possible TPV under RNA interference/ & taxon restrictions

gocentral commented 14 years ago

In GO the definitions of RNA interference is very specific

Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'.

So althought fission yeast has and RNAi "type" of process, the term I should use is GO:0031048 chromatin silencing by small RNA

So now my problem is that I used children of RNAi,

"production of siRNA involved in RNA interference"

which is a child of RNAi, so can we have

GO NEW production of siRNA (child of gene silencing by RNA?) --GO NEWproduction of siRNA involved in chromatin silencing by small RNA --GO:0030422production of siRNA involved in RNA interference

and i can move my existing annotation

Thanks

val

Taxon restictions I'm not sure which species RNA interference, as defined applies to but you can restrict fungi (I think), may have to check about N. crassa, though, can exclude yeast anyway. I also noticed there were bacterial annotations, but should probably exclude bacteria?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7226

gocentral commented 14 years ago

Here is another suggestion, RNA interference is probably more often used as a general term for all of the RNA mechanisms, (see response from liz Bayne working on anotyher fission yeast RNAi gene below). So we could make the more general term RNA interference, and make RNA interference RNA interference by post-transcriptional mechanism (or similar) if this is more in line with current usage of "RNA interference"

OK, I think you are right. Often "RNA interference" is used as a
general term to cover all related pathways, but here the definition is
quite clear in being specific for post-transcriptional mechanisms, so
I think just using "chromatin silencing by small RNA" is correct. (I
don't really like "RNAi-like chromatin silencing" because as I said
RNAi is often taken to include chromatin silencing and so to me this
would suggest something different again).

Thanks, Liz.

Original comment by: ValWood

gocentral commented 14 years ago

The 1st author of this paper also thinks that RNAi should be a more general term:

. 2010 Mar 5;140(5):666-77. Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Bayne EH, White SA, Kagansky A, Bijos DA, Sanchez-Pulido L, Hoe KL, Kim DU, Park HO, Ponting CP, Rappsilber J, Allshire RC.

In fact it was Liz Bayne who suggested initially that these gene products should be annotated to RNAi and the process is generally referred to as palin RNAi in fission yeast where it is intensly studied.

Original comment by: ValWood

gocentral commented 14 years ago

Hi Becky,

Can you take this one? Similar questions have come up a couple times before, so there's some background in the mailing list archive and in SF:

http://fafner.stanford.edu/pipermail/go/2007-August/015122.html (and following msgs) https://sourceforge.net/tracker/?func=detail&aid=2845544&group\_id=36855&atid=440764

cheers, m

Original comment by: mah11

gocentral commented 14 years ago

assigned_to: nobody --> rfoulger

Original comment by: mah11

gocentral commented 14 years ago

Hi Val,

We've already got the new terms you suggest (Midori added them in after one of your previous SF items: https://sourceforge.net/tracker/?func=detail&aid=2845544&group\_id=36855&atid=440764)

gene silencing by RNA ; GO:0031047 --<production of small RNA involved in gene silencing by RNA ; GO:0070918 ----%production of siRNA involved in chromatin silencing by small RNA ; GO:0070919 ----%etc...

Given all the extra terms in this part of GO now, are you happy with us keeping the restricted definition of RNAi? Are there sufficient RNA silencing terms for yeast and prokaryotes now?

thanks, Becky

Original comment by: rebeccafoulger

gocentral commented 14 years ago

Hi Becky,

The problem here is that the fission yeast community refers to the RNA phenomena observed in fission yeast as RNAi. The meaning of the term "RNAi" has changed over recent years to desribe the generic mechanism, rather than the way is is defined in GO as the post transcriptional mechanism.

This probably wouldn't be such a bit deal, but pombe is one of the pirimary organisms for the study of RNAi. If you Google pombe and "RNA interference" you get 33,300 hits.

Most people studying the RNAi mechism, use fission yeast to disect this pathway (over 200 papers), and many of the popular reviews are written by pombe reserchers or people using pombe as one of their model systems, whi refer to this orocess as RENAi and RNI interfernece in the abstrcts and titkles of their papers. Buhler & Moazed 2007 Grewal and Jia 2007 Kloc and Martienssen 2008

So my final suggestion to be more in line with community usage, (sorry this changed from my original request!) was to rename gene silencing by RNA to "RNA interference", and than to rename any of the specific child terms as necessary (particularly the existing RNAi term and its children which is too narrow as it only refers to post transcriptional silencing)

This means that I can move my existing annotations (and various IEA mappings) to RNAi (which are wrong) to the term GO:0031047 gene silencing by RNA. This move would also mean that future Interpro mappings made to RNAi for components of the RNAi pathway would be corrcet. It would also make my comminuty happy as they always suggest that their genes should be annotated to RNAi but at present this would be wrong.

I think you are right that all of the existing terms are in place, and I just need to move any annotations to production, targeting etc to the branch of the ontology under "chromatin silencing by small RNA" Val

Original comment by: ValWood

gocentral commented 14 years ago

HI Val,

I'm reading PMID:16162338, which Ranjana passed on about posttranscription and transcriptional RNAi gene silencing. So we definately need to change RNA interference ; GO:0016246 to posttranscriptional RNA interference ; GO:0016246

and add 'posttranscriptional' into its children.

The review counts miRNA gene silencing as RNAi-like (not classical RNAi). In the yeas community, do they include miRNAs in their use of RNAi? How about chromatin silencing?

I don't think we should change the top level term gene silencing by RNA ; GO:0031047 to be RNAi. PMID: 19898526 for instance says: S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation.

So there is still gene silencing by RNA that is NOT RNAi.

We need to make a new generic RNAi term... we just need to work out which of the existing terms should go under it.

Original comment by: rebeccafoulger

gocentral commented 14 years ago

In pombe they call the RNAs siRNAs (small interfering RNAs) iI'm not sure how these differ from miRNAs?

The existing term chromatin silencing by small RNA has exact synonym RNA interference-like chromatin silencing

and has only been used by fission yeast and arabidopsis for annotation of RNAi genes (no cerevisiae annotations, so it hasn't been used int e context below). This could be renamed as "chromatin silencing by RNAi" to make this clearer that it is si RNA and not other types of non-coding RNA by a non-RNAi mechanism. The definiiton should also be changed to make sure it mentions the RNA machinery (this is what we meant when the term was made but we didn't consider that it could be interpreted to mean other typed of ncRNA). If a term is required for this, it could be added as a parent of this term, but not under the general RNAi parent.

The ones which refer specifically to RNAi are

cotranscriptional gene silencing by small RNA chromatin silencing by small RNA posttranscriptional gene silencing by RNA production of small RNA involved in gene silencing by RNA small RNA loading onto RISC

as all of these are defined to involve the RNAi machinery or have exact synonyms which include RNAi

Does that help?

Val

nferred but at preednt it could also cover cases of the cerevisie type which do not involved RNAi, we weren't

Original comment by: ValWood

gocentral commented 14 years ago

summary: possible TPV under RNI interference/ & taxon restrictions --> possible TPV under RNA interference/ & taxon restrictions

Original comment by: ValWood

gocentral commented 14 years ago

When this is resloved can a comment be posted on https://sourceforge.net/tracker/index.php?func=detail&aid=2973116&group\_id=36855&atid=605890 (the outcome will dictate whether the existing mappings can be kept)

Val

Original comment by: ValWood