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.