queries RNA-mediated gene silencing

[gocentral]

RNA-mediated gene silencing needs a parent RNA-mediated chromatin silencing

as the same process results in gene inactivation at other repeat regions such as the heterochromatin of the centromere

see PMID:14704433

it is similar to the transcriptional gene silencing/chromatin silencing issue.

I suspect all of this area is going to be a bit messy. RNA-mediated gene silencing also has a parent development which is a TVP for S. pombe (and for the conserved processes in other eukaryotes which will be regulated by RNAi (i.e heterochromatin formation at the centromere)

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2091":https://sourceforge.net/p/geneontology/ontology-requests/2091

[gocentral]

Logged In: YES user_id=516865

Also not all RNA-mediated silencing is posttranscriptional

RNA mediated silencing --RNA mediated transcriptional silencing --RNA mediated post transcriptional silencing

Thsi is the same as what I said above but more terms are affected than I reilised initially see also PMID: 15371329

Original comment by: ValWood

[gocentral]

• labels: --> Other term-related request
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

It's actually not that bad. (I hardly ever say that about a SourceForge item!)

> it is similar to the transcriptional gene > silencing/chromatin silencing issue.

Remember, we merged transcriptional gene silencing and chromatin silencing! So this doesn't make sense:

> RNA-mediated gene silencing > needs a parent > RNA-mediated chromatin silencing

There is a term, RNA-mediated gene silencing (GO:0035194), that really seems to refer to RNA mediated post-transcriptional silencing. I'll make the wording more specific and add a generic term.

A specific term for RNA mediated chromatin silencing is proposed in SF 1037129, so that'll be taken care of.

As for the 'development' parentage, the problem is that regulation of gene expression, epigenetic (GO:0040029) is directly under development. I can't find anything that explains why, so I'll just remove that parentage.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

Its not that bad !

so somting like

RNA-mediated silencing --RNA-mediated chromatin silencing --RNA interference --miRNA-mediated gene silencing

?

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423

very like -- it's now

gene silencing GO:0016458

• RNA-mediated gene silencing GO:0031047 (new) -- small RNA-mediated chromatin silencing GO:0031048 (new) % chromatin silencing -- RNA-mediated posttranscriptional gene silencing GO:0035194 (reworded) --- miRNA-mediated gene silencing GO:0035195 --- RNA interference GO:0016246

also removed development parent from 40029 as promised

Original comment by: mah11

[gocentral]

• milestone: --> 224410
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865

What about the term name as

"RNA-mediated silencing"

with the synonym "RNA-mediated gene silencing" and including in the def that it doesn't necessarily apply to the silencing of 'genes' but can also include the silencing of heterologous reporter genes in non coding regions like the centromere ?

Original comment by: ValWood

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11