GO:0033562 cotranscriptional gene silencing by small RNA

[gocentral]

Hi Tanya, This is the feedback I mentioned on CTGS:

GO:0033562 cotranscriptional gene silencing by small RNA is defined: A process in which the targeting of nascent transcripts by the RITS complex mediates chromatin modifications and promotes the degradation of nascent transcripts synthesized in heterochromatic regions.

Our users have suggested a rename Co-transcriptional gene silencing by RNA interference machinery and modify def a process in which the RNAi machinery mediates the degradation of nascent transcripts in association with chromatin

Rationale: "It may be better to leave out the chromatin modification part, since this probably only occurs at heterochromatic regions, while CTGS at euchromatic regions occurs without H3K9 methylation."

Note as a consequence we need to ensure that the reasoner does not add GO:0016246 RNA interference as a parent (in GO this term refers specifically to post-transcriptional gene silencing)

PMID:21151114 and PMID:22431512

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10377

[gocentral]

Hi Val,

Do you think this is really a case for a rename instead of a new term? I can only find one annotation to this term right now and it's an Arabidopsis gene product. Haven't had a chance to read the supporting paper.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

My understanding is that this is the correct term/process, but that it isn't heterochromatin specific. The name change is an independent thing, would just make it clearer that it is RNAi machinery ( CTGC always refers to RNAi based, but there might be other types of cootranscriptional silencing? I'm not sure)

So based on this the suggestions seemed to make sense to me.

This is speculation (by me) but the "methylation independent" part of this abstract might indicate why the "CGTS" annotation was made here?:

These results suggest that DTF1 is an atypical component of RdDM and has both DNA methylation-dependent and -independent roles in transcriptional gene silencing. We suggest that besides DNA methylation, siRNAs may cause some other uncharacterized epigenetic modifications that lead to transcriptional gene silencing.

v

Original comment by: ValWood

[gocentral]

Hi Val,

I'm pretty sure that this is where the annotation is from:

"Neither trans-acting siRNA255 nor microRNA171 was affected in ros1dtf1-1 and ros1nrpe1 (Figure 3B), supporting that DTF1 specifically functions in 24-nt siRNA-directed transcriptional gene silencing."

But maybe siRNA-directed transcriptional gene silencing != CTGS. Maybe that annotation should be more general.

I'll think about the annotation some more. Input welcome.

I'll modify the term tomorrow.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Yep, I would say this should probably be more general? but I'm not sure what the processes which are not affected are referring to, so I'm not sure....

Original comment by: ValWood

[gocentral]

Modified the primary name and changed the annotation. GO:0016246 RNA interference was not added as a parent and should not be inferred by the reasoner.

Original comment by: tberardini

[gocentral]

• status: open --> closed-fixed

Original comment by: tberardini