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 201 to 272, in pages of 100, sorted by symbol for reading. The order carries no ranking.

Genes Reactome places in this human pathway, page 3 of 3
Gene	Authority id	Mapping file id	Evidence codes
GenePHF2	AuthorityHGNC:8920	Mapping file id5253 NCBI file	EvidenceTAS
GenePHF20	AuthorityHGNC:16098	Mapping file id51230 NCBI file	EvidenceTAS
GenePHF21A	AuthorityHGNC:24156	Mapping file id51317 NCBI file	EvidenceTAS
GenePHF8	AuthorityHGNC:20672	Mapping file id23133 NCBI file	EvidenceTAS
GenePRDM16	AuthorityHGNC:14000	Mapping file id63976 NCBI file	EvidenceTAS
GenePRDM9	AuthorityHGNC:13994	Mapping file id56979 NCBI file	EvidenceTAS
GenePRMT1	AuthorityHGNC:5187	Mapping file id3276 NCBI file	EvidenceTAS
GenePRMT3	AuthorityHGNC:30163	Mapping file id10196 NCBI file	EvidenceTAS
GenePRMT5	AuthorityHGNC:10894	Mapping file id10419 NCBI file	EvidenceTAS
GenePRMT6	AuthorityHGNC:18241	Mapping file id55170 NCBI file	EvidenceTAS
GenePRMT7	AuthorityHGNC:25557	Mapping file id54496 NCBI file	EvidenceTAS
GeneRBBP4	AuthorityHGNC:9887	Mapping file id5928 NCBI file	EvidenceTAS
GeneRBBP5	AuthorityHGNC:9888	Mapping file id5929 NCBI file	EvidenceTAS
GeneRBBP7	AuthorityHGNC:9890	Mapping file id5931 NCBI file	EvidenceTAS
GeneRCOR1	AuthorityHGNC:17441	Mapping file id23186 NCBI file	EvidenceTAS
GeneRELA	AuthorityHGNC:9955	Mapping file id5970 NCBI file	EvidenceTAS
GeneREST	AuthorityHGNC:9966	Mapping file id5978 NCBI file	EvidenceTAS
GeneRIOX2	AuthorityHGNC:19441	Mapping file id84864 NCBI file	EvidenceTAS
GeneRPS2	AuthorityHGNC:10404	Mapping file id6187 NCBI file	EvidenceTAS
GeneRUVBL1	AuthorityHGNC:10474	Mapping file id8607 NCBI file	EvidenceIEA
GeneRUVBL2	AuthorityHGNC:10475	Mapping file id10856 NCBI file	EvidenceIEA
GeneSAP130	AuthorityHGNC:29813	Mapping file id79595 NCBI file	EvidenceIEA
GeneSAP18	AuthorityHGNC:10530	Mapping file id10284 NCBI file	EvidenceTAS
GeneSAP30	AuthorityHGNC:10532	Mapping file id8819 NCBI file	EvidenceTAS
GeneSAP30L	AuthorityHGNC:25663	Mapping file id79685 NCBI file	EvidenceTAS
GeneSETD1A	AuthorityHGNC:29010	Mapping file id9739 NCBI file	EvidenceTAS
GeneSETD1B	AuthorityHGNC:29187	Mapping file id23067 NCBI file	EvidenceTAS
GeneSETD2	AuthorityHGNC:18420	Mapping file id29072 NCBI file	EvidenceTAS
GeneSETD3	AuthorityHGNC:20493	Mapping file id84193 NCBI file	EvidenceTAS
GeneSETD6	AuthorityHGNC:26116	Mapping file id79918 NCBI file	EvidenceTAS
GeneSETD7	AuthorityHGNC:30412	Mapping file id80854 NCBI file	EvidenceTAS
GeneSETDB1	AuthorityHGNC:10761	Mapping file id9869 NCBI file	EvidenceTAS
GeneSETDB2	AuthorityHGNC:20263	Mapping file id83852 NCBI file	EvidenceTAS
GeneSGF29	AuthorityHGNC:25156	Mapping file id112869 NCBI file	EvidenceIEA
GeneSMARCA2	AuthorityHGNC:11098	Mapping file id6595 NCBI file	EvidenceTAS
