Fig. 4

a, b Differential analyses of chromatin accessibility between WT and ctcf^−/− embryos at 24 (a) and 48 hpf (b) from ATAC-seq data (n = 2 biological replicates per condition). The log₂ normalized read counts of WT ATAC peaks versus the log₂ fold-change of accessibility are plotted. Regions showing statistically significant differential accessibility (adjusted P-value < 0.01) are highlighted in blue (increased) or red (decreased). The total number of differential peaks is shown inside the boxes. c, d Motif enrichment analyses for the increased and decreased ATAC peaks in ctcf^−/− embryos at 24 (c) and 48 hpf (d). The three motifs with the lowest p-values are shown for each case. e Heatmaps plotting normalized ATAC-seq signal in WT and ctcf^−/− embryos (red), as well as CTCF ChIP-seq signal (green) at 48 hpf, for the differentially accessible regions (DARs) from (b) overlapping or not with CTCF sites. f Box plots showing the expression fold-change in ctcf^−/− embryos at 48 hpf of all DEGs or only those associated with increased or decreased DARs, overlapping or not with CTCF sites. Boxplots represent the centerline, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; notches, 95% confidence interval of the median. Statistical significance was assessed using a two-sided Wilcoxon’s rank-sum test. g GO enrichment analyses of biological processes for the genes associated with decreased DARs in ctcf^−/− embryos at 48 hpf, overlapping or not with CTCF sites. GO terms showing an FDR < 0.05 are considered enriched.