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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Should 'Integrator complex' and mediator complex' be part of 'DNA-directed RNA polymerase II complex'? #15979

Closed pgaudet closed 6 years ago

pgaudet commented 6 years ago

Continuing the work from #15870

@bmeldal @krchristie are 'Integrator complex' and mediator complex' part of 'DNA-directed RNA polymerase II complex'?

Thanks, Pascale

bmeldal commented 6 years ago

From https://www.ebi.ac.uk/complexportal/complex/CPX-3227:

"Plays an essential role in gene expression regulation by acting as a bridge between DNA-binding transcription factors and the RNA polymerase II (RNAPII) transcription machinery, serving as a central scaffold within the pre-initiation complex. The Mediator complex is also targeted by sequence-specific, DNA-binding transcription factors and appears to regulate RNAPII at both the initiation and elongation stages of transcription. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and unfolds to an extended conformation and partially surrounds RNAPII specifically interacting with the unphosphorylated form of its C-terminal domain. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. Reversibly associates with the CKM complex (CPX-3232, CPX-3263). Mediator lacking the CKM complex has a stimulatory effect on basal transcription. In contrast, Mediator containing the sub-complex represses basal transcription."

So, no, not part of RNAPII. Will also need to change holocomplex in our def!

bmeldal commented 6 years ago

Have you got proteins for Integrator complex? I don't think we've curated that one yet.

GO:0032039 integrator complex "A protein complex that stably associates with the C-terminus of RNA polymerase II and mediates 3'-end processing of small nuclear RNAs generated by RNA polymerase II."

So no, I'd say not part of RNAPII either. It interacts with it.

pgaudet commented 6 years ago

@ValWood I was referring to 'core mediator' GO:0070847 - this one is part of GO:0016591 DNA-directed RNA polymerase II, holoenzyme

ValWood commented 6 years ago

OK so core mediator merges into mediator? fine by me. We only use mediator.

pgaudet commented 6 years ago

I just wanted core mediator moved to NOT be a 'part of' GO:0016591 DNA-directed RNA polymerase II, holoenzyme.

I can merge core mediator and mediator, I don't know of the distinction is important.

pgaudet commented 6 years ago

integrator complex -> change parent from 'nucleoplasm part' to 'part of' some nucleus (when it's active it's mot in the nucleoplasm)

core mediator complex -> change parent from 'nucleoplasm part' to 'part of' some nucleus(when it's active it's mot in the nucleoplasm)

ValWood commented 6 years ago

https://en.wikipedia.org/wiki/Mediator_(coactivator) some subunits are not always present, and there are different modules, but I don't see the advantage in annotating a core vs holo...

ValWood commented 6 years ago

core is without the cdk module

ValWood commented 6 years ago

the cdk module is not essential but many subunits are. not sure...

pgaudet commented 6 years ago

Yeah we can leave the mediator and the core mediator separate for now. I'm just removing them from 'part of pol II holoenzyme'.

Pascale