[Ontology-editors] forward and reverse transcription

Wed Dec 3 02:36:42 PST 2008

p.s. It also sounds as though "transcription" has been used with more than 
one meaning, so GO may end up not having a term named simply 
"transcription", but instead keeping only terms with more specific names.

m

On Wed, 3 Dec 2008, Midori Harris wrote:

> 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
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Ontology-editors mailing list
>>>>>>> Ontology-editors at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>>>>>> 
>>>>> 
>>> 
>> 
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>