Figure 3.

TATA Box Stabilizes Binding of the PIC

(A and B) Single-locus examples of TATA-less (A) versus TATA-containing (B) promoters. Shown are average methylation levels (top panel, black dots connected by a black line) and single-molecule stacks measured by targeted amplicon bisulfite sequencing, sorted into five states using the classification algorithm (methylated Cs, accessible, light gray; unmethylated Cs, protected, black). The vertical side bar depicts the frequency of each state using the same color code as in 2D. Red dashed line depicts position of the TSSs. The percentages of molecules in PIC- or Pol-II-bound states are indicated on the right side of the plot.

(C) Composite footprinting profiles around TATA-containing or TATA-less highly active promoters (red and blue lines, respectively) showing strong differences in PIC footprints between the categories.

(D) Heatmap showing state frequencies for transcriptionally active promoters. k-means clustering was used to organize the heatmap. Side bars indicate presence (colored) or absence (black) of core promoter elements, revealing that TATA-containing promoters cluster due to the increased abundance of PIC footprint.

(E) TATA-box presence alters state distribution, depleting accessible molecules and increasing the number of molecules bound by PIC (with or without Pol II binding). Shown are p values (–log) of a Wilcoxon rank-sum test multiplied by the sign of the statistic parameter to account for directionality of the differences.