def transcription factor TFIID complex

[gocentral]

TFIID complex pays a central role in core promoter recognition and (the regulation of ?) transcription initiation by PolII. TFIID is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs).

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1530":https://sourceforge.net/p/geneontology/ontology-requests/1530

[gocentral]

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Hi Val,

The 'central role in core promoter recognition' is probably sufficient. I don't think I'd include 'transcription initiation' at all, since even after RNA Pol II is bound at the promoter, 2 other factors, TFIIE and TFIIH, are still required for transcription to occur.

Would you happen to have a good reference for this?

cheers,

-Karen

Original comment by: krchristie

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• assigned_to: nobody --> kchris

Original comment by: krchristie

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I was reading PMID: 14574615 a review of RNA pol II trancription app. in S. p

The definition was sort of 'derived' from the statement

"TFIID which plays a central role in transcription initiation by Pol II, consists of TBP and multiple TBP-associated factors.

Would it be useful to reword this to keep 'transcription initiation' but reword so the 'central role' didn't apply to transcription initiation.

Anyway Karen I defer to you....

Original comment by: ValWood

[gocentral]

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I wound up looking at this term (en route to working on a neighboring term), and came up with:

A complex that binds the TATA element present within most RNA polymerase II promoters; includes the TATA-binding protein (TBP), which recognizes the TATA sequence, and several TBP-associated proteins (TAFs); the total mass is typically about 800 kDa.

Although I don't think it's essential to have process information in a component term def, it would be easy to add something about promoter recognition. Also, if TFIID binding is necessary for transcription initiation, that's consistent with an important role even if it's not sufficient. So what do you think of including something like:

'TFIID plays a central role in core promoter recognition, and its binding to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.'

m

Original comment by: mah11

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Hi Midori,

I think we have to be careful about saying "TFIID binds the TATA element", because I think TFIID is also involved in promoter recognition in TATA-less promoters. Otherwise, I like your suggestion. I think I like your suggestion about 'TFIID plays a central role in core promoter recognition', maybe even as the opening sentence.

But, I'll check on TATA-less promoters and suggest something.

thanks,

-karen

Original comment by: krchristie

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As long as it is true that TFIID binds the TATA box in promoters that have one, it's perfectly OK to say so. I'll keep the 'central role' phrase, tho probably in roughly the same position as in the earlier draft, because I'm reluctant to put process information first in a component definition (even in a case like this, where it helps explain what the complex is).

Another try, with the aim of rewording so as not to imply that TFIID is only relevant at TATA promoters:

A complex that binds the TATA element present within most RNA polymerase II promoters; includes the TATA-binding protein (TBP), which recognizes the TATA sequence, and several TBP-associated proteins (TAFs); the total mass is typically about 800 kDa. TFIID plays a central role in core promoter recognition at both TATA-containing and TATA-less promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

Let me know if you find anything to enhance or contradict this.

m

Original comment by: mah11

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Starting it off with the stuff about binding TATA still puts process info first.

How about:

A complex composed of TATA binding protein (TBP) and TBP Associated Factors (TAFs) with a total mass typically about 800 kDa. Most of the TAFs are conserved across species. In TATA- containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. However, TFIID is involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

using ISBN: 0879695501, SGD:krc, GO:mah, and whatever ref you got the molecular weight from as refs.

-Karen

Original comment by: krchristie

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> Starting it off with the stuff about binding TATA still puts process info first.

erm, no it doesn't, because TATA binding is not a process ...

but the point about whether, and where, process or function info should go in a component definition still holds. We can't really avoid some function information, because the subunits of TFIID have been named for their functions .... we run into this with a lot of component names.

Anyway, I think it could use a little more adjustment for style, but the content is (finally!) in pretty good shape. Unless this has got something garbled, I'll put it in:

A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA- containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.

m

Original comment by: mah11

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I agree, it's impossible to avoid putting process and/or function info into component defs. I misspoke, my point was really that the def should start with component info before the process or function info.

Anyway, your grammatical revisions look good to me, so feel free to put it in.

thanks,

-Karen

Original comment by: krchristie

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OK, it's in at last! Thanks for all the help.

m

Original comment by: mah11

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• labels: --> Other term-related request
• status: open --> closed-fixed

Original comment by: mah11

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• milestone: --> PomBase

Original comment by: mah11