Fig. 2

Dynamics of p63 binding during development in zebrafish embryos. a Picture illustrating zebrafish developmental stages in which most experiments were performed. b Heatmaps of the 30,597 p63 binding sites (BSs) obtained from ChIPmentation in 80% of epiboly, 24 and 36 hpf stages (n = 2 biological replicates per stage). Peaks were clustered using k-means clustering, obtaining four groups: cluster a (n = 656), cluster b (n = 3,956), cluster c (n = 3,801) and cluster d (n = 22,184). Average profiles of cluster b, which was used as the group of early p63 BSs, and cluster c, as late p63 BSs, are shown on top. c Top-10 enrichment of WT expression patterns of the genes corresponding to early (top) and late (bottom) p63 BSs. The -log₁₀ of p-value for each term is shown. d Motif enrichment analysis of the early (top) and late (bottom) p63 BSs. Five representative motifs of the top-10 were chosen. Motif logos are represented with their position in the top-10, the transcription factor (TF) name and the enrichment p-value in a color scale. e Heatmaps of the early (top) and late (bottom) p63 BSs clustered according to chromatin marks H3K4me3, H3K4me1 and H3K27ac in 80% of epiboly and 24 hpf. Peaks were clustered using k-means clustering, obtaining three sub-clusters per each group: b1 (n = 875), b2 (n = 912), b3 (n = 2,169), c1 (n = 396), c2 (n = 330) and c3 (n = 3,075). f Box plots showing the distance of the peak sub-clusters from (e) to the transcription start sites (TSS) of the nearby genes. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. Source data are provided as a Source Data file. g Motif enrichment analyses of the peak sub-clusters from (e) representing the most enriched motif in each one, their motif logos, percentage of peaks containing the motif and associated enrichment p-value. See also Supplementary Fig. 1