(A)-(C) Normalized ChIP-seq signal of RpaA (red), RpaB (blue), RNAP (green) and mock IP (black) upstream of the sigma factor genes (A) rpoD6, (B) rpoD5, and (C) sigF2. The location of the gene is located on the plot with a gray bar with an arrow indicating directionality of the gene. The location of RpaA, RpaB, and RNAP peaks are indicated on top of the plot with red (RpaA), blue (RpaB), and green (RNAP) bars. See Materials and methods, ChIP-seq analysis for more details. (D)-(F) Changes in enrichment of RpaA (red), RpaB (blue), and RNAP (green) and downstream sigma factor gene expression (black) after exposure to the High Light pulse (triangles) or the Shade pulse (circles) upstream of rpoD6 (D), rpoD5 (E), and sigF2 (F). See Materials and methods, ChIP-seq analysis for more details. (G)-(L) Gene expression dynamics of rpoD6 (G,J), rpoD5 (H,K), and sigF2 (I,L) under Low Light vs High Light pulse (G)-(I) and Clear Day vs Shade pulse (J)-(L) conditions. RpaA and RpaB binding changes in a correlated manner upstream of these genes. RpaA and RpaB binding also correlates with changes in RNAP enrichment and sigma factor expression levels.