NTR: determinant of selective removal (DSR) -dependent heterochromatin formation

[ValWood]

Please provide as much information as you can:

• Suggested term label:

~si independent pericentric heterochromatin formation~

• Definition (free text) ~standard def, but maybe include the components (YTH family RNA-binding protein (Mmi1 In pombe), CPF +?~ see below

• Reference, in format PMID:#######

PMID: 31269446 CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing

This paper also describes a roe for this pathway in pericentromeric heterochromatin formation, in parallel to RNAi

• Gene product name and ID to be annotated to this term

• Parent term(s)

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

• Cross-references

• For enzymes, please provide RHEA and/or EC numbers.

• Can also provide MetaCyc, KEGG, Wikipedia, and other links.

• Any other information

@colinlog @pgaudet can discuss Friday?

[pgaudet]

We removed the 'x-independent' terms because they really meant, that we could exclude one mechanism, but not others, so in these case we should annotate to the parent.

Looks like you are looking into a specific pathway though, perhaps we could create something along the lines of 'YTH family-mediated pericentric heterochromatin formation?

[ValWood]

OK I can do that, it will be clear which pathway it is.

[ValWood]

I think a better label would be determinant of selective removal (DSR) -dependent heterochromatin formation (at least for the facultative pathway)

BUT, that does not seem to apply to the centromeric pathway (there is such a lot in this paper!) I can just annotate the ones implemented in the pericentromeric pathway to pericentric heterochromatin formation" (GO:0031508)

I will keep this ticket for determinant of selective removal (DSR) -dependent heterochromatin formation I could repurpose GO:0033621 | nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts for this and improve the term. This is the same meaning, but I don't know if the pathway is specific for only meiotic genes in other species.

@colinlog

GO:0033621
nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts

[ValWood]

Should this be modelled as "gene silencing'. (It is to prevent ectopic expression of meiotic gene during vegetative growth), or as an RNA catabolic process? or both?

(Sorry this ticket has changed topics somewhat!)

[ValWood]

note also that we still have terms like siRNA-independent facultative heterochromatin formation

Perhaps these could be MTREC/NURS dependent/mediated facultative heterochromatin formation? Also, not that there is a mismatch between the siRNA-mediated terms and their regulatory children which still say dependent