[go]

[Jim Hu]

Hi Midori

I'll find an expert here at the the phage meeting to help me  
formulate an SF request then.

On Aug 9, 2007, at 10:38 AM, Midori Harris wrote:

> Yes, the degradation seems to fit the GO:0035194 df, and we could  
> add a more specific child; the other process would go under GO: 
> 0045947.
>
> m
>
> On Thu, 9 Aug 2007, David Hill wrote:
>
>> I'm no expert in this area, but it sounds like there might be two  
>> things going on, one is the degradation and the other is the  
>> negative regulation of translation initiation. Is this all part of  
>> the same process. I think we should start a SF request for this.
>>
>> David
>>
>> Midori Harris wrote:
>>> Hi Jim,
>>> I don't think we've yet added a term in this area that was  
>>> specifically motivated by prokaryote-annotation needs. From your  
>>> brief description, I agree that RNA interference is wrong, but  
>>> would its parent be suitable?
>>> id: GO:0035194
>>> name: RNA-mediated posttranscriptional gene silencing
>>> def: "Any process of gene inactivation (silencing) in which small  
>>> RNAs trigger degradation of mRNA." [PMID:15020054, PMID:15066275,  
>>> PMID:15066283]

I'm concerned that the true path takes that up to silencing, which  
requires that the effect be long-term.  I don't think these are.

Jim


>>> If you need a different term, either as a child of GO:0035194 or  
>>> placed elsewhere, we're happy to add something. It will help  
>>> immensely if you can suggest a name, definition and parent(s).
>>> Midori
>>> On Thu, 9 Aug 2007, Jim Hu wrote:
>>>> Is there an existing process term for RNA-mediated inhibition of  
>>>> translation as it works in prokaryotes?  There are many examples  
>>>> of small RNAs that bind around the translation start site to  
>>>> block initiation (often with the help of hfq) or promote RNA  
>>>> degradation.  I'm seeing these annotated by others to
>>>>     GO:0016246 ! RNA interference,
>>>> but this strikes me as very wrong.  No dsRNA, and the processes  
>>>> are evolutionarily unrelated.
>>>> I'm not crazy about
>>>>
>>>>     GO:0042868 ! antisense RNA metabolic process
>>>> for this either.  It also goes into the epigenetic path, which I  
>>>> don't think applies here.
>>>> Jim
>>>> =====================================
>>>> Jim Hu
>>>> Associate Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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