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Source ontology files for the Gene Ontology
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chromatin silencing at LTR #10531

Closed gocentral closed 9 years ago

gocentral commented 11 years ago

chromatin silencing at LTR

SO:0000286 pmid:21151114

Reported by: antonialock

Original Ticket: geneontology/ontology-requests/10332

gocentral commented 11 years ago

I was thinking about this some more...

Generally I think we should have new GO terms for differnet processes (different genes are involved/different pathways). There is a precedent for specifying different regions (centromere, telomere, mating type region), but the processes which operate at these locations are different. However, later once the differences are fully quantifiable it might be better to re-represent these terms to represent the mechanistic differences and put the occurs_at (SO:centromere) etc in an extension.

So, because this is "normal" RNAi machinery dependent chromatin silencing, a better way to represent this is probably "chromatin silencing by small RNA ; GO:0031048" with "occurs_at(SO:0000286)" as an extension.

The abstract says that this is histone methyltransferase independent, but I am not sure that this gene is required for canonical GO:0031048 (it is currently annotated to GO:0031048 but we should look at this annotation too). If Clr4 isn't part of the normal pathway, I think you could also put independent_of(clr4) in the extension, otherwise you might need to represent this pathway difference histone methyltransferase independent chromatin silencing by small RNA

(sorry this is slightly different from our discussion the other day!)

Val

Original comment by: ValWood

gocentral commented 11 years ago

they say that histone methylation at the centromeres helps recruiting the silencing machinery, so it's a bit of a positive feedback loop (so maybe it should be pos reg of GO:0031048 for clr4?).

Original comment by: antonialock

gocentral commented 11 years ago

and establishment and maintenance of heterochromatin formation + silencing by small rna for dcr and the others?

Original comment by: antonialock

gocentral commented 11 years ago

Original comment by: jl242

gocentral commented 11 years ago

So do you actually need any new terms then?

Original comment by: jl242

gocentral commented 11 years ago

Can we wait for Val to reply? I think she is busy preparing for someone's viva..

Original comment by: antonialock

gocentral commented 11 years ago

Its a complicated paper.... I'll read it and see if I can figure it out. It is likely we will need to converse with the authors to check, so it might take a while but it is on ,my list. Val

Original comment by: ValWood

gocentral commented 11 years ago

Original comment by: ValWood

gocentral commented 11 years ago

I don't think we need the terms. The authors are happy with the annotations http://curation.pombase.org/pombe/curs/e64102699ced97dc/ro/ turned out to be cotranscriptional gene silencing by small RNA the authors have suggested some minor changes to term which I will submit shortly

Original comment by: ValWood