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 1 to 100, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 1 of 3
Gene	Authority id	Mapping file id	Evidence codes
GeneACTB	AuthorityHGNC:132	Mapping file id60 NCBI file	EvidenceIEA
GeneACTL6A	AuthorityHGNC:24124	Mapping file id86 NCBI file	EvidenceIEA, TAS
GeneACTL6B	AuthorityHGNC:160	Mapping file id51412 NCBI file	EvidenceTAS
GeneAEBP2	AuthorityHGNC:24051	Mapping file id121536 NCBI file	EvidenceTAS
GeneARID1A	AuthorityHGNC:11110	Mapping file id8289 NCBI file	EvidenceTAS
GeneARID1B	AuthorityHGNC:18040	Mapping file id57492 NCBI file	EvidenceTAS
GeneARID2	AuthorityHGNC:18037	Mapping file id196528 NCBI file	EvidenceTAS
GeneARID4A	AuthorityHGNC:9885	Mapping file id5926 NCBI file	EvidenceTAS
GeneARID4B	AuthorityHGNC:15550	Mapping file id51742 NCBI file	EvidenceTAS
GeneARID5B	AuthorityHGNC:17362	Mapping file id84159 NCBI file	EvidenceTAS
GeneASH1L	AuthorityHGNC:19088	Mapping file id55870 NCBI file	EvidenceTAS
GeneASH2L	AuthorityHGNC:744	Mapping file id9070 NCBI file	EvidenceTAS
GeneATF2	AuthorityHGNC:784	Mapping file id1386 NCBI file	EvidenceTAS
GeneATF7IP	AuthorityHGNC:20092	Mapping file id55729 NCBI file	EvidenceTAS
GeneATXN7	AuthorityHGNC:10560	Mapping file id6314 NCBI file	EvidenceIEA
GeneATXN7L3	AuthorityHGNC:25416	Mapping file id56970 NCBI file	EvidenceIEA
GeneBRD1	AuthorityHGNC:1102	Mapping file id23774 NCBI file	EvidenceTAS
GeneBRD8	AuthorityHGNC:19874	Mapping file id10902 NCBI file	EvidenceIEA
GeneBRMS1	AuthorityHGNC:17262	Mapping file id25855 NCBI file	EvidenceTAS
GeneBRPF1	AuthorityHGNC:14255	Mapping file id7862 NCBI file	EvidenceTAS
GeneBRPF3	AuthorityHGNC:14256	Mapping file id27154 NCBI file	EvidenceTAS
GeneBRWD1	AuthorityHGNC:12760	Mapping file id54014 NCBI file	EvidenceTAS
GeneCARM1	AuthorityHGNC:23393	Mapping file id10498 NCBI file	EvidenceTAS
GeneCCND1	AuthorityHGNC:1582	Mapping file id595 NCBI file	EvidenceTAS
GeneCDK4	AuthorityHGNC:1773	Mapping file id1019 NCBI file	EvidenceTAS
GeneCHD3	AuthorityHGNC:1918	Mapping file id1107 NCBI file	EvidenceTAS
GeneCHD4	AuthorityHGNC:1919	Mapping file id1108 NCBI file	EvidenceTAS
GeneCLOCK	AuthorityHGNC:2082	Mapping file id9575 NCBI file	EvidenceIEA
GeneCOPRS	AuthorityHGNC:28848	Mapping file id55352 NCBI file	EvidenceTAS
GeneCREBBP	AuthorityHGNC:2348	Mapping file id1387 NCBI file	EvidenceIEA
GeneDMAP1	AuthorityHGNC:18291	Mapping file id55929 NCBI file	EvidenceIEA
GeneDNMT3A	AuthorityHGNC:2978	Mapping file id1788 NCBI file	EvidenceTAS
GeneDOT1L	AuthorityHGNC:24948	Mapping file id84444 NCBI file	EvidenceTAS
