To directly identify regulatory regions, we mapped the binding locations of 119 different DNA-binding proteins and a number of RNA polymerase components in 72 cell types using ChIP-seq (Table 1, Supplementary Table N1, ref 19); 87 (73%) were sequence-specific TFs (TFSS). Overall, 636,336 binding regions covering 231Mb (8.1%) of the genome are enriched for regions bound by DNA-binding proteins across all cell types. We assessed each protein-binding site for enrichment of known DNA-binding motifs and the presence of novel motifs. Overall, 86% of the DNA segments occupied by TFSS contained a strong DNA-binding motif and in most (55%) cases, the known motif was most enriched (Pouya Kheradpour and Manolis Kellis, personal communication).
