obsolete GO:0097393 telomeric repeat-containing RNA transcription

[ValWood]

Please provide as much information as you can:

• GO term ID and Label obsolete GO:0097393 telomeric repeat-containing RNA transcription

• Reason for deprecation

There is no evidence that any of this is functionally relevant, could be cryptic transcription. I just kept the phenotypes

https://www.pombase.org/reference/PMID:22139915

since these are the only EXP I think this term should be obsoleted

• Are there annotations to this term?
• How many EXP: pombe only, removed

[pgaudet]

Dear all, The proposal has been made to obsolete GO:0097393 telomeric repeat-containing RNA transcription. The reason for obsoletion is that there is no evidence that any of this is functionally relevant, could be cryptic transcription. There are no manual annotations to this term (EXP has been removed); no mappings; these terms are not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/23260

Thanks, Pascale

[pgaudet]

Note there there are children terms -

• GO:0097394 telomeric repeat-containing RNA transcription by RNA polymerase II
• • [regulates relation] GO:1901580 regulation of telomeric RNA transcription from RNA pol II promoter
• • • GO:1901581 negative regulation of telomeric RNA transcription from RNA pol II promoter
• • • GO:1901582 positive regulation of telomeric RNA transcription from RNA pol II promoter

And one annotation to the positive regulation term by BHF @RLovering PMID:26055325

[RLovering]

Hi Pascale

I can't remove this annotation until the required replacement term is available. Please create the term: GO:0140747 regulation of ncRNA transcription

is a child: positive regulation of ncRNA transcription Definition:Any process that increases the frequency, rate or extent of the synthesis of ncRNA. PMID:28847004 Exact Synonym: positive regulation of non-protein coding gene transcription Exact Synonym: positive regulation of non-coding RNA transcription Add child terms [GO:0060196]positive regulation of antisense RNA transcription [GO:1905382]positive regulation of snRNA transcription by RNA polymerase II [GO:0140543]positive regulation of piRNA transcription [GO:1902895]positive regulation of miRNA transcription [GO:1901838]positive regulation of transcription of nucleolar large rRNA by RNA polymerase I

Perhaps it is also worth creating the negative sibling too: GO:0140747 regulation of ncRNA transcription

is a child: negative regulation of ncRNA transcription Definition: Any process that decreases the frequency, rate or extent of the synthesis of a ncRNA. PMID:33767452 PMID:33913806 Exact Synonym: negative regulation of non-protein coding gene transcription Exact Synonym: negative regulation of non-coding RNA transcription Add child terms [GO:0060195]negative regulation of antisense RNA transcription [GO:1905381]negative regulation of snRNA transcription by RNA polymerase II [GO:0140744]negative regulation of lncRNA transcription [GO:1902894]negative regulation of miRNA transcription [GO:1901837]negative regulation of transcription of nucleolar large rRNA by RNA polymerase I

I may have missed some of the child terms that would need to be added.

Note that the ncRNA that is being transcribe does not have an RNAcentral ID because it is TERRA: Telomeric repeat–containing RNA (TERRA) is a long non-coding RNA transcribed from telomeres - repetitive nucleotide regions found on the ends of chromosomes. Consequently it will not be possible to specify the has-input in the AE field, I am not sure these will ever get RNAcentral IDs. - which might suggest the term should stay.

Thanks

Ruth

[RLovering]

ps did you check wikipedia? https://en.wikipedia.org/wiki/TERRA_(biology)

[paolaroncaglia]

Hi @ValWood @pgaudet @RLovering In case it helps with the decision, please find the original request here (by Antonia while at PomBase; at the time - 2012 - she did indeed mention that there was no evidence for the process or pathway). @ukemi edited the term following a discussion here. I don't feel strongly one way or another, but I was curious to track this term down as it was one of mine. Thanks and take care! Paola

[pgaudet]

Hi @RLovering

For the two papers you cite:

• for positive regulation of nc transcription: we already have a specific term for piRNA transcription: GO:0140543 positive regulation of piRNA transcription (see #19530)
• ~for the negative regulation: the paper states "ZC3H4 is a candidate transcription termination factor", "ZC3H4 depletion stabilises unproductive transcripts." -> this is not referring to functional ncRNAs, but to 'unproductive transcripts' . I think we should distinguish the two; ZC3H4 is rather involved in a QC mechanism.~ sorry, this was probably pasted in the wrong ticket

What do you think?

[pgaudet]

@RLovering

We went over this with @colinlog and @ValWood

For GO:1901582 positive regulation of telomeric RNA transcription from RNA pol II promoter : Looking at PMID:24500201, ATRX seems to be involved in (among other processes), the Alternative Lengthening of Telomeres pathway. We have a GO term that mentions 'Alternative Lengthening of Telomeres pathway', defined as 'A telomere maintenance process that results in the formation of a telomeric circle, or t-circle. A t-circle is an extrachromosomal duplex or single-stranded circular DNA molecule composed of t-arrays. T-circles are involved in the control of telomere length via alternative-lengthening of telomeres (ALT) pathway and telomere rapid deletion (TRD).'

but this term is part_of 'telomere maintenance via telomere trimming', which does not not mention the t-circle.

It seems like the paper you've annotated to GO:1901582 positive regulation of telomeric RNA transcription from RNA pol II promoter](http://amigo.geneontology.org/amigo/term/GO:1901582#display-lineage-tab), PMID:26055325, is probably just an effect of the role ATRX plany in the ALT pathways?

---

See also https://www.researchsquare.com/article/rs-362334/v1 "deletion of ATRX and SETD2, commonly mutated in high grade gliomas (HGGs), elicits induction of ALT."

so I am not sure anymore which way around this goes

[pgaudet]

For PMID:20211137 (GO:1901581 negative regulation of telomeric RNA transcription from RNA pol II promoter), @colinlog proposes to annotate to GO:0006334 nucleosome assembly occurs_in GO:0000781 chromosome, telomeric region.

What do you think?

[ValWood]

I'm having second thoughts about this. The regulation terms are probably OK, if we are allowing RNA species-specific terms ( but in these cases it is confusing to have non- regulation terms like "GO:0097393 telomeric repeat-containing RNA transcription" available.

[pgaudet]

@RLovering changed the annotation of P46100 | ATRX from positive regulation of telomeric RNA transcription from RNA pol II promoter to to subtelomeric heterochromatin formation

Ready for obsoletion.