'promoter' as a cellular component

[gocentral]

Possibly this has been raised previously, and there is a reason as to why promoter/enhancer is not within the cellular component ontology.

However, based on PMID:17505061, specifically the ChIP assay in Fig 2, I would like to propose that promoter and enhancer are added to the CC ontology. I don't feel that ChIP analysis is sufficient evidence to support annotation to the MF terms 'promoter binding' or 'enhancer binding', as it is possible that the subject of the ChIP asssy is part of a protein complex in those regions, and it is another protein that is actually binding the DNA.

However I would appreciate other people's thoughts on this, if it is generally felt that ChIP analysis is sufficient for annotation to these MF terms, I will go ahead and add these annotations.

Thanks, V

Reported by: vkhodiyar

Original Ticket: geneontology/ontology-requests/8412

[gocentral]

This was discussed at a GO meeting in Cambridge in 2007. In the minutes (link below), search for "Overlap/connections between GO and SO?"

http://wiki.geneontology.org/index.php/GO\_Consortium\_Meeting.

With the development of column 16, it may make more sense to use a more general GO component term and put a specific SO term ID in column 16.

In addition, please note that the single word "promoter" is ambiguous as to exactly which portion of the transcription regulatory region is being referred to and is thus being removed from the MF ontology. So if there is a decision to make terms in CC for these types of regions, please make sure that the terms use phrasing consistent with what is in the MF ontology for the "transcription regulatory region DNA binding" terms.

-Karen

Original comment by: krchristie

[gocentral]

Commenting on your last question regarding whether "ChIP analysis is sufficient for annotation to these MF terms", no, CHiP analysis tells you which proteins can be localized to a given region, NOT which ones are directly binding. Many may be localized via protein-protein interactions with other proteins that actually bind DNA/chromatin.

Also, please note that the term "promoter binding" has been agreed to be obsoleted, see wiki:

http://wiki.geneontology.org/index.php/Proposal\_to\_obsolete\_%22promoter\_binding%22\_and\_child\_terms

-Karen

Original comment by: krchristie

[gocentral]

Here's the SF item from the previous discussion: https://sourceforge.net/tracker/index.php?func=detail&aid=1587313&group\_id=36855&atid=440764

Since 'enhancer binding' and 'promoter binding' can not be consistently defined (hence their obsoletion), I don't think it makes sense to have the enhancer or promoter terms in CC.

Can you annotate to 'chromatin ; GO:0000785'?

Original comment by: rebeccafoulger

[gocentral]

Thanks both for your comments, I will use GO:0000790 nuclear chromatin for my current annotations. Regards, V

Original comment by: vkhodiyar

[gocentral]

Ok- will close this item then. Thanks!

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-invalid

Original comment by: rebeccafoulger