post-transcriptional RNA stability regulator Mkt1 - check and update

[ValWood]

@Antonialock Is all of this related to mkt1?

From that 2020 paper 31822915 they say

A possible consequence of impaired post-transcriptional downregulation of pericentromeric transcripts could be increased accumulation of these transcripts on chromatin, possibly resulting in increased DNA:RNA hybrid formation, which has been implicated in defective heterochromatin assembly (57,58).

Then they did some experiments where they observed increased DNA:RNA hybrids, and that suppressing them promoted heterchromatin formation

"suggesting that suppressing DNA:RNA hybrid accumulation can partially rescue the heterochromatin defect"

"These findings are consistent with a model whereby, when transcription at pericentromeres is high (either in an establishment scenario, or when transcriptional silencing is impaired), RNAi- and Mkt1-dependent post-transcriptional silencing promotes heterochromatin assembly at least in part through prevention of over-accumulation of pericentromeric transcripts on chromatin."

so mkt1 is involved in "RNAi-mediated silencing"

the abnormal heterochromatin assembly is an indirect phenotype resulting from lots of RNA sticking to the DNA obstructingheterochromatin formation?

[ValWood]

and mkt1 product description update from

• [x] XP-G family nuclease Mkt1 to

post-transcriptional RNA stability regulator Mkt1 ?

[ValWood]

"RNAi-mediated silencing" happens via heterochromatin assembly BUT All the BP annotations appear to be indirect phenotypes. I removed them this morning while revising some transcription stuff. They should be phenotype only.

~ this the one we were discussing last night? If so it has a conserved role in mRNA processing?!~

• [ ] annotate process to match post-transcriptional RNA stability regulator Mkt1 ?

[ValWood]

@Antonialock do my 2 actions make sense to you? DO you have anything I can ISS to?

[ValWood]

Interesting. I found the paper we looked at https://www.ncbi.nlm.nih.gov/pubmed/24470144

and I think pombe Zc3H11 might be https://www.pombase.org/gene/SPAC3A11.02

anyway for now I updated the product. Also need to report and suppress the InterPro mapping

[Antonialock]

Yes I thought https://www.ncbi.nlm.nih.gov/pubmed/24470144 was a very good characterization paper.

I am annotating Q587E3 (trypanosome mkt1) to mRNA stabilization I know we discussed this term but in comparison to neg reg of mrna catabolism it does have the additional parent posttranscriptional regulation of gene expression which might be useful? It can be merged into something else automatically if the ontology changes...

I'm not great at pitching product descriptions, do you like

post-transcriptional RNA stability regulator Mkt1 or Post-transcriptional regulator MKT1

better?

[Antonialock]

Zc3H11 is zfs1 you are thinking of lsm12?

[ValWood]

also mailed InterPro about the description here: http://www.ebi.ac.uk/interpro/entry/InterPro/IPR022039/

[ValWood]

no i have

Ortholog species	Ortholog gene	Ortholog description	Reference
Homo sapiens	ZFP36L1 (HGNC:1107)	ZFP36 ring finger protein like 1
Homo sapiens	ZFP36L2 (HGNC:1108)	ZFP36 ring finger protein like 2
Homo sapiens	ZFP36 (HGNC:12862)	ZFP36 ring finger protein

for zfs1?

[ValWood]

essentially waiting for Q587E3 https://www.uniprot.org/uniprot/Q587E3 GO terms to make a better process ISS

[Antonialock]

I annotated it to mRNA stabilization https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=Q587E3

I know it is on your do not annotate term set, but I didn't know what else to annotate to. see discussion in https://github.com/geneontology/go-ontology/issues/16360

[Antonialock]

hang on, that GO ticket is about protein stabilization, not mRNA stabilization (so ignore that GO ticket here) - maybe mRNA stabilization is ok?