NTR: siRNA processing

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Please add:

name: siRNA processing definition: Any process involved in the conversion of a primary small interfering RNA transcript into a mature small interfering RNA molecule. reference: TAIR:tb parentage: isa RNA processing GO:0006396

Thanks,

Tanya

Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/2074":https://sourceforge.net/p/geneontology/ontology-requests/2074

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Hi Tanya,

I recently submitted a proposal to reorganize some of the RNAi related terms. The item's still open, SF #1037129. I'd be interested to know if the structure and terms will work for your group.

Nick

Original comment by: nastover

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Hi Nick,

Your proposal will work for our group. Thanks for the reorganization. Is this term ok in that context?

Thanks,

Tanya

Original comment by: tberardini

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Hi Tanya,

I think it will come down to definitions actually. After the reorganization we'd be left with two similar terms:

id: GO:0030422 name: RNA interference, production of guide RNAs namespace: process def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides." [PMID:11524674] is_a: GO:0016070 relationship: part_of GO:0016246

and

id: GO:0035196 name: miRNA-mediated gene silencing, production of miRNAs namespace: process def: "Cleavage of stem-loop RNA precursors (pre-miRNAs) that are encoded within plant and animal genomes into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein." [PMID:15066283, PMID:15066275] exact_synonym: "microRNA-mediated gene silencing, production of microRNAs" [] is_a: GO:0010195 relationship: part_of GO:0035195

The first one covers the production of interfering RNAs from an exogenous dsRNA, while the second covers the production of interfering RNAs from an transcript encoded in the genome. The vague definitions and variable usage of the words "siRNA", "miRNA", "guide RNA", and "RNAi", along with the fact that some of these are holdover terms from two converging fields, makes this tough.

A quote from PMID: 15211354 makes the point: Fundamentally, siRNAs and miRNAs are similar in terms of their molecular characteristics, biogenesis and effector functions. So, the current distinctions between these two species might be arbitrary, and might simply reflect the different paths through which they were originally discovered.

From the definition you provided, it looks like "miRNA-mediated gene silencing, production of miRNAs" might be a synonym for the term you're requesting. Will that work, if an appropriate synonym is included for this term?

Nick

Original comment by: nastover

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Hi Nick,

Hmmm...from this paper: PMID:15024409, it does appear that the two (miRNAs and siRNAs) are two distinct entities. Perhaps they should remain separate for now. If it does come out that they are one and the same, we can then merge the annotations.

Thanks for pointing out GO:0030422. By definition, this looks like the term I'm looking for, however, I would have never found it by looking at the name alone. Would a synonym "siRNA processing" be appropriate here? I think so. I'm not too sure I like the primary term name. Maybe Midori can comment on its origins - I haven't heard of guide RNAs. (Then again, this isn't my field so that term could be as common as say 'DNA.')

BTW, there is currently no relationship between 'miRNA-mediated gene silencing, production of miRNAs' GO:0035196 and 'RNA processing' GO:0006396? I kind of think there should be.

Thanks for your help.

Tanya

Original comment by: tberardini

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Hi Tanya,

Actually yes, you're right, I should have proposed siRNA processing (or siRNA production) as a synonym for GO:0030422 in the larger proposal. (I think I actually put it in the graphic in the proposal but didn't follow through on it.) I was focusing more on the structure at the time, but a large number of the term names in that tree could use renaming.
Problem is, the field's still in flux, and many synonyms exist for small RNAs with similar, if not identical, biological functions.

Some of the terms that may or may not be synonymous are: guide RNA small inhibitory RNA short inhibitory RNA siRNA microRNA miRNA short temporal RNA small temporal RNA stRNA short hairpin RNA shRNA small non-messenger RNA snmRNA repeat-associated short interfering RNA rasiRNA scan RNA scnRNA

Much work is being done in the field now to determine how these small RNA species are related, and it's beyond me to figure out which ones need their own terms and which should be synonyms. There's a lot of history in there. Andy Fire is a member of the Genetics department here

• maybe I should just ask him about this.

One important thing that slipped my mind about GO:0030422 though: "guide RNA" (or "gRNA") is a term more often associated with RNA editing in trypanosomes than with RNAi. (PMID: 10580144). This term should actually be renamed to "production of siRNA" with "production of guide RNA" as a sensu 'everything but Kinetoplastida' synonym (if GO has those).

Synonyms aside, with the new structure it should be pretty easy to add and merge terms as needed without disturbing others. So as the field evolves, the new terms can be captured in GO. Many "production of xxRNA" terms can exist as children of "dsRNA fragmentation" (which I introduced as a child of 'RNA processing: GO:0006396', to answer the last question in your post - hope that works).

Good night, off to my birthday dinner. :) Nick

Original comment by: nastover

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Hi Nick,

Belated Happy Birthday then!

>Andy Fire is a member of the Genetics department here > - maybe I should just ask him about this.

Yes! We could use all the expertise we can get our hands on.

>One important thing that slipped my mind about GO:0030422 >though: "guide RNA" (or "gRNA") is a term more often >associated with RNA editing in trypanosomes than with RNAi. >(PMID: 10580144). This term should actually be renamed to >"production of siRNA" with "production of guide RNA" as a sensu >'everything but Kinetoplastida' synonym (if GO has >those).

Yes, please. Then I can use that term for annotating.

>Synonyms aside, with the new structure it should be pretty >easy to add and merge terms as needed without disturbing >others. So as the field evolves, the new terms can be >captured in GO. Many "production of xxRNA" terms can exist as >children of "dsRNA fragmentation" (which I introduced as a child >of 'RNA processing: GO:0006396', to answer the last >question in your post - hope that works).

Sounds good to me. When are you planning to put your changes into GO?

Cheers,

Tanya

Original comment by: tberardini

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Hi Tanya,

SF #1037129 is still open, and Midori's working on it. It would be worthwhile to draw her attention to this thread and the specific term we talked about, so she can work it in. Unfortunately she'll probably be done putting up the new terms and structure before I get a chance to talk to Andy, to figure out all the synonyms we should have.

Nick

Original comment by: nastover

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OK. I've forwarded the current discussion to Midori.

Thanks,

Tanya

Original comment by: tberardini

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Hi,

No problem, I've been following this (I get aaaalllll the SourceForge comments ...). I may or may not get to the RNAi changes this week. If I do, shall I go ahead and do what we agreed on in that one, and make further adjustments when there's more info from Andy? Or should the whole thing wait?

m

p.s. even more belated happy birthday to Nick!

Original comment by: mah11

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Hi Midori,

Thanks!

Please go ahead and include the change mentioned in the comments here. I think the remaining synonyms should wait until after the initial restructuring. It will just get too confusing otherwise, and I don't have all the proposals ready yet. I emailed Andy, but haven't heard back - not surprising, he's a busy guy. I suspect other curators will find more synonyms to request and slight definition changes as they run across examples in the literature. Better to get the terms out there and start the flow.

Nick

Original comment by: nastover

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OK, I've made the change to GO:0030422 as described below.

I just made the synonym exact because it refers to the same phenomenon; it doesn't much matter which communities use which wording. But I can change it to a narrower synonym if that makes more sense.

I'll leave this item open for you to add more when you hear from Andy.

m

Original comment by: mah11

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Has there been any further word on this?

m

Original comment by: mah11

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No, I'm sorry, I don't have anything more to add to this item.

Nick

Original comment by: nastover

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• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: mah11

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OK, in that case I'll close it. It'll be easy enough to open a new one if the need arises.

m

Original comment by: mah11

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• assigned_to: nobody --> gomidori

Original comment by: mah11