[Ontology-editors] forward and reverse transcription

[Karen Christie]

This all seems to hinge upon the definition of transcription (txn). In my 
old biology text book and in the biological definitions obtained from 
www.dictionary.com, transcription is defined simply and absolutely as 
making an RNA copy from DNA, which would exclude Harold's case of making 
an RNA copy from RNA. Harold is defining it as making RNA. However, if one 
defined txn as something like making a single stranded copy of nucleic 
acid, then all three discussed cases would be included.

Personally, I think it's worth checking into the situation, and perhaps 
with people in the field, to make sure that we do something that is 
consistent with current thinking before we make changes in this area. I 
would be willing to check with my PhD advisor, who was interested in both 
old school txn and reverse txn to get her opinion, or suggestions for 
better people to contact.

-Karen


On Tue, 2 Dec 2008, Harold Drabkin wrote:

> Midori Harris wrote:
>> Wait, I'm confused now about what you guys favor. RNA-dependent synthesis 
>> of RNA isn't transcription at all; it's RNA replication.
>
> As it is described above, you do not know if it is replication or 
> transcription (note, in my original post, is some cases a "transcript" is 
> made by copying RNA, not DNA. (as is the case for some viruses).
> Reverse transcription as originally coined in the literature by Temin and 
> Baltimore was refering to the synthesis of a DNA strand using an RNA 
> template.
>
>> 
>> Transcription is the interconversion of DNA and RNA by synthesizing one on 
>> a template made of the other. Synthesis of RNA on a DNA template is 
>> considered "forward" because it's by far the more common direction.
> I don't think that was the idea. Forward is more because it fits the paradigm
>
> In the case of the single-stranded viral genome life cycles, a transcript is 
> made by copying RNA.
> 1. do we limit the definition of "transcript" to only an RNA made from a DNA 
> template or
> 2. does labeling something a transcript imply ultimate usage (mRNA, 
> functional RNA, etc.).
>
> Thus:
> Is the product of  the RNA dependent generation of an mRNA (certain viruses) 
> a transcript or not? If is is read by ribosomes to translate a protein 
> product, then is it not an mRNA?
> SO, are all mRNAs transcripts?
>
> My original post was looking at the term name and it's def, which did not 
> agree.
> id: GO:0006410
> name: transcription, RNA-dependent
> namespace: biological_process
> def: "The synthesis of DNA on a template of RNA."
>
> Synthesis of DNA from RNA is a reverse of transcription (Temin, Baltimore), 
> it is NOT a type of transcription; it makes DNA, not RNA.
>> 
>> m
>> 
>> On Mon, 1 Dec 2008, David Hill wrote:
>> 
>>> I agree with Harold.  Reverse transcription refers to the process of 
>>> reversing the transcription process, not a type of transcription.
>>> 
>>> Harold Drabkin wrote:
>>>> Hmm, from  the def of 64101, the term name really doesn't fit, since to 
>>>> me, RNA -dependent transcription would be a process whereby an RNA 
>>>> template is transcribed to create another RNA molecule. As it's defined, 
>>>> it is "reverse" transcription.
>>>> Based on the def, I would vote to merge them.
>>>> Posted to SF also
>>>> 
>>>> 
>>>> Midori Harris wrote:
>>>>> Hi,
>>>>> 
>>>>> A couple of questions have come up in SF 2354289:
>>>>> 
>>>>> 1. Should these terms be merged?
>>>>>
>>>>>   id: GO:0006278
>>>>>   name: RNA-dependent DNA replication
>>>>>   def: "The process whereby new strands of DNA are synthesized, using 
>>>>> RNA
>>>>>   as a template for RNA-dependent DNA polymerases (e.g. reverse
>>>>>   transcriptase) that synthesize the new strands."
>>>>>
>>>>>   id: GO:0006410
>>>>>   name: transcription, RNA-dependent
>>>>>   namespace: biological_process
>>>>>   def: "The synthesis of DNA on a template of RNA."
>>>>> 
>>>>> 2. Should reverse transcription be considered part of gene expression 
>>>>> (at present it is, by transitivity, but if it shouldn't be, it's easy to 
>>>>> change)?
>>>>> 
>>>>> Comments here or on the SF item much appreciated.
>>>>> 
>>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=2354289&group_id=36855&atid=440764 
>>>>> Midori
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>