Necessity of H3K4me2, H3K4me3, H3K9ac and H3K27ac in RNAPII recruitment. A) We defined thresholds based on 95 percentiles for the presence of H3K4me2, H3K4me3, H3K9ac and H3K27ac marks in the promoter region(+/-1000 nt), and then counted how many promoters that have 0, 1, 2, 3 or all marks. For each group we counted how many of the promoters that had RNAPII signals exceeding the threshold in the vicinity of the TSS(+/-300). In each subplot the left bar represent the promoters that have no RNAPII present while the right bar represents those that have RNAPII present. B) We repeated the same analysis in panel A, but instead counted how many genes that had higher RNAPII signal in the gene body than expected by random. We note that most promoters either have no marks or all four marks. Furthermore, ~95% of the promoters with no marks present have no RNAPII signal, while 89% of promoters with all marks have significant signals for RNAPII in the promoter. This tendency is not as strong when measuring RNAPII in the gene body, suggesting that the four marks are necessary for recruitment but not sufficient for the elongation of RNAPII.
Chen et al. BMC Genomics 2011 12:544 doi:10.1186/1471-2164-12-544