Methylation of lysine 4 on histone H3 (H3K4me) is a more specific marker of transcription factor clusters than is open chromatin (OCR). (A) Relative numbers of unique and shared regions for OCR and H3K4me. To compensate for the smaller region lengths in OCR compared to H3K4me, all unique OCR regions within 600 bp of each other were merged. Still, there are about threefold more unique OCR regions (black) than unique H3K4me regions (white). Thus H3K4me is a more precise marker than OCR when comparable fractions of transcription factor (TF) clusters overlap with these regions. (B) Percentage of TF clusters that overlap with H3K4me, OCR and combined acetylated lysine 27 on histone 3 (H3K27ac) and H3K9ac. (C) Same as graph (B), but with CTCF and Rad21 removed from the clusters. CTCF/Rad21 was the most frequent TF pair encountered in K562. We did not have high-throughput sequencing coupled with chromatin immunoprecipitation data for Rad21 in Gm12878, resulting in more singleton peaks for CTCF in Gm12878, which is the reason for the improved overlap observed in (B) for Gm12878.