[Ontology-editors] forward and reverse transcription

[Harold Drabkin]

And just checking our  Oxford Bible of Biochemistry and Mol Biol, THEY 
say "the synthesis of either RNA on a template of DNA or DNA on a 
template of RNA.

I think the latter part of that def. does not agree with many other sources:

Lewin (genes VII) : "transcription generates a single-stranded RNA 
identical in sequence with one of the strands of the duplex DNA"
Stryer (Biochemistry): "the synthesis of RNA from a DNA template is 
called transcription"
Lodish, Baltimore, etc. (Mol Cell Biology)  "the process of 
transcription, the information stored in DNA is copied into ribonucleic 
acid (RNA).

.. and 4-5 other genetics, biochemistry, and  texts.


SO, I guess it appears transcription is RNA from a DNA template, period.
Generation of an mRNA from an RNA template evidently does not fall into 
this category even if both are capable of making an mRNA transcript.

But I still think the two terms in question should be merged if we agree 
that making DNA from RNA is not transcription, but a term that is called 
reverse-transcription  which means copying DNA from RNA.
h


Karen Christie wrote:
> 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
>>
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