[Ontology-editors] forward and reverse transcription

Tue Dec 2 15:35:26 PST 2008

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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>>> 
>