Figure 3. Bcd drives chromatin accessibility primarily at concentration-sensitive targets.

(A) Heatmaps showing chromatin accessibility (top) and probability of nucleosome occupancy (bottom) around Bcd-bound peaks from ATAC-seq experiments. Peak regions are arranged by decreasing accessibility in wild-type embryos. bcd^E1 mutant embryos show a loss of accessibility and increased nucleosome occupancy most strongly at the Concentration-Sensitive I and II peaks. zld^- embryos show reduced accessibility across all sensitivity classes. (B) Subset of 132 Bcd-bound peaks selected from (A) that become inaccessible in the absence of Bcd. Accessibility at these peaks increases with increasing concentrations of uniform Bcd. Odds ratios and p-values calculated from Fisher's exact test show significant overrepresentation of the Concentration-Sensitive I and II classes in the Bcd- and Zld-dependent peaks. n values indicate the number of peaks in each sensitivity class that are Bcd or Zld dependent.

Figure 3—figure supplement 1. Enrichment of Bcd sensitivity classes in Zld bound peaks.

(A) Overlap between Zld ChIP-seq peaks from Harrison et al. (2011) and Bcd ChIP-seq peaks defined in this study. A total of 732 of Bcd ChIP peaks (71.3%) overlap with Zld peaks. (B) Odds ratios and p-values calculated from Fisher's exact tests for enrichment of each Bcd peak class in peaks that are also bound by Zld. In contrast to Zld dependence as defined by reduced chromatin accessibility in zld^– embryos, Concentration Sensitive I and II classes show a greater enrichment for Zld binding than the Concentration Sensitive III and Insensitive classes. (C) Odds ratios and p-values calculated from Fisher's exact tests for enrichment of each Bcd peak class in Zld dependent peaks, separated into those bound and not bound by Zld. Concentration insensitive peaks that are bound by Zld are overrepresented in Zld dependent peaks, while Concentration Sensitive I peaks are underrepresented. In Bcd peaks that are not bound by Zld, no sensitivity class is significantly enriched for Zld dependence. (D) Odds ratios and p-values calculated from Fisher's exact tests for enrichment of each Bcd peak class in Bcd dependent peaks, separated into those bound and not bound by Zld. Concentration Sensitive I and II peaks that are also bound by Zld are overrepresented in Bcd dependent peaks, while Concentration Sensitive III and Insensitive peaks are underrepresented. In Bcd peaks that are not bound by Zld, no sensitivity class is significantly enriched in for Bcd dependence.