transcription factor function enquiry

[gocentral]

I am looking at 2 terms and I can't figure out why they are not related as parent/child

1. GO:0000991 core RNA polymerase II binding transcription factor activity Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

2. GO:0001076 RNA polymerase II transcription factor binding transcription factor activity Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

Oh and another one, 990 appear to have an identical child.... GO:0000991 core RNA polymerase II binding transcription factor activity

(not that at SGD the first 2 are used to describe SPN1, and appears to be describing the same activity which is how I spotted it)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9303

[gocentral]

ignore the 3rd point/ I see the difference between 990/991 is core RNA pol vs core RNA II pol

Original comment by: ValWood

[gocentral]

From the names and defs, it looks like the difference is that 991 binds RNA pol II, whereas 1076 binds a transcription factor, i.e. something other than the polymerase.

If Spn1p binds to both the polymerase and a transcription factor, then it's correct to use both terms for it.

Original comment by: mah11

[gocentral]

Ah got it, (a bit)

I don't think that SPN1 binds to a "RNA polymerase II transcription factor" ? if not RNA polymerase II transcription factor binding transcription factor activity is still going to confuse everyone. I remember now I have made this mistake before and SGD curators have clearly done the same. Its a bit ambiguous.

If this is what it means, why isn't it sequence-specific DNA binding RNA polymerase II transcription factor binding transcription factor activity "RNA polymerase II transcription factor" does not exist in the ontology

Maybe extend the def to Interacting selectively and non-covalently with a sequence-specific DNA binding RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.

or maybe this term is capturing the fact that SPN1 interacts with SPT6 but they both bind RNA POLII so this isn't really describing a different function of SPN1, just an additional binding partner.....

If this was the case SPN1 and SPT6 would both have RNA polymerase II transcription factor binding transcription factor activity describing their binding to each other which seems a bit bonkers? Still confused......

Original comment by: ValWood

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: jl242

[gocentral]

Hi Val,

The term 991 is for transcription factor activities that bind "core RNA polymerase II".

The term 1076 is for transcription factor activities that bind a "RNA polymerase II transcription factor".

Core RNA polymerase II is not considered to be a transcription factor and an RNA polymerase II transcription factor is not considered to be core RNA polymerase. So these should not have a parent child relationship in either direction.

As for SPN1, the description on the SGD page says "Protein involved in RNA polymerase II transcription; interacts genetically or physically with RNAP II, TBP, TFIIS, and chromatin remodelling factors; central domain highly conserved throughout eukaryotes; mutations confer an Spt- phenotype", so it looks to me like it is probably binding to both RNAP II and to one or more other transcription factors at the same time, which would be pretty typical activity for a transcription factor.

-Karen

Original comment by: krchristie

[gocentral]

• status: open --> closed-invalid

Original comment by: krchristie

[gocentral]

Val, I have no idea what you mean with this bit:

I don't think that SPN1 binds to a "RNA polymerase II transcription factor" ? if not RNA polymerase II transcription factor binding transcription factor activity is still going to confuse everyone. I remember now I have made this mistake before and SGD curators have clearly done the same. Its a bit ambiguous.

Perhaps you could clarify before I try to answer.

thanks,

-Karen

Original comment by: krchristie

[gocentral]

OK I thought then that

RNA polymerase II transcription factor binding transcription factor activity was referring to a sequence specific transcription factor, but it could be any transcription factor which is NOT RNA pol II right?
I get it now...

Val

Original comment by: ValWood

[gocentral]

• status: closed-invalid --> open-invalid

Original comment by: ValWood

[gocentral]

Just to confirm, yes Val, the transcription factor being bound could be any txn factor, DNA binding or protein binding.

-Karen

Original comment by: krchristie

[gocentral]

• status: open-invalid --> closed-invalid

Original comment by: krchristie