DNA/RNA-templated transcription

[gocentral]

When Jane and I were making and rearranging the viral replication/transcription terms, we kept getting confused by RNA/DNA-dependent terms. Could we rename the following two terms, and any related children:

from: transcription, RNA-dependent ; GO:0001172 transcription, DNA-dependent ; GO:0006351 to: RNA-templated transcription ; GO:0001172 DNA-templated transcription ; GO:0006351

Becky

.... have assigned to David so you and Karen can double-check. Assign back to me for any edits.

Reported by: rebeccafoulger

Original Ticket: geneontology/ontology-requests/10475

[gocentral]

Hi Becky,

I don't see any problem with changing these names as you suggest, providing we convert the DNA-dependent and RNA-dependent names to synonyms. These names predate the transcription overhaul and I suspect are based in the way people use to talk about biochemical assays for transcription as being dependent on either DNA or RNA. But if you think the -templated names are clearer, it's fine with me.

-Karen

Original comment by: krchristie

[gocentral]

Hi again Becky,

Regarding the questions in your email:

Also, we're trying to work out what's covered by transcription, RNA-dependent ; GO:0001172

-Do you know if there is any ss versus ds criteria for the input and output? -Is GO:0001172 the same as RNA replication, or is it part of (or a type of) RNA replication?

I am not aware of there being any criteria for ss vs ds RNA for the template for transcription. I'm pretty sure that either ss RNA or ds RNA can be used as a template for RNA transcription. However, I'm less clear on the product. It seems like it would need to be ss RNA to be used a a substrate for translation, but don't depend on my memory for that.

As I understand it, the "distinction" between "RNA-templated transcription" and "RNA replication" is probably messy. I talked to Julie Park, and I think also Harold, about RNA (templated) transcription versus RNA replication during the transcription overhaul. If I recall correctly, Julie seemed to think that there is sometimes not a mechanistic difference between RNA-templated transcription and RNA replication, but rather more of a difference in semantics and "ultimate purpose" of a given RNA copy made from an RNA template, which may depend on the timing in the life cycle of the virus, and that "ultimate purpose" may even depend a bit on the perspective of the person writing the paper, depending on what their primary research interest was. At the time, we felt we were not prepared to spend any time looking into the various viral life cycles to make a call.

If I remember correctly, there may be some viruses where replication of the RNA genome may be as simple as merely transcribing a copy. However, transcription alone is often not able to copy the entire viral genome RNA as transcription generally starts internally, so there are cases where you could consider "RNA-templated transcription" to be a step of "RNA replication" where "RNA replication" requires some additional steps to complete the replication since transcription often can't copy the entire viral genome. I don't know if it would work to call "RNA-templated transcription" the process of making an RNA copy from an RNA template, and "RNA replication" everything which is required to make a copy of an RNA genome, which might sometimes be only "RNA-templated transcription", and sometimes will be that plus some additional things, one of which might be making the second RNA strand of a dsRNA genome (assuming you can exclude that from txn).

That's about the limit of my knowledge/memory of viral transcription. It's pretty complex and varied.

-Karen

Original comment by: krchristie

[gocentral]

Hi Karen,

We had much the same thoughts on the viral replication/transcription front. Viralzone group transcription and replication where necessary (http://viralzone.expasy.org/all_by_species/915.html). In GO, we've been making viral genome replication terms, which have HAS_PART links to transcription terms. Which is how we came across GO:0001172.

We were also rather confused about 'RNA-dependent DNA replication ; GO:0006278' and 'reverse transcription ; GO:0001171' being under DNA replication, but that's probably another story.

Glad you've no objections to the 'templated' name changes. cheers, Becky

Original comment by: rebeccafoulger

[gocentral]

Hi Becky,

I have some additional comments I can share from when I was doing the transcription overhaul.

Prior to the transcription overhaul, the term "reverse transcription" was incorrectly placed under "transcription" which was, if I recall correctly, badly defined as "either the synthesis of RNA from a DNA template or the synthesis of DNA from an RNA template". Julie, Harold, and I felt that this was an inaccurate conflation of the two different uses of the word "transcription" that failed to recognize that "reverse transcription" is not a type of transcription at all, but rather the reverse of it, at least as per the simplistic "central dogma" definition of transcription as RNA from DNA.

Julie knew more about viral replication than I did, but if I recall correctly, "reverse transcription" only occurs in the context of certain types of viruses with a complex life cycle where there is a DNA genome that is transcribed into RNA at some point, and which requires "reverse transcription" as part of the process of regenerating the DNA genome to be packaged into the virion.

Then, I see that "telomere maintenance via telomerase" is also under "RNA-dependent DNA replication". Telomerase, like reverse transcriptase, also uses an RNA template, in this case an intrinsic part of the telomerase complex, to synthesize DNA.

Basically, I think you could think of "RNA-dependent DNA replication" as "RNA-templated DNA biosynthetic process"

-Karen

Original comment by: krchristie

[gocentral]

Thinking about this now, I wonder if reverse transcription should be is a DNA biosynthetic process, but be a part of the replication. Replication would also include second strand synthesis?

Original comment by: ukemi

[gocentral]

• status: open --> closed-accepted

Original comment by: ukemi

[gocentral]

Replication and transcription terms are now all changed to 'templated' with 'dependent' synonyms added.

Original comment by: ukemi