[Ontology-editors] forward and reverse transcription

Harold Drabkin hjd at informatics.jax.org
Wed Dec 3 06:49:45 PST 2008 

The fact that term has been used in a different scope from which it was 
originally intended means that there is extreme ambiguity in it's use, 
which is sloppy.

We need to ask
1. what IS transcription; who coined the term and in what circumstances.
2. more related to Midori's 1rst question: is the reverse of the process 
a type of the process; I would say no in any case I can think of.
So, reverse transcription is not a type of transcription, no matter what 
we decide IS "transcription.

and, choking on the dust I'm bushing off from a box in my attic,  from 
a  textbooks over 30 years old" Transcription is the process by which 
information contained in DNA is copied, by base paring, to form a 
complementary sequence of ribonucleotides, a RNA chain.."and similar 
scattered references in a 1966 Cold Spring Harbor Symposium volume (XXXI).

But I would still be comfortable distinguishing DNA based transcription 
from RNA based transcription

Alexander Diehl wrote:
> Harold and Karen,
>
> In viruses, such as Corona and Toga viruses, (+)-strand subgenomic 
> RNAs that act as mRNA are made from a negative stranded genomic RNA 
> template.  Virologists refer to this process as "transcription" in 
> hundreds of papers, a usage which dates back over 30 years 
> (PMID:173940).  This not RNA replication, but a different process 
> (using many of the same enzymes to be sure) under a different type of 
> regulation.
>
> I really don't think you should rely on undergraduate textbooks, no 
> matter how notable the authors, to decide this issue.
>
> Thanks,
>
> Alex
>
>
> Karen Christie wrote:
>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Ontology-editors mailing list
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>>>>>>>
>>>>>
>>>
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