Fig. 2. Pre-existing chromatin accessibility, DNA binding motifs and pluripotency TF binding, underlie GATA6 binding dynamics.

A Heatmaps depicting chromatin accessibility (ATAC-seq) and GATA6 enrichments, over 4kb-long regions centered on GATA6 summits, ranked by decreasing accessibility in ES cells at each GATA6 cluster. B Occurrence and quality (identity score to the consensus of the best motif of each region, z-scored to scale between different motifs) of DNA binding motifs across the regions shown in (A), in the same order as in (A). Within each score panel is shown the global median of all regions per cluster (blue) and a trend line (red) of the data (gray). C Analysis of pluripotency TF binding (reads per million; RPM) across the 3 GATA6 clusters, presented and ordered as in (A). D Example of different behaviors of GATA6 and pluripotency TFs (PTF). E Left; average profile of OCT4 (O), SOX2 (S) and ESRRB (E) at the 3 groups of regions illustrated in (D). Right; binding of GATA6 across the same clusters. All four plots show the average profile (RPM) over 4 kb centered on the GATA6 summit. F Distribution of GATA6 motifs around the GATA6 summit (left panel), together with the motif score of the best motif present in each region (right panel, median—bar; 25–75% percentiles—box; 1.5-folds the inter-quartile range—whiskers). G Average profiles of chromatin accessibility (small ATAC-seq fragments) and nucleosomes (measured by long fragments detected by ATAC-seq or by MNase-seq using different concentrations of MNase—Low, Mild, High). ATAC-seq is expressed in RPM and MNase-seq in normalized midpoints per billion reads (MPB; see Methods for details). All plots show the average profile over 8 kb centered on the GATA6 summit. Source data are provided as a Source Data file.