NTR: regulatory RNA binding

[gocentral]

Under the "RNA binding" term, there are currently a number of terms for binding of (eukaryotic) RNA regulators, e.g. piRNA, miRNA and siRNA binding. No terms currently exist for the prokaryotic small regulatory RNAs. I propose a new parent term, regulatory RNA binding, as a child of RNA binding. In addition, I'd like to request creation of a term for "small RNA binding" that would include the bacterial small regulatory RNAs; it could have the "regulatory RNA binding" term as its parent.

Thanks, Ingrid

Reported by: imk07

Original Ticket: geneontology/ontology-requests/10058

[gocentral]

I'm curious how do we define regulatory here? More specifically I'm intrigued by the existing term (s).

GO:0001069 regulatory region RNA binding (is this grouping term required it seems to lump regulation of different processes, so its an odd axis of classification?)

GO:0001068 transcription regulatory region RNA binding is defined: Interacting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon.

How is "regulatory region defined" This doesn't see to make sense, surely the entire RNA is regulatory, not the region being bound by the protein? Maybe I've misunderstood but the def isn't clear

Original comment by: ValWood

[gocentral]

Hi Ingrid,

I'd like to suggest that you propose a different name than 'small RNA binding'. I forsee that this term will be confused in any gene product that binds an RNA that is small in size, an arbitrary distinction. Can you make the term name a bit more specific? Thanks in advance.

As for Val's questions, if you have any comments on them, that would be great. I'm not really up on this field. I will have a look at the current annotations to see if I can make the terms clearer.

David

Original comment by: ukemi

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: ukemi

[gocentral]

Hi David, Val,

I guess it's a bit trickier than I thought.

Re. the existing terms, my "impression" from the definition is that they are talking about a specific regulatory region within a larger RNA. So if you transferred the meaning to a protein, this would be like the allosteric site of an enzyme; the function of the enzyme itself is not to regulate or be regulated. These small RNAs, though, function as regulators. Maybe one could make an argument that within the ontology, RNA binding is RNA binding, and the function of what is bound is not the relevant thing (or should be encoded using "with"); I'll leave that to the philosophers....

Re. the term "small RNA". Aren't biologists the worst at naming things? "Small RNA" is probably the most widely used term here, but I agree that it will be too tempting for unintentional misannotations. I often also read "regulatory small RNA" or "small regulatory RNA", or we could take the lead from pi and si and mi and use sRNA, also a term I read occasionally.

-Ingrid

Original comment by: imk07

[gocentral]

Hi

So, here is some background on the “regulatory region nucleic acid binding” terms that Val brought up. The term GO:0044212, then called “regulatory region DNA binding” existed prior to the transcription overhaul, but if I recall correctly was defined in such a way as to be specific to regulation of transcription. So, we added “transcription” to the name of this term to reflect the existing definition, and then made a parent term for just plain “regulatory region DNA binding” (GO:0000975) to cover sites within the DNA that regulate other DNA-bases processes such as DNA repair or DNA replication.

Then the terms “regulatory region RNA binding” and “transcription regulatory region RNA binding” was made to be parallel to “regulatory region DNA binding” terms described above.

With respect to “transcription regulatory region RNA binding”, the biology behind these is that there are specific sites within nascently transcribed RNAs that interact with regulatory proteins that control transcription elongation or termination, e.g. NusA or NusG in prokaryotes or Tat in a eukaryotic virus (HIV). So, the point here was to indicate binding to a regulatory site within the nascent RNA transcript. Then these two terms (“regulatory region RNA binding”, “regulatory region nucleic acid binding”) were created just for logical structure.

So, I agree with Ingrid that these terms are distinct from the “small regulatory RNA” terms that she wants.

-Karen

Original comment by: krchristie

[pgaudet]

@keseler What do you suggest we do about this ticket; do you want to create 'small regulatory RNA binding'? If you do, please provide a reference and a definition.

Thanks, Pascale

[keseler]

Oh my, that's a long time ago. Yes, I'd still like a "small regulatory RNA binding" term.

Definition? perhaps: "Interacting selectively and non-covalently with a small regulatory RNA, a short RNA (usually 50-350 nt long) that is either independently transcribed or processed from a longer RNA by an RNAse enzyme."
Publications; hmmm. A subset of small regulatory RNAs interact with the Hfq protein; a good publication would be PMID 14622403. Though I think what precipitated my request at the time was a much later publication about RapZ, PMID 23475961.

Thanks, Ingrid

[hattrill]

Looks like piRNAs were forgotten - could you make GO:0034584 piRNA binding a child of GO:0061980 regulatory RNA binding?

Thanks