Extended Data Fig. 8: Developmental dynamics of topologically associated domains and H3K27ac ensemble definition.

a, ATAC-seq signals in GRB (top) and non-GRB (bottom) TADs throughout development. TADs are ordered in a descending order from the top of the heatmap. b, Directionality index in GRB TADs throughout development. c, Distance distribution of enhancer-associated PADREs to the closest promoter within GRB TADs. Bars represents inter-quartile range. d, Enhancer-associated ChromHMM segments in GRB TADs throughout development. TADs are ordered in a descending order from the top of the heatmap. Segments are coloured based on the logarithm of their length. Early stages are dominated by fewer large blocks, which start to be enriched within TADs only at 75%-Epiboly. In late stages, short segments are distributed uniformly throughout the entire TAD length. e, Width distribution of concatenated enhancer-associated ChromHMM segments. Singletons shorter than two bins (400 bp) were excluded. The number of segments is shown above each violin plot. f, Ratio of GRB and non-GRB tads containing H3K27ac ensembles. g, the density of CAGE promoters on ensemble boundaries. h, the number of non-promoter PADREs per 100 kb in TADs containing ensembles. The x-axis shows the developmental stage in which the PADRE is H3K27ac marked (early, late, or both). The location of promoters in respect to the ensemble is shown in different colours. The numbers were compared using two-sided two-sample unpaired Wilcoxon test.