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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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PTN000271860: PAINT ADA2-related issues #1583

Closed hattrill closed 6 years ago

hattrill commented 7 years ago

For the nodes populated for PTN000271860, I am wondering whether the transcription factor terms are appropriate. This is a subunit of HAT complexes, rather than a transcription factor per se. Term: transcription factor activity, sequence-specific DNA binding There is some early evidence for interactions with transcription factors, so perhaps co-activator is ok, but it doesn't seem to feature much in current thinking.

pgaudet commented 6 years ago

Hi @hattrill It seems clear in the literature that SAGA is considered a co-factor: http://genesdev.cshlp.org/content/28/18/1999.long

There are several primary annotations; I suggest that you dispute the primary annotations; what do you think ? @Tanya AT4G16420 @srengel S000002856 (+Candida: CAL0000192402)

Thanks, Pascale

ValWood commented 6 years ago

The problem is that although SAG is considered a cofactor, it completely fits the GO def of TF in that it both 1) binds DNA (ada subunit has a DNA binding domain) and 2) Regulates transcription.

This implies that the def of trancription factor needs refining. Not all types of transctiptional regulation + DNA binding = "transcription factor"

ValWood commented 6 years ago

I'm basing this on the fact that ADa2 has a homeobox. Maybe it does not bind DNA, but for sure some chromatin remodelling type co-factors do. I always felt that something else was required in the def

krchristie commented 6 years ago

With respect to definition of "transcription factor", also remember that not all transcription factors bind DNA.

hattrill commented 6 years ago

Well, I guess it is ok - looking at enhanceosomes, etc. seems that many have HAT activity.

ValWood commented 6 years ago

I checked last night and SAGA binds to TBP and RNA pol II, so co-factor fits for this.

We still have an issue that other non co-factor chromatin remodellers also fit the DNA binding TF def .....

hattrill commented 6 years ago

And, some domains e.g. SANT-MYB, MADF-BESS and ARID domains pop up in cofactors, DNA binding TFs and remodellers.

pgaudet commented 6 years ago

@hattrill @ValWood So, can this issue be closed ? It doesnt seem to be a problem with the annotations of the family.

Thanks, Pascale

hattrill commented 6 years ago

I am ok with closing this.

srengel commented 6 years ago

seems like nothing here to do for Sc ADA2. please let me know if i have misunderstood.

pgaudet commented 6 years ago

Right, I dont think so, the annotations were right.