(a) TMP-seq data were normalized for sequence bias and the average normalized signals surrounding the TSS and TES were determined for expressed (top) and silent (bottom) genes. (b) For each gene and for each corresponding sample, the Pearson's correlation (r) was determined for the 1 kb region surrounding the TSS between TMP-seq and nucleosome occupancy data, and the distribution of the correlation was plotted. (c) The changes in nucleosome occupancy were determined by subtracting the MNase-seq values of control from Topo I- (left) and Topo II- (right) inhibited samples, and were displayed as heat maps with genes ordered by decreasing gene expression in control samples. Contrast = 5. (d) Heat map as in main Fig. 2b with genes arranged by torsion difference (TD). Ctl: control.