Figure 3.

The correlation between sequence-directed nucleosome formation potential and experimentally measured nucleosome occupancy at both promoter classes. Lee et al. have predicted genome-wide nucleosome formation potential based on DNA features [7]. We calculated Pearson correlation coefficient between sequence-directed nucleosome formation potential and experimentally measured nucleosome occupancy [7] at each promoter. Distributions of resulting correlation coefficient values are presented for SDN-enriched promoters (green), SDN-less promoters (red) and all promoters (blue). High positive correlation indicates sequence-dependent nucleosome positioning, while low positive correlation could indicate nucleosome positioning less dependent on the intrinsic DNA sequence. SDN-enriched and SDN-less promoters showed stronger and weaker positive correlation between sequence-directed nucleosome formation potential and experimentally measured nucleosome occupancy than the rest of the promoters, respectively.