[Ontology-editors] forward and reverse transcription

Tue Dec 2 18:16:03 PST 2008

Harold and Karen,

In viruses, such as Corona and Toga viruses, (+)-strand subgenomic RNAs 
that act as mRNA are made from a negative stranded genomic RNA 
template.  Virologists refer to this process as "transcription" in 
hundreds of papers, a usage which dates back over 30 years 
(PMID:173940).  This not RNA replication, but a different process (using 
many of the same enzymes to be sure) under a different type of regulation.

I really don't think you should rely on undergraduate textbooks, no 
matter how notable the authors, to decide this issue.

Thanks,

Alex

Karen Christie wrote:
> rereading the text of Harold's earlier email, with all the defs. The 
> one is GO is from the Oxford "Bible" of Biochemistry and Mol Bio, and 
> even with that one, I've noticed that it is sometimes too simplistic 
> compared to up-to-date literature.
>
> -K
>
>
> On Tue, 2 Dec 2008, Harold Drabkin wrote:
>
>> 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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>>>>>>
>>>>
>>
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-- 
Alexander D. Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
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Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
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