GeneSMARCA4	AuthorityHGNC:11100	Mapping file id6597 NCBI file	EvidenceTAS
GeneSMARCB1	AuthorityHGNC:11103	Mapping file id6598 NCBI file	EvidenceTAS
GeneSMARCC1	AuthorityHGNC:11104	Mapping file id6599 NCBI file	EvidenceTAS
GeneSMARCC2	AuthorityHGNC:11105	Mapping file id6601 NCBI file	EvidenceTAS
GeneSMARCD1	AuthorityHGNC:11106	Mapping file id6602 NCBI file	EvidenceTAS
GeneSMARCD2	AuthorityHGNC:11107	Mapping file id6603 NCBI file	EvidenceTAS
GeneSMARCD3	AuthorityHGNC:11108	Mapping file id6604 NCBI file	EvidenceTAS
GeneSMARCE1	AuthorityHGNC:11109	Mapping file id6605 NCBI file	EvidenceTAS
GeneSMYD2	AuthorityHGNC:20982	Mapping file id56950 NCBI file	EvidenceTAS
GeneSMYD3	AuthorityHGNC:15513	Mapping file id64754 NCBI file	EvidenceTAS
GeneSUDS3	AuthorityHGNC:29545	Mapping file id64426 NCBI file	EvidenceTAS
GeneSUPT20H	AuthorityHGNC:20596	Mapping file id55578 NCBI file	EvidenceIEA
GeneSUPT3H	AuthorityHGNC:11466	Mapping file id8464 NCBI file	EvidenceIEA
GeneSUPT7L	AuthorityHGNC:30632	Mapping file id9913 NCBI file	EvidenceIEA
GeneSUV39H1	AuthorityHGNC:11479	Mapping file id6839 NCBI file	EvidenceTAS
GeneSUV39H2	AuthorityHGNC:17287	Mapping file id79723 NCBI file	EvidenceTAS
GeneSUZ12	AuthorityHGNC:17101	Mapping file id23512 NCBI file	EvidenceTAS
GeneTADA1	AuthorityHGNC:30631	Mapping file id117143 NCBI file	EvidenceIEA
GeneTADA2A	AuthorityHGNC:11531	Mapping file id6871 NCBI file	EvidenceIEA
GeneTADA2B	AuthorityHGNC:30781	Mapping file id93624 NCBI file	EvidenceIEA
GeneTADA3	AuthorityHGNC:19422	Mapping file id10474 NCBI file	EvidenceIEA
GeneTAF10	AuthorityHGNC:11543	Mapping file id6881 NCBI file	EvidenceIEA
GeneTAF12	AuthorityHGNC:11545	Mapping file id6883 NCBI file	EvidenceIEA
GeneTAF5L	AuthorityHGNC:17304	Mapping file id27097 NCBI file	EvidenceIEA
GeneTAF6L	AuthorityHGNC:17305	Mapping file id10629 NCBI file	EvidenceIEA
GeneTAF9	AuthorityHGNC:11542	Mapping file id6880 NCBI file	EvidenceIEA
GeneTBL1X	AuthorityHGNC:11585	Mapping file id6907 NCBI file	EvidenceTAS
GeneTBL1XR1	AuthorityHGNC:29529	Mapping file id79718 NCBI file	EvidenceTAS
GeneTRRAP	AuthorityHGNC:12347	Mapping file id8295 NCBI file	EvidenceIEA
GeneUSP22	AuthorityHGNC:12621	Mapping file id23326 NCBI file	EvidenceIEA
GeneUTY	AuthorityHGNC:12638	Mapping file id7404 NCBI file	EvidenceTAS
GeneVPS72	AuthorityHGNC:11644	Mapping file id6944 NCBI file	EvidenceIEA
GeneWDR5	AuthorityHGNC:12757	Mapping file id11091 NCBI file	EvidenceIEA, TAS
GeneWDR77	AuthorityHGNC:29652	Mapping file id79084 NCBI file	EvidenceTAS
GeneYEATS2	AuthorityHGNC:25489	Mapping file id55689 NCBI file	EvidenceIEA
GeneYEATS4	AuthorityHGNC:24859	Mapping file id8089 NCBI file	EvidenceIEA
GeneZZZ3	AuthorityHGNC:24523	Mapping file id26009 NCBI file	EvidenceIEA

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.