Figure 4

Differences in chromatin accessibility in cell-type specific peak regions suggest cell-type specific regulation. Chromatin accessibility as measured by DNase sensitivity for the two cell types in peak regions that are cell-type specific for K562 (A) and HeLa-S3 (B) and in peak regions that are common for both cell types (blue bars in A and B). Only the 30% highest peaks are analyzed. A) Box-plots showing for K562-specific TF peak regions, the distributions of DNase-seq signal in K562 (red) and HeLa-S3 (green), and for TF peak regions common to K562 and HeLa-S3, the distribution of DNase-seq signal in K562 (blue). The DNase-seq signal was the read per million-normalized number of reads mapping to each peak region divided by the region length. BRF2 has only one box-plot as all BRF2 peaks overlapped in the two cell lines. B) Similar data as in (A), but for HeLa-S3-specific peak regions the DNase-seq signal in HeLa-S3 (green) and K562 (red) and for peak regions common to K562 and HeLa-S3 the DNase-seq signal in HeLa-S3 (blue). Most of the TFs have comparable DNase-seq signals at the common peak regions in the two cell lines (compare blue bars in A and B). Moreover, most of the TFs show symmetric signals at the cell-type specific peak regions, such that the regions that are specific for K562 have higher DNase-seq signals in K562 than in HeLa-S3 (A) and vice versa (B).