[Ontology-editors] forward and reverse transcription
Alexander Diehl
adiehl at informatics.jax.org
Wed Dec 3 07:54:41 PST 2008
Harold,
I don't know of an example of 4 to cite -- it simply follows from the
idea of transcription being "the synthesis of a strand of nucleic acid
of a template strand of nucleic acid." We can obviously by fiat in the
GO state that synthesis of DNA from a DNA template is not a type of
transcription, since this particular usage is not supported by the
literature.
But "reverse transcription" is a named biological process in the
literature, and we must represent it in the GO with the string "reverse
transcription" either as a term name or synonym. Whether we can agree
upon a broad-enough definition of transcription to accommodate this term
as a child is the question. In any case whatever we choose
"transcription" to be in the GO it must cover at a minimum #1 and #2 of
my list, lest we ignore 30+ years of virology, and using my suggested
definition of transcription allows it to accommodate #3 as well.
-- Alex
Harold Drabkin wrote:
> 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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>>>>
>>>
>>
>
--
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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