[Ontology-editors] forward and reverse transcription
Alexander Diehl
adiehl at informatics.jax.org
Wed Dec 3 07:16:48 PST 2008
We represent the language of biologists. Usage changes over the years.
Just because the original meaning of the word has expanded does not mean
other usages are necessarily wrong or sloppy. Furthermore, we have long
accepted that different communities of biologists use the same word in
different ways. It is up to us create the appropriate terms and write
term names and definitions that reflect the different usages we see in
the whole of biology. It is not for us to decide that an accepted usage
of transcription in the phrase "reverse transcription" cannot be
represented in the GO -- it should, perhaps as a term name, perhaps an
an exact synonym.
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.
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
2. transcription of mRNA from an RNA template
3. transcription of DNA from an RNA template
4. transcription of DNA from a DNA template (!)
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.
(please don't fall out of your chair!)
-- Alex
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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