Analyses of human promoters reproduce the distinction between promoter classes. The ratio between nucleosome occupancy at the TSS-proximal and -distal regions is correlated with transcriptional plasticity among the eight yeast (A) or human (B) promoter classes. Lines indicate the linear least-squares fit. Red and blue circles represent clusters corresponding to OPN and DPN, respectively. (C) Human OPN promoters (red bars) are enriched with CpG-poor promoters and TATA boxes, are depleted in H2A.Z, and have lower peak-to-trough ratios compared with human DPN promoters (blue bars). Similar results were obtained in analysis of human nucleosome positions from high-throughput sequencing (Supplemental Fig. 11; Schones et al. 2008). In addition, the ratio of human nucleosome occupancy was also significantly correlated with binding of CTCF and several histone H3 methylations (Supplemental Fig. 12; Barski et al. 2007).
