[Ontology-editors] forward and reverse transcription

[Karen Christie]

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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