[Ontology-editors] forward and reverse transcription

[Midori Harris]

Thanks. Considering everything from this email thread, I think we really 
need input from outside our little GO circle.

m

On Tue, 2 Dec 2008, Karen Christie wrote:

> I've sent an email to my old advisor to see if she has thoughts on this 
> issue.
>
> -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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