definition correction for GO:0045944

[gocentral]

There seems to be an inaccuracy in the definition of “positive regulation of transcription from RNA polymerase II promoter” (GO:0045944). The definition is “Any process that activates or increases the frequency, rate or extent of transcription from the RNA polymerase II promoter”. It should be “…transcription from a RNA polymerase II-specific promoter”. The children of GO:0045944 have definitions that have phrases similar to the suggested phrase.

Reported by: slaulederkind

Original Ticket: geneontology/ontology-requests/7465

[gocentral]

• labels: --> Other term-related request

Original comment by: slaulederkind

[gocentral]

I don't really see the need to change the wording. It seems perfectly appropriate as is. I am not currently aware of any promoters that can be utilized by more than one type of the euk nuclear RNA polymerases, so the addition of the word "specific" seems redundant, since by saying that it's an RNAP II promoter, you've already stated the specificity. I also don't see that the "II-specific promoter" phrasing is used in all the children. It looks like it is used in a very small fraction of terms. I get 16 hits for the query "II-specific promoter" while I get 136 hits for the query "II promoter". Thus if consistency is the issue, I think it may be better to change all instances of "II-specific promoter" to "II promoter".

-Karen

Original comment by: krchristie

[gocentral]

The way it is worded now makes it sound like the term is referring to the promoter for the RNA polymerase II gene, not a promoter acted upon by RNA polymerase II.

Original comment by: slaulederkind

[gocentral]

Hmm, it does not convey that impression to me. The standard terminology in the transcription field does not include the use of the word specific.

-Karen

Original comment by: krchristie

[gocentral]

Although I really don't think annotators should be confused by this, I can see Stan's point.

How about:

“Any process that activates or increases the frequency, rate or extent of transcription from the promoter of a gene transcribed by RNA polymerase II.”

Original comment by: ukemi

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: ukemi

[gocentral]

I like David's wording, I can go with that.

-Karen

Original comment by: krchristie

[gocentral]

That sounds good. You should probably change the parent and sibling term definitions to match the new definition of this term.

Original comment by: slaulederkind

[gocentral]

Hmm, yes, the main reason I'm not so keen on this change. There are over a hundred terms that refer to promoters in this way. It seems like a lot of work, especially now that it's assigned to me, for little gain....

Original comment by: krchristie

[gocentral]

In the course of the transcription overhaul work, I noticed some definitions where the article "the" is used instead of "an" producing the impression that there is only one RNAP II promoter.

Then I realized that's basically the issue in this SF item, where Stan pointed out one specific case, see SF item. The def he points out says "the RNA polymerase II promoter" instead of "an RNA polymerase II promoter". Changing "the" to "an" would remove the impression that it is the promoter of the RNA polymerase gene.

Using OBO-Edit searching for a number of known strings for these definitions gives these counts:

"transcription from an RNA polymerase" = 79 matches "transcription from the RNA polymerase" = 10 matches "I-specific promoter" = 23 matches

David and Karen discussed this on 5/6/2011 and agreed that the problem definitions are the ones using the phrase "the RNA polymerase __ promoter" instead of "an". We are agreed to change both of the less common strings to the most common string, so all will use the "transcription from an RNA polymerase" phrasing.

-Karen

Original comment by: krchristie

[gocentral]

Fixed this. Changed all language to the most common form, as detailed in previous comment. This comment lists the specific terms affected.

-Karen

remove Pol __-specific type language (where ___ is I, II, or III):

GO:0001009 - transcription from RNA polymerase III type 2 promoter GO:0001014 - snoRNA transcription from a type 2 RNA polymerase III promoter GO:0001015 - snoRNA transcription from an RNA polymerase II promoter GO:0001035 - transcription from RNA polymerase III type 3 promoter GO:0001041 - transcription from a RNA polymerase III hybrid type promoter GO:0006360 - transcription from RNA polymerase I promoter GO:0006366 - transcription from RNA polymerase II promoter GO:0006368 - transcription elongation from RNA polymerase II promoter GO:0006383 - transcription from RNA polymerase III promoter GO:0006385 - transcription elongation from RNA polymerase III promoter GO:0010688 - negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter GO:0010689 - negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to chemical stimulus GO:0010690 - negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to stress GO:0010691 - negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels GO:0042789 - mRNA transcription from RNA polymerase II promoter GO:0060962 - regulation of ribosomal protein gene transcription from RNA polymerase II promoter GO:0060963 - positive regulation of ribosomal protein gene transcription from RNA polymerase II promoter

Note that 5 terms with this phrasing in the definitions were not changed because they all about to be obsoleted because they were terms for general/basal/non-specific or specific transcription.

"the RNA polymerase promoter" to "an RNA polymerase promoter" changes (where ___ is I, II, or III)

GO:0045943 - positive regulation of transcription from RNA polymerase I promoter GO:0045944 - positive regulation of transcription from RNA polymerase II promoter GO:0045945 - positive regulation of transcription from RNA polymerase III promoter GO:0046019 - regulation of transcription from RNA polymerase II promoter by pheromones GO:0060260 - regulation of transcription initiation from RNA polymerase II promoter GO:0060261 - positive regulation of transcription initiation from RNA polymerase II promoter GO:0060633 - negative regulation of transcription initiation from RNA polymerase II promoter GO:0070898 - RNA polymerase III transcriptional preinitiation complex assembly GO:0001074 - RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly GO:0001075 - sequence-specific core promoter binding RNA polymerase II transcription factor activity involved in preinitiation complex formation

Original comment by: krchristie

[gocentral]

• status: open --> closed-fixed

Original comment by: krchristie