In Tier 1 and Tier 2 cell types, we identified a mean of 205,109 DHSs per cell type (at FDR 1%), encompassing an average of 1.0% of the genomic sequence in each cell type, and 3.9% in aggregate. On average, 98.5% of the occupancy sites of TFs mapped by ENCODE ChIP-seq (and, collectively, 94.4% of all 1.1 million TF ChIP-seq peaks in K562) lay within accessible chromatin defined by DNaseI hotspots29. However, a small number of factors, most prominently heterochromatin-bound repressive complexes (e.g., the Kap1-SetDB1-Znf274 complex31,32 encoded by the TRIM28, SETDB1 and ZNF274 genes), appear to occupy a significant fraction of nucleosomal sites.
