Too much specificity "tRNA transcription"

[gocentral]

Original query:

Re:
GO:1900446 ; negative regulation of tRNA transcription from RNA polymerase III promoter
biological_process
Any process that stops, prevents or reduces the frequency, rate or extent of tRNA transcription from RNA polymerase III promoter.

From our recent discussion, should GO:1900446 (above) warrant a term ? Unless I am mistaken , there is no specific regulator for negatively regulating tRNA transcription which is separable from general negative regulation of transcription from RNA polymerase III. Is this a case where you would advise users to capture the information in an extension, as it is not a biologically separable process ?

similarly tRNA transcription, is this an process which can be distinguished from
transcription from RNA polymerase III
or
transcription from mitochondrial prompter?

(there is a possibility my biological knowledge is out of date here and RNA pol III does have "gene specific" regulators but I have not seen anything.....)

Val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9410

[gocentral]

Response from Karen:

Everything I know is consistent with what Val has said. I am not aware of a regulator of RNAP III txn that is specific to tRNAs. My understanding of RNAP III txn is that it is constitutively on when the components (e.g. RNAP III, TFIIIA, TFIIIB, TFIIIC, are present), and that there is one highly conserved general negative regulator, Maf1, that generally shuts down all RNAP III txn. So, I also do not see a good reason to have the term GO:1900446. The existing term "negative regulation of transcription from RNA polymerase III promoter" (GO:0016480) should be sufficient for the regulation of RNAP III txn that I am aware of.

Going further, I question the need for the term "tRNA transcription from RNA polymerase III promoter" (GO:0042797). It is not really different from the term "transcription from RNA polymerase III type 2 promoter" (GO:0001009) which we added as part of the txnOH and which, as far as I know, is inclusive of all nuclear tRNA txn in eukaryotes, though GO:0001009 also includes txn of any other RNAs made from a type 2 promoter. Historically, GO:0042797 preceeded the txnOH and was not updated by it. We did not deal with any terms for txn of a specific "type" of RNA, though we have been leaning towards the idea of removing them as they do not represent a specific process, are not well integrated with the terms that do represent known processes, and cause problems like this.

Original comment by: ValWood

[gocentral]

Other comments

The term "tRNA transcription"(or whatever), would become a "narrower than synonym"
A comment could say something along the lines that "tRNA transcription is a "narrow synonym" rather than a more specific child term because the more specific term would be applicable to the same set of genes as the parent (i.e ALL genes which are involved in transcription from RNA polymerase III promoter are also involved in tRNA transcription).

The existence of a single term is much better for annotation consistency.The litmus test is that ALL of the gene products annotated to
transcription from RNA polymerase III promoter
could also be annotated to
tRNA transcription from RNA polymerase III promoter
Establishing child term which provide no additional information about the process, mean that existing annotation is no longer to the most specific term that it could be, a curator would need to move the annotation down, but this is is pointless when the term has the same meaning …

The tRNA's belongs in the extension, the child term is "gene product specific", albeit a group of gene products (tRNAs)

I think that's all the relevant stuff....

Original comment by: ValWood

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: ValWood

[gocentral]

This has been brought up again from Susan:
https://sourceforge.net/tracker/index.php?func=detail&aid=3530547&group\_id=36855&atid=440764

I will go ahead and propose obsoletion of GO:1900446.

Then I'll leave merging of the tRNA terms to you, as necessary Karen. We have:
transcription from RNA polymerase III type 2 promoter ; GO:0001009
tRNA transcription ; GO:0009304
tRNA transcription from RNA polymerase III promoter ; GO:0042797

Becky

Original comment by: rebeccafoulger

[gocentral]

Hi,

In my opinion, this term:
"tRNA transcription from RNA polymerase III promoter ; GO:0042797"

could be merged into this term:
"transcription from RNA polymerase III type 2 promoter ; GO:0001009"

because I am not aware of any tRNA transcription in any eukaryote (the only organisms with RNAP III) that is not from a type 2 promoter.

However, this term:
tRNA transcription ; GO:0009304

cannot be merged into a RNAP III term because tRNAs are not transcribed by RNAP III in organisms which only have a single RNAP, e.g. eubacteria like E. coli, or Archaea.

