Change parent for a bunch of promoter proximal promoters

[ValWood]

And refine def (these are implicitly promoter proximal because the def already mentions promoter, this is just more precise)

Ace2_UAS Update def: An RNA polymerase II proximal promoter element

iron_repressed_GATA_element Update def: An RNA polymerase II proximal promoter element

CRE rename CRE_Proximal Update def: An RNA polymerase II proximal promoter element

CSL_response_element Update def: An RNA polymerase II proximal promoter element

MCB Update def: An RNA polymerase II proximal promoter element

CuRE Update def: An RNA polymerase II proximal promoter element

DRE Update def: An RNA polymerase II proximal promoter element

PCB Update def: An RNA polymerase II proximal promoter element

FLEX_element Update def: An RNA polymerase II proximal promoter element

GATA_box Update def: An RNA polymerase II proximal promoter element

HSE Update def: An RNA polymerase II proximal promoter element

AP_1_binding_site Update def: An RNA polymerase II proximal promoter element

CDRE_motif Update def: An RNA polymerase II proximal promoter element

STREP_motif Update def: An RNA polymerase II proximal promoter element

forkhead_motif Update def: An RNA polymerase II proximal promoter element

zinc_repressed_element Update def: An RNA polymerase II proximal promoter element

CCAAT_motif Update def: An RNA polymerase II proximal promoter element

TR_box Update def: An RNA polymerase II proximal promoter element

[ValWood]

Change parent to http://www.sequenceontology.org/browser/current_svn/term/SO:0001668

[ValWood]

Outstanding, I don't know if these are always proximal and some are not restricted to yeast

AACCCT_box A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site.

sterol_regulatory_element

(For the others, if they are used outside yeast the papers refer to a promoter proximal context)

@pgaudet @RLovering

[ValWood]

• mating_type_M_box

[ValWood]

@RLovering @ukemi

based on the current defs do you agree with this change?

[RLovering]

Hi Val

thanks for pointing to this ticket and also for your comments on the non-mammalian motifs/elements as there are obviously a lot to cover.

To be honest my concern is that I am not sure that some of these are 'always' in the proximal promoter. The other concern is that GATA_box is currently a child of core_promoter_element (no definition) whereas CSL_response_element is a child of promoter_element (no definition but synonym is general transcription factor binding site, core promoter element which is worrying). Neither of these terms have a relation to promoter. possibly it would be safer to just put them under regulatory_element.

Basically I could look up every motif/element in pubmed and see where it appears to lie wrt promoter/enhancer etc, but I would rather get people who are working in this area to confirm which ones are always proximal to the promoter (and have the definition for this region agreed) and which ones are always in enhancers and which ones can be in either region, if indeed these distinctions can be made.

Ruth

[ValWood]

Good points. None of the terms we requested are "core promoter", and references to "core promoter' should be removed. I'm not sure which ones are present outside fungi. Fungal specific ones could be "promoter proximal", but as you say the safest option would be to move all to

TF_binding_site http://www.sequenceontology.org/miso/current_svn/term/SO:0000235

I think the reason they were placed under promoter element is that this is broad in SO. It has 2 descendants regulatory_promoter_element core_promoter_element

but it is also undefined so this isn't very clear.....

I see what you mean ;) I wonder why there are no definitions...

[davidwsant]

Hi @ValWood and @RLovering,

The structure of the terms relating to regulatory regions has been restructured. The terms with no definitions have now also been updated to have definitions. Some of the terms in mention have moved, such as iron_repressed_GATA_element is now a child of GATA_box(SO:0001840), which is a child of core_eukaryotic_promoter_element(SO:0001660), which is a child of promoter_element(SO:0001659).

It looks like you were requesting that many terms that are mostly under promoter_element SO:0001659 be moved to TF_binding_side SO:0000235 . Promoter_element overlaps TF_binding_site. Considering that terms have been restructured, would you mind looking over the changes and determine if you would still like to make any changes? If you would like to move terms, please give specifics.

Thank you,

Dave Sant

[ValWood]

Hi David. I can see some issues. I will open tickets and tag the relevant people. It might not be today...

v

[davidwsant]

Hi Val,

Thanks for looking at them. I think opening new tickets is a good idea. I will close out this issue and look for the new ones as they come.

Thanks,

Dave

[ValWood]

Apologies I only just got chance to look at this.

I think my main concern is housing the transcription factor binding sites under "promoter element" while the definition of "promoter" is unclear and self referencing

"An element that can exist within the promoter region of a gene."

I then found "promoter region" (which isn't a parent oddly)? and this is defined "A region of sequence which is part of a promoter"

This seems even weirder because these 2 concepts now reference each other, but aren't related.

I think the definitions of these promoter terms (exactly what they include, are critical to move forward to evaluate whether other terms are correctly positioned). v