Review annotations to GO:0001076 'transcription factor activity, RNA polymerase II transcription factor binding'

[pgaudet]

Dear all,

For the transcription factor overhaul, we are proposing to obsolete GO:0001076 'transcription factor activity, RNA polymerase II transcription factor binding'. There are not very many annotations, and most proteins are annotated to other MF terms. Please review your annotations:

https://docs.google.com/spreadsheets/d/1NnkTeU8Ph7p5UHICsDUu94EoSsXbAhDg5lLsDsAs4Po/edit#gid=0

Impacted groups:

BHF-UCL @RLovering
ParkinsonsUK-UCL @RLovering
FlyBase @hattrill
IntAct @bmeldal
MGI @ukemi
SGD @suzialeksander
TAIR @tberardini
UniProt @ggeorghiou
WB @vanaukenk
ZFIN @sabrinatoro

There are no InterPro mappings.

Tagging @krchristie

Please fill the Google doc and remove your name from the assignees when done.

[sabrinatoro]

ZFIN annotations have been reviewed.

[RLovering]

Hi Pascale
I have tried to do this but I am not happy with the definition for one of the recommended terms : GO:0001104 RNA polymerase II transcription cofactor activity
Definition: Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.

Surprisingly I am not willing to make the assumption that a co-factor TF that binds a specific TF will also bind a basal TF.

There does not seem to be a GO term with the definition (with the text "and also with the RNAP II basal transcription machinery" and "and the basal RNAP II transcription machinery" removed and with the phrase 'specific and other regulatory or basal' added):
Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between specific and other regulatory or basal transcription factors.

Basically the expts show a regulatory TF (ie cofactor) binding a specific TF, but no evidence for the cofactor binding to basal TFs. As there could be additional proteins in this complex I am not willing to use the term:GO:0001104 RNA polymerase II transcription cofactor activity.

The alternative is to just associate the term GO:0140110 transcription regulator activity.

Please advise and I will then revise our annotations

Best

Ruth

[pgaudet]

Hi @RLovering
You're right - GO:0001104 RNA polymerase II transcription cofactor activity
is not appropriate in this case. I agree GO:0140110 transcription regulator activity is better.

Thanks, Pascale

[RLovering]

FYI GO:0140110 transcription regulator activity has a do not annotate restriction

[RLovering]

BHF annotations all updated

[ukemi]

Assigning to @krchristie for MGI.

[vanaukenk]

WB annotations reviewed

[tberardini]

TAIR annotation reviewed.

[pgarmiri]

The one UniProt annotation has be reviewed and updated.

[pgaudet]

The term is now obsolete. I cam closing this. Some groups have not looked at their annotations (or commented in the spreadsheet):
@bmeldal
@hdrabkin
@RLovering

[hdrabkin]

mgi fixed

[RLovering]

sorry ours were done in July but form not completed completely

[pgaudet]

@bmeldal can you please check the IntAct annotation ?

[bmeldal]

As for Ruth, change was made but I forgot to update the spreadsheet. Sorry.

[pgaudet]

No problem. Thanks for checking.

Pascale