Previously, I believed that Pol II binding peak in ChIP seq indicated a transcription start site (TSS). In most gene, the peaks do overlap with the TSS sites. However, recently I found that the Pol II binding peak presented inside the first introns of two genes. I am wondering, does that mean a new transcript started from there, or Pol II pausing or something that I do not know yet? Could anyone give me some suggestions? Thank you so much!
Hi De-Liang Zhang , it could be a TSS. Pol II pausing usually occurs near the TSS and seldom in the intron. If you have H3K4me1 or H3K4me3 chip data, you can see whether that peak indeed overlaps with a H3K4me3 peak. The reason I include H3K4me1 is that it might be an eRNA... (quite rare though).
Hi, Gen Lin, Thank you so much for the comments. The peaks of H3K4me1 and H3K4me3 do overlap, and the ratio of H3K4me1 vs H3K4me3 is higher in the intronic POL2 site than in the promoter. So..., it might be an enhancer site, and/or eRNA site.... Because the gene plays an essential function, and the site conserves highly in vertebrates, I wonder the function of this site in the regulation of the gene expression. Any comments?
Yes I think it's possible that it's an enhancer. You can check out what are predicted enhancers for this gene (https://www.genecards.org/, http://slidebase.binf.ku.dk/human_enhancers/selector). I guess you need more evidence, like can you find this in cage data for example, for whether the change in PolII signal is correlated with change in gene expression etc..
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