GeneDPY30	AuthorityHGNC:24590	Mapping file id84661 NCBI file	EvidenceTAS
GeneDR1	AuthorityHGNC:3017	Mapping file id1810 NCBI file	EvidenceIEA
GeneEED	AuthorityHGNC:3188	Mapping file id8726 NCBI file	EvidenceTAS
GeneEHMT1	AuthorityHGNC:24650	Mapping file id79813 NCBI file	EvidenceTAS
GeneEHMT2	AuthorityHGNC:14129	Mapping file id10919 NCBI file	EvidenceTAS
GeneELP1	AuthorityHGNC:5959	Mapping file id8518 NCBI file	EvidenceIEA
GeneELP2	AuthorityHGNC:18248	Mapping file id55250 NCBI file	EvidenceIEA
GeneELP3	AuthorityHGNC:20696	Mapping file id55140 NCBI file	EvidenceIEA
GeneELP4	AuthorityHGNC:1171	Mapping file id26610 NCBI file	EvidenceIEA
GeneELP5	AuthorityHGNC:30617	Mapping file id23587 NCBI file	EvidenceIEA
GeneELP6	AuthorityHGNC:25976	Mapping file id54859 NCBI file	EvidenceIEA
GeneENY2	AuthorityHGNC:24449	Mapping file id56943 NCBI file	EvidenceIEA
GeneEP300	AuthorityHGNC:3373	Mapping file id2033 NCBI file	EvidenceTAS
GeneEP400	AuthorityHGNC:11958	Mapping file id57634 NCBI file	EvidenceIEA
GeneEPC1	AuthorityHGNC:19876	Mapping file id80314 NCBI file	EvidenceIEA
GeneEZH2	AuthorityHGNC:3527	Mapping file id2146 NCBI file	EvidenceTAS
GeneGATAD2A	AuthorityHGNC:29989	Mapping file id54815 NCBI file	EvidenceTAS
GeneGATAD2B	AuthorityHGNC:30778	Mapping file id57459 NCBI file	EvidenceTAS
GeneGPS2	AuthorityHGNC:4550	Mapping file id2874 NCBI file	EvidenceTAS
GeneH2AB1	AuthorityHGNC:22516	Mapping file id474382 NCBI file	EvidenceTAS
GeneH2AC1	AuthorityHGNC:18729	Mapping file id221613 NCBI file	EvidenceIEA, TAS
GeneH2AC11	AuthorityHGNC:4737	Mapping file id8969 NCBI file	EvidenceIEA, TAS
GeneH2AC12	AuthorityHGNC:13671	Mapping file id85235 NCBI file	EvidenceIEA, TAS
GeneH2AC13	AuthorityHGNC:4725	Mapping file id8329 NCBI file	EvidenceIEA, TAS
GeneH2AC14	AuthorityHGNC:4727	Mapping file id8331 NCBI file	EvidenceIEA, TAS
GeneH2AC15	AuthorityHGNC:4726	Mapping file id8330 NCBI file	EvidenceIEA, TAS
GeneH2AC16	AuthorityHGNC:4730	Mapping file id8332 NCBI file	EvidenceIEA, TAS
GeneH2AC17	AuthorityHGNC:4735	Mapping file id8336 NCBI file	EvidenceIEA, TAS
GeneH2AC18	AuthorityHGNC:4736	Mapping file id8337 NCBI file	EvidenceIEA, TAS
GeneH2AC19	AuthorityHGNC:29668	Mapping file id723790 NCBI file	EvidenceIEA, TAS
GeneH2AC20	AuthorityHGNC:4738	Mapping file id8338 NCBI file	EvidenceIEA, TAS
GeneH2AC21	AuthorityHGNC:20508	Mapping file id317772 NCBI file	EvidenceIEA, TAS
GeneH2AC25	AuthorityHGNC:20507	Mapping file id92815 NCBI file	EvidenceIEA, TAS
GeneH2AC4	AuthorityHGNC:4734	Mapping file id8335 NCBI file	EvidenceIEA, TAS
