Query GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding

[pgaudet]

Hi @krchristie

What proteins interact with the RNA polymerase II core promoter? I am looking at annotations to 'GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding' and it seems we have many DNA binding transcription factors annotated to this term. Can you please have a look ?

Thanks, Pascale

[krchristie]

DNA binding General Transcription Factors, i.e. GTFs such as TFIID, bind in the core promoter. The majority of the "specific" TFs probably bind in the area proximal to the core promoter, not the core promoter itself. I'll take a look @pgaudet

[pgaudet]

Hi @krchristie just checking if you had time to look at this.

Thanks, Pascale

[krchristie]

Hi @pgaudet - Is this ticket still something you are interested in pursuing?

I took a really quick look today at the 57 experimental annotations, and categorized things as a GTF, histone, histone modifier, holoenzyme, mediator, or possible specific TF just by eye looking at the gene names. The number of things that are clearly labeled as mediator subunits, or that I don't recognize as GTFs and thus seem likely to be specific TFs suggests that an annotation review of the annotations made to this term might be useful.

The table with my categories and the counts of experimental annotations is below. But I wanted to check with you if this ticket is still current before I do anything else.

Thanks,

-Karen

Category	# annotations
GTF	10
histone	4
histone modifier	2
holoenzyme	4
mediator	17
specific TF?	20
	57

[pgaudet]

Thanks @krchristie , this is very useful.

I'll open an annotation review ticket. (Note to self: The manual annotations are here: https://docs.google.com/spreadsheets/d/1Xfq61ALrCoQB1VS6Z4639I0Dr87m6STGnr9q7An--Fo/edit#gid=0

I need to first merge proximal/distal promoter binding).

[krchristie]

@pgaudet - I've gone ahead and reviewed one paper because the combination of annotations to this term for mouse seemed odd. I have deleted all of them and marked them in the spreadsheet you linked to above.

[krchristie]

@pgaudet - added you to the assignees list so it stays on your radar to make an annotation review ticket when you're ready

[colinlog]

I expect to have a rather comprehensive listing of the promoter-associated protein complexes in hand in June 2020. To this end we will use existing EBI and other on-line and the review "Koster, M.J., B. Snel, and H.T. Timmers, Genesis of chromatin and transcription dynamics in the origin of species. Cell, 2015. 161(4): p. 724-36." as starting point. Happy to hear of other scientists so as to join efforts, if desired.