NTR: RNA polymerase II transcription initiation surveillance

[sylvainpoux]

Hi GO,
I would need a new term for a transcription elongation quality control process. The integrator complex mediates transcription termination of transcripts that are unfavorably configured for transcriptional elongation.

Thanks

Sylvain

Term: RNA polymerase II transcription elongation surveillance
Definition: A process that promotes premature RNA polymerase II transcription termination of transcripts that are unfavorably configured for transcriptional elongation.
child of GO:0006369 termination of RNA polymerase II transcription
child of GO:0034243; P:regulation of transcription elongation by RNA polymerase II 
PubMed=33385327
PubMed=34762484

See updated request here: #29516 (comment)

[raymond91125]

@sylvainpoux I collected related issues into a Project https://github.com/orgs/geneontology/projects/228 to help coordinate discussions and actions. Please let me know if there are other tickets that should be included. Thanks.

[sylvainpoux]

Hi @raymond91125, thanks for the information. For the moment I don't need more terms. The only issue is that I 'store' a lot of curation work waiting for new terms. If the discussion takes long, it will be difficult for me to keep up with curation work and GO-CAM models that are pending.

Thanks

Sylvain

[raymond91125]

Understood. I've made terms for the INTAC complex and integrator complex assembly. For the process terms, I think the decision has wider implications. I will reach out to @pgaudet for prioritization. Apologies for the delay.

Hi @raymond91125, thanks for the information. For the moment I don't need more terms. The only issue is that I 'store' a lot of curation work waiting for new terms. If the discussion takes long, it will be difficult for me to keep up with curation work and GO-CAM models that are pending.

Thanks

Sylvain

[sylvainpoux]

Dear all,

Please find some updated version following our meeting with @pgaudet and @colinlog

Name: RNA polymerase II transcription initiation surveillance
Definition: A process that promotes premature RNA polymerase II transcription termination
of transcripts that are unfavorably configured for transcriptional elongation.
Child of GO:0006367 transcription initiation at RNA polymerase II promoter
PubMed=33385327
PubMed=34762484

Thanks

Sylvain

[ValWood]

Can I suggest some changes? I have been working on transcription vs surveillance (ontology and curation) for the past year or so. I haven't proposed many changes yet because there is a lot to consider, and I still have reviews to read and papers to curate. However, the current ontology structure is largely correct.

transcription and RNA surveillance should be largely 'disjoint' (although they could be connected by 'negative regulation of the aborted transcription process). The surveillance occurs during transcription (or splicing) but these terms are not modelled as part of transcription (biosynthesis) but as part of 'RNA catabolism'.

Instead of being a child of
GO:0006367 transcription initiation at RNA polymerase II promoter
RNA polymerase II transcription initiation surveillance

should be a child of
GO:0071027 nuclear RNA surveillance
Definition A process that identifies and degrades defective or aberrant RNAs within the nucleus. PMID:18644474
which provides the catabolism parentage.

and for
Term: RNA polymerase II transcription elongation surveillance
Definition: A process that promotes premature RNA polymerase II transcription termination of transcripts that are unfavorably configured for transcriptional elongation.
child of GO:0006369 termination of RNA polymerase II transcription
child of GO:0034243; P:regulation of transcription elongation by RNA polymerase II
here
GO:0006369 termination of RNA polymerase II transcription
should be replaced by GO:0071027 nuclear RNA surveillance
This term is defined
A transcription termination process that completes the production of a primary RNA polymerase II transcript.
and this is a non-productive transcript

if
child of GO:0034243; P:regulation of transcription elongation by RNA polymerase II
is kept, it should be changed to 'negative regulation of'

Note that although termination is how these processes are observed the critical event that is controlled by the signalling through CTD code is the cleavage event (which obviously triggers premature termination).

A major outstanding issue with the ontology is that we have different axes for the classification of mRNA, lncRNA, etc, when these are clearly the same processes.
Here the premature cleavage and termination is used to suppress phosphate metabolism, so these are currently annotated by PomBase as lncRNA 3-end processing, when they are clearly also 'transcription surveillance'
https://www.pombase.org/reference/PMID:30355770
https://www.pombase.org/reference/PMID:32546512
https://www.pombase.org/reference/PMID:34389684

I haven't fully figured out how to reconcile this.

[pgaudet]

@ValWood

I think you are describing a different process - this is transcription initiation surveillance, ie at pausing, there is a no-no go decision that takes place.

[sylvainpoux]

Hi @ValWood, could you please consider the updated definition and not the initial? We change the hierarchy of terms

[ValWood]

Actually there must be some transcription based on the definition
Definition: A process that promotes premature RNA polymerase II transcription termination
of transcripts.

This is still RNA surveillance as defined.

[ValWood]

If a transcript is formed at all, it's surveillance

[sylvainpoux]

Please find an updated definition:

Name: RNA polymerase II transcription initiation surveillance
Definition: A process that promotes premature RNA polymerase II transcription termination of transcripts that are unfavorably configured for transcriptional elongation by releasing RNA polymerase II from bound DNA or promoting RNA polymerase II degradation.
Child of GO:0006367 transcription initiation at RNA polymerase II promoter
child of GO:0071025 RNA surveillance
PubMed=33385327
PubMed=34762484

Please note that I did not selected GO:0071028 nuclear mRNA surveillance as parent, since this process does not always involve mRNA catabolic process (the integrator complex degrades mRNA but not the BCR(ARMC5) complex, which degrades the polymerase

Thanks

Sylvain

[ValWood]

Sounds good!

re:
Please note that I did not selected GO:0071028 nuclear mRNA surveillance as parent, since this process does not always involve mRNA catabolic process (the integrator complex degrades mRNA but not the BCR(ARMC5) complex, which degrades the polymerase

Can we use
GO:0071027 nuclear RNA surveillance
I am trying to separate surveillance that occurs in the nucleus during or immediately post-transcription from cytoplasmic pathways.

[raymond91125]

+[Term]
+id: GO:0160240
+name: RNA polymerase II transcription initiation surveillance
+namespace: biological_process
+def: "A process that promotes premature RNA polymerase II transcription termination of transcripts that are unfavorably configured for transcriptional elongation by releasing RNA polymerase II from bound DNA or promoting RNA polymerase II degradation." [PMID:33385327, PMID:34762484]
+is_a: GO:0071027 ! nuclear RNA surveillance
+relationship: part_of GO:0006367 ! transcription initiation at RNA polymerase II promoter
+property_value: term_tracker_item "#29516" xsd:anyURI
+created_by: rynl
+creation_date: 2025-01-30T00:34:21Z

[raymond91125]

Please let me know if there's anything needs fixing.