GO:0035068 micro-ribonucleoprotein complex parentage

[gocentral]

Hi,

I'm wondering whether GO:0035068 micro-ribonucleoprotein complex Def: A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA.

should be a child of GO:0016442 RISC complex Def: A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.

See final paragraph of http://genesdev.cshlp.org/content/16/9/1025.full.html - are the miRISC and miRNP the same thing?

Looking at the annotations to miRNP term, these are all proteins expected to be in the RISC complex, except maybe Fmr1 (Q9NFU0), but which has also been annotated to RISC complex.

If it should be a child of RISC complex, then there should be an equivalent term for siRNAs, i.e. siRISC complex (See http://www.ncbi.nlm.nih.gov/pubmed/15691656).

Thanks, Rachael.

Reported by: rachhuntley

Original Ticket: geneontology/ontology-requests/11664

[gocentral]

Does look like miRNP is just what they call the thing before they realised it was RISC. The review is from 2002. From a sratch of pubMed it looks like miRNP is still used, but perhaps just synonymously with miRISC

http://www.ncbi.nlm.nih.gov/pubmed/?term=miRNP http://www.ncbi.nlm.nih.gov/pubmed/25240885

Or perhaps that miRNP is sligltly broader in that it - RISC + other proteins, varying with miRNA?

Looking through more refs to get a clearer picture.

Original comment by: dosumis

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: paolaroncaglia

[pgaudet]

@bmeldal Do you have any comment about this ?

[bmeldal]

I'm not sure, Pascale. I looked at the review from 2002 and then just checked Wikipedia as I haven't curated RISC yet. Looks like RISC is at minimum an argonaute protein (ago1 or ago2 or other equivalents) (drome has R2D2 :) ) and a non-coding RNA. Then they call the complex dep on which RNA is incorporated.

We have the RISC-loading complex in the CP, which Rachel requested and I curated.

[pgaudet]

So maybe this term is not required anymore and this ticket can be closed ? @rachhuntley

[rachhuntley]

If, as the definition suggests, this term is referring only to mature (~22nt long) miRNAs, then this would be synonymous with miRISC (a sub-type of RISC), which is composed of miRNA and Argonaute-type proteins. However, there are annotations to DICER, TARBP2 and RAN, which bind the pre-miRNA (the longer stem-loop structure that is processed to form the mature miRNA) and there are existing terms that cover these complexes, e.g. RISC-loading complex, RNA nuclear export complex.

MGI have annotated RNAs from 8 papers, but looking at just a few, these seem to be referring to the microRNA-containing RISC complex.

Either we should obsolete this term and move the annotations to the existing terms, or we could re-name this term "miRISC complex" and make it a child of RISC complex. The latter would mean the MGI annotations can remain associated with this term (potentially, after a review of the 8 papers) and the other 23 annotations to this term would need to be moved to existing terms.

[bmeldal]

In that case I agree that miRISC and miRNP are indeed the same thing. I'd follow Rachael's suggestion and re-house those annotations that are not to argonaute proteins to RISC-loading complex or similar.

Btw, I looked at UniProt entries, too, not just Wikipedia - written in haste ;-) and UniProt also don't have very defined defs for the RISC complex beyond argonaute+types of ncRNAs

[pgaudet]

So, is a merge OK @bmeldal ?