cis_regulatory_module
SO:0000727
Definition: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.
Comments and references
Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.
Definition references: PMID:19660565, SO:SG
Synonyms
| Scope | Value |
|---|---|
| exact | CRM |
| exact | TF module |
| exact | cis regulatory module |
| exact | transcription factor module |
Identifiers and subsets
Accession: SO:0000727
Persistent URL: http://purl.obolibrary.org/obo/SO_0000727
Alternate IDs: None
Subsets: SOFA
Cross references: None
History summary
Term history is reconstructed from the Git-era ontology files by comparing ontology classes across revisions. Earlier SVN-era changes will be added at a future date.
First seen in Git-era editable history: 2016-12-05 in commit 92e3cae
Most recent Git-era change: 2021-02-16 in commit 7777cdf
Number of changes: 8
Ontology neighborhood diagram
Relationships
Parents
Children
http://purl.obolibrary.org/obo/so#part_of (incoming)
Change history
This timeline summarizes changes identified in SO’s GitHub commit history, including updates to labels, definitions, parent terms, synonyms, subsets, and obsoletion status. It is a best-effort reconstruction and may not include every change to a term. Since only history from GitHub is included at the moment, any term added before the migration from SVN to Git will show as being created in 2016. This will be addressed once SVN history is incorporated.
| Date | Change | Summary | Evidence |
|---|---|---|---|
| 2021-02-16 | definition changed | Definition updated Before: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. After: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs. | 7777cdf#534 |
| 2021-02-08 | synonym added | Synonym added: CRM Scope: exact | 9fa74b8#526 |
| 2021-02-08 | label changed | Label changed from CRM to cis_regulatory_module Before: CRM After: cis_regulatory_module | 9fa74b8#526 |
| 2021-01-21 | definition changed | Definition updated Before: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the basal promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. After: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. | 415172f |
| 2020-11-10 | definition changed | Definition updated Before: A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. After: A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the basal promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. | c421726 |
| 2020-11-09 | definition changed | Definition updated Before: A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. After: A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. | 442c88d |
| 2020-08-13 | edited | Term stanza touched in repository history | 56fcc6a |
| 2016-12-05 | created | Term introduced into the editable ontology history Initial label: CRM Initial definition captured. Initial parent: SO:0001055 | 92e3cae |