[Ontology-editors] forward and reverse transcription

[Harold Drabkin]

That's why I think I like the concepts of a DNA transcripiton and an RNA 
transcripiton, both of which yield a transcript.


Midori Harris wrote:
> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>
>>>>
>>>
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