gocentral
commented
18 years ago Logged In: YES user_id=473890
I completely agree that a term called "transcription factor activity, enhancer binding" should not specify promoter binding as part of its definition and completely agree with Alison's statements defining enhancers.
-Karen
Original comment by: krchristie
Hi,
Can GO please consider the following request related to Molecular Function term #3705: RNA polymerase II transcription factor activity, enhancer binding. Currently the definition is "Functions to initiate or regulate RNA polymerase II transcription by binding a promoter or enhancer region of DNA." We would like to recommend that the defintion of this term be narrowed to "Functions to initiate or regulate RNA polymerase II transcription by binding an enhancer region of DNA" removing reference to "the promoter region".
For the following reasons: The issue is that a promoter and an enhancer are different functional units with different functional characteristics. A promoter is loosely considered a DNA region that leads to transcription of a gene. You can take that region and place it in front of another gene, and it will likely drive transcription of the heterologous gene. An enhancer is a DNA element that augments transcription from a promoter. It will work independent of position and in the inverse orientation, so it is sequence independent to a certain degree. You cannot invert the promoter and have it work. And I can't think of a promoter that will work when it is placed kilobases away from its gene. Enhancers can work far away from a gene. I would like to suggest if they want to be as accurate as possible that they modify the term definition.
Thanks,
-Alison
Reported by: awg1
Original Ticket: "geneontology/ontology-requests/3337":https://sourceforge.net/p/geneontology/ontology-requests/3337