Sigma factors and RNAP binding at RpoD promoter regions. (A) Heatmap of occupancy distribution of the indicated protein targets as measured by ChIP-exo. Transcription units (TUs; rows, N = 638 TUs) are aligned by their ATG start codons (5′-3′, left to right) and sorted by RpoD occupancy (summed −80 to +80 bp from TU ATG start) at 30°C. ATG starts were used instead of TSSs because TSSs have more experimental error, condition-specific biological variability, and variance among strains compared with DNA elements. Sense and antisense tags were shifted in the 3′ direction by 6 bp (to adjust for the headroom of lambda exonuclease) and merged. Data files have an x-axis bin size of 2 bp. (B) Relative occupancy level in arbitrary units (AUs) on a linear scale for individual target proteins, rank ordered by their occupancy level at 638 TUs from panel A. The dashed line represents the approximate midpoint observed with targets that are expected to be background. (C) Heatmap matrix of correlation coefficients for co-occupancy of targets from panel A (from −500 to +100 of a TU ATG start). Heat shock, or H, denotes instantaneous change from 30°C to 42°C for 6 min. (D) Composite (averaged) plots of RpoD, RpoA, and MglB occupancy from panel A (30°C) and from Supplemental Figure S1 (6 min, 42°C). AU denotes arbitrary linear units. Data files have an x-axis bin size of 2 bp. The MglB data are the same in both panels. To compare y-axis magnitudes between same-target samples from 30°C and 42°C, gene-averaged y-axis values were empirically scaled (i.e., one scaling factor per data set) to achieve similar y-axis minima values in the x-axis window (i.e., to achieve similar average local background). This assumes that the minima are background.
