I am working on a gene whose enhancers I would like to know. Instead of the conventional P element based enhancer trap, is there any prediction tool which can predict the enhancer of the given gene with appreciable accuracy?
I am not familiar with the fly system, Rohit, but can you mine databases like the UCSC genome browser and look for H3K4me1+H3K27ac? The former alone is a mark for an enhancer, and both these marks indicate an "active" enhancer. Now, the actual enhancer element would be expected to map right in the middle--that is, the H3K4me1+H3K27ac domains would "flank" the enhancer.
Another way to look at--if there are such datasets available--is to select indiscriminately all possible transcription factors that the genome browser has mapped in Drosophila, and look at the locus of your interest. If you see a multitude of TFs binding to your locus of interest--and very few binding the adjoining sequences--then you may have identified the enhancer. You know that enhancers are bound to TF clusters.
These above two approaches are NOT absolutely accurate ways to map enhancers, but are simple ways that you can do sitting in your chair for an hour. Once you get a feeling from these two analysis, you can get a motif analysis done for free online to see if this region has any binding sequence for a pioneer factor like a FOXA1 homolog or CBP/P300. Many ways will open up once you get there.
Can I get a collaboration from a person who's sound in computational bio and/or bioinfo?
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