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PTN000122628 IPR017071 #4151

Closed ValWood closed 1 year ago

ValWood commented 2 years ago

GO:0006357 | regulation of transcription by RNA polymerase II | IBA with FBgn0040273 , PTN000122628 , O00267 , 1563807 , ZDB-GENE-001207-1 , S000004470

"regulation of transcription" doesn't seem correct here.

I annotated to co-transcriptional chromatin reassembly

which is a descendant of [transcription elongation from RNA polymerase II promoter]

it is part_of this process, not regulating it

@colinlog do you agree?

(also affects IPR017071, I am filtering both annotations)

colinlog commented 2 years ago

What SPT5/4 DSIF is involved is really GO:0001111 promoter clearance from RNA polymerase II promoter See PMID: 34608338 for a recent review on this topic. The latest research results says that it does this by stabilising the largest subunit of RNA pol II against culin-mediated degradation on the promoter.

Do you have a publication for the "chromatin reassembly " part of your proposed annotation Val?

On Wed, May 11, 2022 at 7:39 AM Val Wood @.***> wrote:

  • PTHR ID & PTN node:

GO:0006357 | regulation of transcription by RNA polymerase II | IBA with FBgn0040273 , PTN000122628 , O00267 , 1563807 , ZDB-GENE-001207-1 , S000004470

"regulation of transcription" doesn't seem correct here.

I annotated to co-transcriptional chromatin reassembly

which is a descendant of [transcription elongation from RNA polymerase II promoter]

it is part_of this process, not regulating it

@colinlog https://github.com/colinlog do you agree?

(also affects IPR017071, I am filtering both annotations)

-

Type of Issue: Erroneous source or erroneous propagation, or other issue

Add the label 'high priority' if needed. Generally high priority issues affect a lot of proteins, and annotations are incorrect (as opposed to just imprecise).

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ValWood commented 2 years ago

I made this annotation because I thought we discussed that all DSIF and FACT were transcriptional chromatin reassembly (maybe I misread my notes). I used https://www.pombase.org/reference/PMID:33846633 as a placeholder because there are no annotattiond currently (I thought that this was the same thing as passage through a nucleosome), maybe I am getting really confused.

If so, what is the correct term to use for "promoter clearance" and/or should these be just "chromatin remodelling"? and which complexes should be annotated to the "co-transcriptional chromatin reassembly" term?

marcfeuermann commented 1 year ago

Many regulation terms have been annotated for this family. At the PAINT level, I've removed the propagation of the "regulation" term. Cannot do more for the moment since none of the terms you've mentioned in the discussion are available for PAINTing. Please feel free to conclude the discussion and close the issue if you think it is okay for the moment.