[Ontology-editors] forward and reverse transcription
Alexander Diehl
adiehl at informatics.jax.org
Wed Dec 3 06:47:21 PST 2008
Perhaps it is better to be completely clear in either the term name or
in an exact synonym:
DNA transcription = RNA transcription from a DNA template
RNA transcription = RNA transcription from an RNA template
reverse transcription = DNA transcription from an RNA template
-- Alex
Harold Drabkin wrote:
> 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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--
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
email: adiehl at informatics.jax.org
work: +1 (207) 288-6427
fax: +1 (207) 288-6131
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