[Ontology-editors] forward and reverse transcription

[Harold Drabkin]

Interestingly, the Alberts et al  (Mol. Biol of the Cell) almost hedge 
their bets:

They say RNA made from DNA template is "DNA transcription"

This to me implies they were thinking of an "RNA transcription", but 
they do not use the term.
h


Karen Christie wrote:
> Harold,
>
> Thanks! for checking into this.
>
> However, while textbooks have their place, they do sometimes 
> oversimplify. Thus, I still think it might be worth checking with 
> people in the field on this. I can see arguments either way, so I 
> think a reality check with researchers would be good.
>
> -Karen
>
>
> On Tue, 2 Dec 2008, Harold Drabkin wrote:
>
>> 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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>>