I've recently done a ChIP-seq analysis with a protein I'm interested in and found that this protein is highly enriched in intergenic and intron regions. I suppose that most of the genomic sequences are intergenic, so it should not be surprising that it is enriched in intergenic regions. But it is much more abundant in introns than exons. I am not very familiar with this field, anyone knows what this might implicate in its function, or this is just a general phenomenon?
Occupancy of your protein of interest predominately in the intronic region imply two things:
1. It could be a splice factor, may have some residual tendency to bind also DNA in addition to RNA.
2. It could be a transcription factor, binding to enhancer motif. You can test this by a multiple alignment of all the underlying DNA sequences resulting from your ChIP-seq experiment. If this reveals a recurring binding motif, then it’s more likely a transcription factor.
Hope this helps!
All the best,
Manjunatha
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