GeneH2AC6	AuthorityHGNC:4733	Mapping file id8334 NCBI file	EvidenceIEA, TAS
GeneH2AC7	AuthorityHGNC:4729	Mapping file id3013 NCBI file	EvidenceIEA, TAS
GeneH2AC8	AuthorityHGNC:4724	Mapping file id3012 NCBI file	EvidenceIEA, TAS
GeneH2AJ	AuthorityHGNC:14456	Mapping file id55766 NCBI file	EvidenceTAS
GeneH2AX	AuthorityHGNC:4739	Mapping file id3014 NCBI file	EvidenceTAS
GeneH2AZ2	AuthorityHGNC:20664	Mapping file id94239 NCBI file	EvidenceTAS
GeneH2BC1	AuthorityHGNC:18730	Mapping file id255626 NCBI file	EvidenceIEA, TAS
GeneH2BC10	AuthorityHGNC:4756	Mapping file id8346 NCBI file	EvidenceIEA, TAS
GeneH2BC11	AuthorityHGNC:4761	Mapping file id8970 NCBI file	EvidenceIEA, TAS
GeneH2BC12	AuthorityHGNC:13954	Mapping file id85236 NCBI file	EvidenceIEA, TAS
GeneH2BC13	AuthorityHGNC:4748	Mapping file id8340 NCBI file	EvidenceIEA, TAS
GeneH2BC14	AuthorityHGNC:4750	Mapping file id8342 NCBI file	EvidenceIEA, TAS
GeneH2BC15	AuthorityHGNC:4749	Mapping file id8341 NCBI file	EvidenceIEA, TAS
GeneH2BC17	AuthorityHGNC:4758	Mapping file id8348 NCBI file	EvidenceIEA, TAS
GeneH2BC18	AuthorityHGNC:24700	Mapping file id440689 NCBI file	EvidenceIEA, TAS
GeneH2BC21	AuthorityHGNC:4760	Mapping file id8349 NCBI file	EvidenceIEA, TAS
GeneH2BC26	AuthorityHGNC:20514	Mapping file id128312 NCBI file	EvidenceIEA, TAS
GeneH2BC3	AuthorityHGNC:4751	Mapping file id3018 NCBI file	EvidenceIEA, TAS
GeneH2BC4	AuthorityHGNC:4757	Mapping file id8347 NCBI file	EvidenceIEA, TAS
GeneH2BC5	AuthorityHGNC:4747	Mapping file id3017 NCBI file	EvidenceIEA, TAS
GeneH2BC6	AuthorityHGNC:4753	Mapping file id8344 NCBI file	EvidenceIEA, TAS
GeneH2BC7	AuthorityHGNC:4752	Mapping file id8343 NCBI file	EvidenceIEA, TAS
GeneH2BC8	AuthorityHGNC:4746	Mapping file id8339 NCBI file	EvidenceIEA, TAS
GeneH2BC9	AuthorityHGNC:4755	Mapping file id8345 NCBI file	EvidenceIEA, TAS
GeneH3C1	AuthorityHGNC:4766	Mapping file id8350 NCBI file	EvidenceIEA, TAS
GeneH3C10	AuthorityHGNC:4775	Mapping file id8357 NCBI file	EvidenceIEA, TAS
GeneH3C11	AuthorityHGNC:4771	Mapping file id8354 NCBI file	EvidenceIEA, TAS
GeneH3C12	AuthorityHGNC:4774	Mapping file id8356 NCBI file	EvidenceIEA, TAS
GeneH3C13	AuthorityHGNC:25311	Mapping file id653604 NCBI file	EvidenceIEA, TAS
GeneH3C14	AuthorityHGNC:20503	Mapping file id126961 NCBI file	EvidenceIEA, TAS
GeneH3C15	AuthorityHGNC:20505	Mapping file id333932 NCBI file	EvidenceIEA, TAS
GeneH3C2	AuthorityHGNC:4776	Mapping file id8358 NCBI file	EvidenceIEA, TAS
GeneH3C3	AuthorityHGNC:4768	Mapping file id8352 NCBI file	EvidenceIEA, TAS

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.