[Ontology-editors] forward and reverse transcription

Harold Drabkin hjd at informatics.jax.org
Wed Dec 3 07:27:28 PST 2008 

Alexander Diehl wrote:
>
>
> Furthermore, in 1966, reverse transcription had not even been 
> discovered, and was probably considered impossible by biologists of 
> the time, so no definition would contain a reference to it.
But a reverse of a process is still not and instance or part of a 
process I would think.
>
> To me, transcription simply means the synthesis of a strand of nucleic 
> acid of a template strand of nucleic acid.  Types of transcription 
> include:
>
> 1.  transcription of mRNA from an DNA template 
agree
> 2.  transcription of mRNA from an RNA template
agree
> 3.  transcription of DNA from an RNA template
agree
> 4.  transcription of DNA from a DNA template (!)
>
Alex, can you give me an instance where #4 above is/was used?

> Furthermore transcription is part of the process of
> 4.  genomic RNA replication in RNA viruses
> 5.  DNA replication
>
> and probably some other processes as well.

What transcription is a part of is not the question at the moment 
(certainly creation of the RNA primer for DNA synthesis is part of some 
DNA replication).
I still contend that the use of "transcription" is at least confined to 
a process of making RNA molecule


>
> (please don't fall out of your chair!)
>
I don't have enough room in my cubicle to do that 8-)

>
>
> Harold Drabkin wrote:
>> 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
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>
>>>>>
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