Fig. 6

(A) Stacked bar plot showing the percentage of N/P/S-bound Group 1 regions that require one, two, or three NPS factors to rescue accessibility. All regions were ranked by average nucleosome occupancy score and then divided into quartiles. (B) Violin plot comparing the nucleosome occupancy scores between Nanog-bound regions that are rescued by single, double, or triple factor combination (two-sample t-test, *** P <0.001). On the x-axis, ^† denotes regions that require two or three factors for rescue. (C) Violin plot comparing nucleosome occupancy between low and high dosage groups in Figure 5D (two-sample t-test, *** P <0.001, ** P <0.01). (D) Heatmaps of Omni-ATAC, H3, and NPS binding signal, and nucleosome occupancy score (nuc score) at N/P/S-bound Group 1 regions that can be rescued by any single/double/triple NPS factors. Heatmaps are centered at Omni-ATAC peak summits and ranked by average intensity of Omni-ATAC signal in wild-type (WT) embryos. (E) Line plot of nucleosome occupancy score, H3 signal in MZnps embryos, and H3 signal (top 25% accessible) in WT embryos at the regions in (D). (F) Violin plot comparing the nucleosome occupancy between N/P/S-bound accessible regions and inaccessible regions (two-sample t-test, *** P <0.001). (G) Heatmaps showing accessibility enrichment for TF motifs (Figure 4B) in different quartiles ranked by nucleosome occupancy score, and H3 ChIP-seq signal in MZnps and WT. (H) Schematic illustrating how nucleosome occupancy facilitates pioneering activity. See also Figure S6.