Fig. 5

Effect of Exd/Hth on Hox binding. a Plot showing the number of cofactor-enhanced binding regions based on differential binding (fdr ≤ 0.01, logFC ≥ 1 and both replicates bound at macs q1e−2). Regions more bound in the presence of Exd/Hth (Hth+Hox) are shown in colour as positive numbers, regions more bound in Hox alone compared to Hth+Hox are shown in grey underneath. b Boxplot of ATAC scores in Hox group peaks for Hox proteins in the absence (Hox) or presence (Hox+Hth) of Exd/Hth. The Hth regions are bound by Hth-GFP and the Exd+Hth regions are bound by Exd-GFP in the presence of Hth. Numbers of bound regions are indicated above the plot. c Density plots of mean ATAC-seq scores for Hox group peaks bound by Dfd, Ubx, and Abd-B with and without Exd/Hth showing the effect of the cofactors on the chromatin accessibility profile. Solid lines: Hox alone, dotted lines: Hox in presence of Exd/Hth. d Boxplot comparing chromatin accessibility of Exd/Hth enhanced regions (Hox ENH) versus common regions (bound similarly in the presence or absence of Exd/Hth; Hox COM). Numbers for Hox ENH regions are given above the plot and the same number of randomly selected common regions was used for Hox COM. e Plot showing lack of effect of Exd/Hth on the Hox selectivity profile plotting percentage of regions in each of the Hox selectivity classes for Hox alone (Hox) and in the presence of Exd/Hth (Hox+Hth). This lack of effect is a robust observation across both low (q1e−2) and high (q1e−10) stringency binding regions. f Motif analysis comparing motif enrichment for binding regions for Hox alone (Hox), Hox in the presence of Exd/Hth (Hox+Hth), and Exd/Hth cofactor enhanced binding regions (Hox ENH) using 500 randomly selected regions from each class for selected Hox proteins Lab, Dfd, Ubx and Abd-B. Motifs are HoxA* (grey; see Fig. 2), Abd-B (purple, see Fig. 2), and the Exd and Hth motifs (light blue)