Below is a UCSC Genome Browser screen shot centred on the start of the ACTB gene that shows ENCODE ChIP-Seq signal for H3K4Me3 for the HSMM cell line (I turned off all other cell lines).
My question is, what is the cause of the dip near the promoter of this gene? The H3K4Me3 histone mark is associated with promoters and if anything, I would expect to see an enrichment at the promoter. Is this due to poised RNA polymerases binding at the TSS and thus somehow affecting the antibody binding? How does this affect peak calling?
Thanks in advance