gocentral
commented
14 years ago - I'm leery of using "communication" in this context, at least in the term name. Happy to use it as a synonym.
- This sounds very similar to the fairly new term 'gene looping', except that it's more narrowly defined:
[Term] id: GO:0090202 name: gene looping namespace: biological_process def: "The formation and maintenance of DNA loops that juxtapose the promoter and terminator regions of RNA polymerase II-transcribed genes." [GOC:dph, GOC:rb, GOC:tb, PMID:19933150] is_a: GO:0006325 ! chromatin organization created_by: tanyaberardini creation_date: 2009-12-18T11:56:00Z
[Term] id: GO:0090203 name: transcriptional activation by gene looping namespace: biological_process def: "The formation and maintenance of DNA loops that juxtapose the promoter and terminator regions of RNA polymerase II-transcribed genes and activate transcription from an RNA polymerase II promoter." [GOC:dph, GOC:rb, GOC:tb] synonym: "transcriptional activation by memory gene loops" RELATED [GOC:dph, GOC:rb, GOC:tb] is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter is_a: GO:0090202 ! gene looping created_by: tanyaberardini creation_date: 2009-12-18T11:58:32Z
PMID:19923429 refers to enhancer-promoter chromatin loops, so I think it would be entirely reasonable to broaden the definition of GO:0090202 to encompass looping between any parts of a gene and its regulatory regions, and add another child term, e.g. 'regulation of transcription by promoter-enhancer looping' or 'transcriptional activation by promoter-enhancer looping1 (or both; if we want the latter, we would probably also want to rename GO:0090203 to 'transcriptional activation by promoter-terminator looping').
Oh, and do you happen to know if the enhancer-promoter looping is specific to genes transcribed by RNA pol II?
Assigning to Tanya to elicit comments ;) (I'm happy to edit if my suggestions make sense.)
cheers, m
Original comment by: mah11
Another request from the UK curator pre-jamboree meeting...
PMID:15060134 shows that Drosophila Nipped-B regulates transcription via an enhancer by structurally facilitating enhancer-promoter communication. We wondered if we could have a new term to captures this aspect of long-range transcriptional regulation. See also review PMID:10508687. Not sure what the best way to capture this is...
How about: name: long-range enhancer-promoter communication namespace: biological_process def:Any process that enables promoter elements to be brought into close physical proximity with enhancer elements that lie distant from the promoter during gene activation. is_a: GO:0034401 ! chromatin organization during transcription relationship: part_of GO:0006355 ! regulation of transcription, DNA-dependent? I'm not sure if it would be helpful to have a new term for long-range regulation of transcription or regulation of transcription via enhancer - maybe we could discuss this at the jamboree?
Could we also have the three regulates terms for this please too?
Thanks, Susan
Reported by: stweedie
Original Ticket: geneontology/ontology-requests/7070