PTN001236278 positive regulation of transcription by RNA polymerase II - PTHR47636

[ValWood]

• PTHR ID & PTN node:

GO:0045944 | positive regulation of transcription by RNA polymerase II | IBA with PTN001236278 , S000004680

• Sequences with problematic annotation (ID + gene/protein name): This is a member of Rpd3S/Clr6-CII complex (GO:0032221) This is a histone deacetylase complex. All other members in pombe are annotated to repression. @colinlog does this seem correct? It's a bit confusing...

[ValWood]

We should probably look at these on a call. I'm picking up PAINT inferences for pombe cph1,cph2 (S.c SCO1 ; Human PHF12) (here there is one human annotation, looked incorrect to me) https://www.uniprot.org/citations/19041327 should this be +ve reg?

and pombe clr6 (S.c RPD3; Human HDAC1 & 2) Quite a lot of annotations. Some of the human ones I spot-checked looked incorrect and the S. cerevisiae ones are really old.

Maybe @colinlog can advise on the current consensus here? Could this be 'interference'?

[pgaudet]

Hi @ValWood This is a small family with no human orthologs. The annotations were propagated from cerevisiae RCO1 https://www.yeastgenome.org/locus/S000004680 Positive regulation of transcription is citing this paper: PMC3866184

Anyway, with @colinlog we have agreed to use 'regulation of transcription' rather than positive/negative, at least for dbTFs. I dont know that this systematically applies to coTFs, maybe their function (depending on the chromatin modification they catalyze) is more easily classifiable into positive or negative regulation, but based on the paper cited (PMC3866184), I was not able to tell, they used KO's, and I am not sure of the mechanism, so I moved the annotation to 'chromatin remodeling' and 'regulation of transcription'.

@srengel Do you want to have a look at that paper?

Thanks, Pascale

[ValWood]

Just to note, this is positive regulation of meiosis specific genes. This gene negatively regulates antisense transcripts, and a lot of meiosis genes are negatively regulated by antisense transcripts so although this annotation seems odd for a repressor, it looks odd. Would we therefore end up with every repressor of antisense RNAs annotated to both +ve and -ve regulation of transcription? I guess so?

[pgaudet]

Hi @ValWood Is the "repressor of antisense RNAs" a random example, or it is relevant to this ticket? Generally, an inhibitor of an inhibitor is a positive regulator, yes @ukemi @vanaukenk

Thanks, Pascale

[ValWood]

It is relevant to this ticket. So it seems that Rpd3S/Clr6-CII complex is a corepressor, but is involved in positive and negative regulation of specific gene expression, due to it's effect on both mRNA and antisense RNA transcription. I guess this would be true for most repressors and co-repressors