I might suggest asking Jim Hu and Debbie Siegele about whether they think there is any need for a tRNA specific term for prokaryotes. If not, I would be inclined to obsolete this term as not representing a specific process. David and I were somewhat inclined to obsolete all of the transcription terms mentioning a specific "type" of RNA in the txn OH because the "type" of RNA is not the distinguishing characteristic of any transcriptional process, but decided it was too much to deal with at the time.

If JIm & Debbie do think that there is a process specific to tRNA txn in prokaryotes, then based on the rules we followed in the txnOH, a term should be made specific to prokaryotes.

-Karen

-Karen

Original comment by: krchristie

[gocentral]

• assigned_to: kchris --> ukemi

Original comment by: krchristie

[gocentral]

Hi,

In my opinion, this term:
"tRNA transcription from RNA polymerase III promoter ; GO:0042797"

could be merged into this term:
"transcription from RNA polymerase III type 2 promoter ; GO:0001009"

because I am not aware of any tRNA transcription in any eukaryote (the only organisms with RNAP III) that is not from a type 2 promoter.

However, this term:
tRNA transcription ; GO:0009304

cannot be merged into a RNAP III term because tRNAs are not transcribed by RNAP III in organisms which only have a single RNAP, e.g. eubacteria like E. coli, or Archaea.

I might suggest asking Jim Hu and Debbie Siegele about whether they think there is any need for a tRNA specific term for prokaryotes. If not, I would be inclined to obsolete this term as not representing a specific process. David and I were somewhat inclined to obsolete all of the transcription terms mentioning a specific "type" of RNA in the txn OH because the "type" of RNA is not the distinguishing characteristic of any transcriptional process, but decided it was too much to deal with at the time.

If JIm & Debbie do think that there is a process specific to tRNA txn in prokaryotes, then based on the rules we followed in the txnOH, a term should be made specific to prokaryotes.

-Karen

-Karen

Original comment by: krchristie

[ukemi]

@jimhu-tamu can you please have a look at this old ticket and comment? I'm trying to clean up some old GH tickets.

[jimhu-tamu]

I don't think we need this level of granularity for bacterial transcription either. There are differences in the regulation of tRNAs and rRNAs from most other mRNAs, but it's the same RNA polymerase in the eubacteria.

[pgaudet]

What I propose to do now:

•  obsolete GO:1900446 (1 annotation SGD)
•  Merge
  "tRNA transcription from RNA polymerase III promoter ; GO:0042797"
  into
  "tRNA transcription ; GO:0009304"

OK @krchristie @jimhu-tamu ?

Outstanding question: there are a number of other polII terms; right now I was not planning to do anything with those; if anyone wants something done, do let me know.

• '5S class rRNA transcription from RNA polymerase III type 1 promoter'
• 'snRNA transcription from RNA polymerase III promoter'
• 'transcription from a RNA polymerase III hybrid type promoter'
• 'transcription from RNA polymerase III type 2 promoter'
  -- 'snoRNA transcription from a type 2 RNA polymerase III promoter'
• 'transcription from RNA polymerase III type 3 promoter'

Thanks, Pascale

[pgaudet]

Obsoletion notice sent Nov 23
Dear all,

The proposal has been made to obsolete 'GO:1900446 negative regulation of tRNA transcription from RNA polymerase III promoter’. The reason for obsoletion is that there is no specific regulator for negatively regulating tRNA transcription which is separable from general negative regulation of transcription from RNA polymerase III.
There is a single protein annotated to this term by SGD. Comments can be added to the ticket:

#9617

We’d like to proceed and obsolete this term on Nov 30, 2017. Unless objections are received by Nov 30, 2017, we will assume that you agree to this change.

