file id23210 NCBI file	EvidenceTAS
GeneKANSL1	AuthorityHGNC:24565	Mapping file id284058 NCBI file	EvidenceTAS
GeneKANSL2	AuthorityHGNC:26024	Mapping file id54934 NCBI file	EvidenceTAS
GeneKANSL3	AuthorityHGNC:25473	Mapping file id55683 NCBI file	EvidenceTAS
GeneKAT14	AuthorityHGNC:15904	Mapping file id57325 NCBI file	EvidenceIEA
GeneKAT2A	AuthorityHGNC:4201	Mapping file id2648 NCBI file	EvidenceIEA
GeneKAT2B	AuthorityHGNC:8638	Mapping file id8850 NCBI file	EvidenceIEA
GeneKAT5	AuthorityHGNC:5275	Mapping file id10524 NCBI file	EvidenceIEA
GeneKAT6A	AuthorityHGNC:13013	Mapping file id7994 NCBI file	EvidenceTAS
GeneKAT6B	AuthorityHGNC:17582	Mapping file id23522 NCBI file	EvidenceTAS
GeneKAT7	AuthorityHGNC:17016	Mapping file id11143 NCBI file	EvidenceTAS
GeneKAT8	AuthorityHGNC:17933	Mapping file id84148 NCBI file	EvidenceTAS
GeneKDM1A	AuthorityHGNC:29079	Mapping file id23028 NCBI file	EvidenceTAS
GeneKDM1B	AuthorityHGNC:21577	Mapping file id221656 NCBI file	EvidenceTAS
GeneKDM2A	AuthorityHGNC:13606	Mapping file id22992 NCBI file	EvidenceTAS
GeneKDM2B	AuthorityHGNC:13610	Mapping file id84678 NCBI file	EvidenceTAS
GeneKDM3A	AuthorityHGNC:20815	Mapping file id55818 NCBI file	EvidenceTAS
GeneKDM3B	AuthorityHGNC:1337	Mapping file id51780 NCBI file	EvidenceTAS
GeneKDM4A	AuthorityHGNC:22978	Mapping file id9682 NCBI file	EvidenceTAS
GeneKDM4B	AuthorityHGNC:29136	Mapping file id23030 NCBI file	EvidenceTAS
GeneKDM4C	AuthorityHGNC:17071	Mapping file id23081 NCBI file	EvidenceTAS
GeneKDM4D	AuthorityHGNC:25498	Mapping file id55693 NCBI file	EvidenceTAS
GeneKDM5A	AuthorityHGNC:9886	Mapping file id5927 NCBI file	EvidenceTAS
GeneKDM5B	AuthorityHGNC:18039	Mapping file id10765 NCBI file	EvidenceTAS
GeneKDM5C	AuthorityHGNC:11114	Mapping file id8242 NCBI file	EvidenceTAS
GeneKDM5D	AuthorityHGNC:11115	Mapping file id8284 NCBI file	EvidenceTAS
GeneKDM6A	AuthorityHGNC:12637	Mapping file id7403 NCBI file	EvidenceTAS
GeneKDM6B	AuthorityHGNC:29012	Mapping file id23135 NCBI file	EvidenceTAS
GeneKDM7A	AuthorityHGNC:22224	Mapping file id80853 NCBI file	EvidenceTAS
GeneKMT2A	AuthorityHGNC:7132	Mapping file id4297 NCBI file	EvidenceTAS
GeneKMT2B	AuthorityHGNC:15840	Mapping file id9757 NCBI file	EvidenceTAS
GeneKMT2C	AuthorityHGNC:13726	Mapping file id58508 NCBI file	EvidenceTAS
GeneKMT2D	AuthorityHGNC:7133	Mapping file id8085 NCBI file	EvidenceTAS
GeneKMT5A	AuthorityHGNC:29489	Mapping file id387893 NCBI file	EvidenceTAS
GeneKMT5B	AuthorityHGNC:24283	Mapping file id51111 NCBI file	EvidenceTAS
GeneKMT5C	AuthorityHGNC:28405	Mapping file id84787 NCBI file	EvidenceTAS
GeneMBD3	AuthorityHGNC:6918	Mapping file id53615 NCBI file	EvidenceTAS
GeneMBIP	AuthorityHGNC:20427	Mapping file id51562 NCBI file	EvidenceIEA
GeneMCRS1	AuthorityHGNC:6960	Mapping file id10445 NCBI file	EvidenceTAS
GeneMEAF6	AuthorityHGNC:25674	Mapping file id64769 NCBI file	EvidenceIEA, TAS
GeneMECOM	AuthorityHGNC:3498	Mapping file id2122 NCBI file	EvidenceTAS
GeneMORF4L1	AuthorityHGNC:16989	Mapping file id10933 NCBI file	EvidenceIEA
GeneMORF4L2	AuthorityHGNC:16849	Mapping file id9643 NCBI file	EvidenceIEA
GeneMRGBP	AuthorityHGNC:15866	Mapping file id55257 NCBI file	EvidenceIEA
GeneMSL1	AuthorityHGNC:27905	Mapping file id339287 NCBI file	EvidenceTAS
GeneMSL2	AuthorityHGNC:25544	Mapping file id55167 NCBI file	EvidenceTAS
GeneMSL3	AuthorityHGNC:7370	Mapping file id10943 NCBI file	EvidenceTAS
GeneMTA1	AuthorityHGNC:7410	Mapping file id9112 NCBI file	EvidenceTAS
GeneMTA2	AuthorityHGNC:7411	Mapping file id9219 NCBI file	EvidenceTAS
GeneMTA3	AuthorityHGNC:23784	Mapping file id57504 NCBI file	EvidenceTAS
GeneNCOA1	AuthorityHGNC:7668	Mapping file id8648 NCBI file	EvidenceTAS
GeneNCOA2	AuthorityHGNC:7669	Mapping file id10499 NCBI file	EvidenceTAS
GeneNCOR1	AuthorityHGNC:7672	Mapping file id9611 NCBI file	EvidenceTAS
GeneNCOR2	AuthorityHGNC:7673	Mapping file id9612 NCBI file	EvidenceTAS
GeneNFKB1	AuthorityHGNC:7794	Mapping file id4790 NCBI file	EvidenceTAS
GeneNFKB2	AuthorityHGNC:7795	Mapping file id4791 NCBI file	EvidenceTAS
GeneNSD1	AuthorityHGNC:14234	Mapping file id64324 NCBI file	EvidenceTAS
GeneNSD2	AuthorityHGNC:12766	Mapping file id7468 NCBI file	EvidenceTAS
GeneNSD3	AuthorityHGNC:12767	Mapping file id54904 NCBI file	EvidenceTAS
GeneOGT	AuthorityHGNC:8127	Mapping file id8473 NCBI file	EvidenceTAS
GenePADI1	AuthorityHGNC:18367	Mapping file id29943 NCBI file	EvidenceTAS
GenePADI2	AuthorityHGNC:18341	Mapping file id11240 NCBI file	EvidenceTAS
GenePADI3	AuthorityHGNC:18337	Mapping file id51702 NCBI file	EvidenceTAS
GenePADI4	AuthorityHGNC:18368	Mapping file id23569 NCBI file	EvidenceTAS
GenePADI6	AuthorityHGNC:20449	Mapping file id353238 NCBI file	EvidenceTAS
GenePAX3	AuthorityHGNC:8617	Mapping file id5077 NCBI file	EvidenceTAS
GenePBRM1	AuthorityHGNC:30064	Mapping file id55193 NCBI file	EvidenceTAS

