[Ontology-editors] forward and reverse transcription

[Karen Christie]

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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