Check F-P link for "GO:0001026 TFIIIB-type transcription factor activity"

[ValWood]

GO:0001026 TFIIIB-type transcription factor activity currently is linked to GO:0006359 regulation of transcription from RNA polymerase III promoter but many of the core transcription factors are directly involved in , not regulating.... maybe a logical definition issue?

https://github.com/geneontology/go-annotation/issues/1522 https://github.com/geneontology/go-annotation/issues/1523

[ukemi]

@krchristie can you look at this?

[krchristie]

@ukemi - When we asked the RNA pol III researchers whether transcription factors such as TFIIIC were regulatory or part of the process, we got a bit of a mixed response, but slightly over half of the RNAP III researchers we contacted felt that transcription factors such as TFIIIC, and thus similarly TFIIIB, were both regulatory and part of the process. Yes, they are required for transcription to occur at all, but they are also regulating when that transcription occurs. Thus, we chose to make links saying that these types of transcription factors are both regulatory and part of the process.

That's the original logic.

[ValWood]

Was this referring to when general transcription occurs? or gene specific transcription? or both?

I presume some signal transduction would regulate when transcription occurs, in which case would these be considered the termination of a signalling pathway? Or are they another molecular function regulator?

It might be useful to have this level of knowledge if we add regulatory links into the ontology between a function and a process.

If not its fine as is, (although it might be best to omit these links if this is at all unclear) - I only queried it because these were some of the very few essential genes which were both "involved directly in a process", and "regulating a process", and the mechanism regulation was not clear (usually they are within process molecular function regulators).

[krchristie]

Both. While transcription factors are part of the mechanism of building the complex to get the RNAP (whichever one) to the right place, they are also regulating when transcription occurs.

[tberardini]

Any ontology edits necessary?

[ValWood]

I think the F-P relationship should be removed:

transcription factor activity, core RNA polymerase III binding
for some annotations:

[ValWood]

I don't understand my comments from 18 hours ago (maybe meant for a different ticket?)

I still think we probably shouldn't add F-P links based only on author statements. I'd prefer it if I could see some experiments demonstrating that TFIIIB was also regulating transcription. I don't see any in GO at present...

[tberardini]

Awaiting further clarification/approval of necessary ontology edits.

[ValWood]

Yep can close. There are IDA annotations to the regulation term, not sure why I didn't see them. I checked paper and is required for activation, so is regulation

[tberardini]

Thank you Val!