Evidence codes on this page: IEA, TAS, as the mapping file writes them; a row carrying two was written twice by the file, once under each. The mapping file id says which file placed the gene: an NCBI Gene id from NCBI2Reactome_All_Levels.txt, an Ensembl gene id from Ensembl2Reactome_All_Levels.txt. The two files can disagree about a code, so a row's codes are the one file's view. Measured by this site's build over this release on 2026-09-09: of the 138,908 human pathway-gene pairs both files place, 207 (0.149 per cent, over 47 genes) carry TAS in the Ensembl file where the NCBI rows carry IEA alone.

Reactome mapping files, the human rows for this pathway · Reactome release 97 · read 2026-09-09 · Reactome downloads"NCBI2Reactome_All_Levels.txt" and "Ensembl2Reactome_All_Levels.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.

03The hierarchy

Parents and children in this release's hierarchy

Parents

Chromatin organizationR-HSA-4839726380 genes

Children

Reactome's hierarchy is a graph rather than a tree: a pathway can sit under more than one parent, and the gene counts are each pathway's own placements at every level under it, so a parent's count is not the sum of its children's.

Reactome, the human pathway list and hierarchy relationship file · Reactome release 97 · read 2026-09-09 · Reactome downloads"ReactomePathways.txt" and "ReactomePathwaysRelation.txt", Reactome, release 97, https://reactome.org/download-data/ (date of access 2026-09-09). Data CC0; attribution encouraged.