#945 PANTHER:PTHR11829_AN0

[Valerie Wood]

Fission yeast has a number of mappings from this family to
GO:0003705
sequence-specific distal enhancer binding RNA polymerase II transcription factor activity

as far as I'm aware, fission yeast don't have "distal enhancers" so this may warrant a taxon filter?

Also, there are sill mappings to terms like "promoter binding " which hve been obsolete for a while.

We would like to include the PAINT annotations for fission yeast, but I notice there are still a number of false annotation reported on the tracker (I checked and the most recent paint file is December, is that correct?), so we'll wait a while until the current issues are fixed before we try to load again.

Thanks

Val

[Rama balakrishnan]

Hi,

I don't think there has been much PAINT curation in the recent months.

Rama

[Pascale Gaudet]

See also sourceforge.net/p/geneontology/ontology-requests/10848/

Quoting Chris:
"If you look in AmiGO you can see the IBA annotations propagated from this Opisthokont node:
http://www.pantree.org/node/annotationNode.jsp?id=PTN000215025

The non-metazoan annotations seem unjustified to me. Either the common ancestor used these genes for tissue development (unlikely) or there was convergence (intriguing but requires more evidence)."

We need to take a look at those annotations

• Pascale

[rach_huntley]

Does this issue still need working on? The ontology SF issue referred to above has been resolved.

[Valerie Wood]

I don't know, it depends if the PAINT annotations are resolved.

i.e yeast should not have annotations to
GO:0003705
sequence-specific distal enhancer binding RNA polymerase II transcription factor activity

I can't check this as we aren't importing PAINT annotation right now (waiting for the SF tracker items to be fixed, and then we'll import)

val

[rach_huntley]

I can't see any PAINT annotations to this term, but there are manual annotations from CGD (to Q1WCU5 and Q1WCU6) and one from SGD (to P07261).

[Valerie Wood]

Thats odd. I thought this "sequence-specific distal enhancer" didn't apply to yeast. I was going to request a taxon restriction for this. Maybe it doesn't mean what I thought, not toatally clear from the def, but odd that there is only one annotation. Will check with SGD.

Val

[Valerie Wood]

RNA polymerase II distal enhancer sequence-specific DNA binding

The binding term
GO:0000980
Name RNA polymerase II distal enhancer sequence-specific DNA binding
has the following comment:

Comment Note that distal enhancers of the type found in mammalian cells are not known to occur in either Saccharomyces cerevisiae or Schizosaccharomyces pombe. While some S. cerevisiae literature does refer to sequences distal to the initiation site, these distal sites do not seem to function independently of position or orientation as mammalian distal enhancers do and are not considered to be enhancers.

So I think the taxon restriction should be added for all ascomycetes for any term containing "distal enhancer" in the absence of any
good experiment to demonstrate otherwise ....

I will open a ticket for this on the ontology tracker. This can then be closed as the taxon restriction will override the PAINT annotations (I hope?)

val

[Valerie Wood]

I see Panther mappings for S.c. too:
http://amigo.geneontology.org/amigo/search/annotation?q=:&fq=regulates_closure:%22GO:0003705%22&sfq=document_category:%22annotation%22

[Rama balakrishnan]

Hi Val, all,

I am checking the SGD manual annotation to this term. I am pretty sure yeast doesn't have distal enhancers. But the paper used for the manual annotation mentions that yeast Gcr1 binds to the enhancer and UAS sequence of Ty-2.
http://www.ncbi.nlm.nih.gov/pubmed/9271107
I don't think the authors use the word 'enhancer' as it is used in humans and other mammals. I have written to Karen to confirm. I will keep you posted.

Rama

[Rama balakrishnan]

Hi,

Karen confirmed that the word enhancer was used in yeast literature early on in the
sense of the region proximal to the core promoter, that increases maximal
activation over the amount you could get with a more minimal promoter
sequence.

I have removed the manual annotations in SGD (will take until next week for you to see this change though). Sure, please add taxon constraints.

Rama