Hi, I have a proboscis monkey genome that I had annotated the gene location for chr18. There are total 411 genes returned by AUGUSTUS. Now I would like to identify the enhancer regions in those genes. May I know what are the methods I can use to find out the regions? I prefer to use software tools since I'm not from a biological background person.
Enhancer regions are difficult to identify. Their definition is .. scattered, and I don't know of any database that has a reference list of all enhancers in the human genome much less the monkey genome. You might want to take a look at Vista Enhancer Browser.
Typically to identify enhancer regions you would rely heavily on ChIP-seq data: primarily histone modifications. H3K4me1 is known to be found at most enhancer regions whether active or poised so this is probably the biggest one. H3K27Ac is known to be found at active enhancers. H3K4me2 has also been used in some literature as a enhancer marker. For transcription factors, p300 is primarily found at enhancer regions. There's quite a few more histone modifications associated with enhancers as well.
I suggest you read a couple of reviews on enhancer definitions, it's not as simple as you may think it is. Here is a good starting review.
I've also interested in this question, and I made a simple google search, that may be useful to you.
https://www.google.ru/#newwindow=1&q=how+to+identify+enhancer+elements
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@natasha: While I understand your desire to help, posting links for a google search with keywords as a new answer is not really helping the person asking the original question.
Other mods may have an opinion on this as well.
Sorry, my fault. I should not have done it. I hope allyson will disregard my comment.
Should we just close posts like this, if not really helping the OP?
No, while the answer is better off as a comment. The google search brought up a few papers and materials that I feel are extremely beneficial to the original question. It is up to the OP to make use of it.
The question here is of precedent.
While the google search may have brought up useful materials it is not providing direct information that can be readily used (like your answer did). Instead of a link for the google search it would be better to post a few direct links for useful material identified using that search.
I see, OK. Thank you!