Thanks, Pascale

[pgaudet]

Hello,

As a last action for this ticket I propose to merge the following terms into their parent (ie removing terms with 'type x' promoter. This can be captured in the MF. These are

GO ID	Label	EXP	Merge into
GO:0001009	transcription from RNA polymerase III type 2 promoter	16	GO:0006383 transcription by RNA polymerase III
GO:0001035	transcription from RNA polymerase III type 3 promoter	1	GO:0006383 transcription by RNA polymerase III
GO:0001041	transcription from a RNA polymerase III hybrid type promoter	8	GO:0006383 transcription by RNA polymerase III
GO:0042791	5S class rRNA transcription from RNA polymerase III type 1 promoter	8	rename '5S class rRNA transcription from RNA polymerase III' -> '5S class rRNA transcription by RNA polymerase III'
GO:0001014	snoRNA transcription from a type 2 RNA polymerase III promoter	0	rename 'snoRNA transcription by RNA polymerase III'
GO:0001022	transcription initiation from RNA polymerase III type 1 promoter	0	GO:0006384 transcription initiation from RNA polymerase III promoter
GO:0001036	transcription initiation from RNA polymerase III hybrid type promoter	0	GO:0006384 transcription initiation from RNA polymerase III promoter
GO:0001023	transcription initiation from RNA polymerase III type 2 promoter	0	GO:0006384 transcription initiation from RNA polymerase III promoter
GO:0001024	transcription initiation from RNA polymerase III type 3 promoter	1	GO:0006384 transcription initiation from RNA polymerase III promoter
GO:0001020	RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly	1	GO:0070898 RNA polymerase III transcriptional preinitiation complex assembly
GO:0001043	RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly	0	GO:0070898 RNA polymerase III transcriptional preinitiation complex assembly
GO:0000999	RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly	0	GO:0070898 RNA polymerase III transcriptional preinitiation complex assembly
GO:0001021	RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly	0	GO:0070898 RNA polymerase III transcriptional preinitiation complex assembly
GO:0001189	RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript	2	GO:0001188 RNA polymerase I transcriptional preinitiation complex assembly
GO:0042790	transcription of nucleolar large rRNA by RNA polymerase I		rename 'nucleolar large rRNA transcription by RNA polymerase I'

I attach a file with the exact annotations to keep as reference.

Thanks, Pascale

ticket-9617-RNApolIII_types-BP-annotations.xlsx

[pgaudet]

@krchristie @ValWood @RLovering Is this OK with you ?

Thanks, Pascale

[RLovering]

I agree with the majority of the proposals. However:

GO:0042791 | 5S class rRNA transcription from RNA polymerase III type 1 promoter | 8 | rename '5S class rRNA transcription from RNA polymerase III'
to be consistent with the other renaming should be rename '5S class rRNA transcription by RNA polymerase III'
I am not sure about

GO:0001022 | transcription initiation from RNA polymerase III type 1 promoter | 0 | GO:0006384 transcription initiation from RNA polymerase III promoter
should this be GO:0006384 transcription initiation at RNA polymerase III promoter (need to agree text and apply to all initiation terms if appropriate

Ruth

[krchristie]

Like Ruth, I agree with most of the merges and other changes.

Regarding Ruth's two suggestions:

GO:0042791 | 5S class rRNA transcription from RNA polymerase III type 1 promoter | 8 | rename '5S class rRNA transcription from RNA polymerase III'
to be consistent with the other renaming should be rename '5S class rRNA transcription by RNA polymerase III'

I agree that having dropped the word promoter out of the term name, that it should also now say "by" RNA polymerase III, rather than "from".

I am not sure about
GO:0001022 | transcription initiation from RNA polymerase III type 1 promoter | 0 | GO:0006384 transcription initiation from RNA polymerase III promoter
should this be GO:0006384 transcription initiation at RNA polymerase III promoter (need to agree text and apply to all initiation terms if appropriate

It sounds fine to me to say transcription initiation "from" RNA polymerase x promoter, so I don't think this needs to be changed to use the word "at" instead. I would use "at" if I were talking about the initiation site, but the promoter isn't a specific site, but a region. Personally, I don't think this one is worth the work, especially if "from" is already used in other terms.

[pgaudet]

Thanks for the feedback @krchristie and @RLovering

I left the naming of the 'initiation' as is (" transcription initiation from RNA polymerase III promoter" etc), and fixed the one that was inconsistent.

I'll merge this one.

Thanks, Pascale