Fig. 4

p63 regulates Sox3 binding to neural enhancers and the neural program. a Differential analysis of Sox3 binding between WT and tp63^−/− at 36 hpf, calculated in a set of 147,588 Sox3 BSs (FDR < 0.05) from ChIPmentation (n = 2 biological replicates per condition). The log₂ base mean Sox3 binding levels in the WT versus the log₂ fold-change of expression are plotted. Peaks showing a statistically significant differential expression (p < 0.01) are highlighted in blue (downregulated) or red (upregulated). b Heatmaps and average profiles of the Sox3 BSs at 36 hpf from (a) in WT and tp63^−/− embryos. Peaks were separated according to the differential analysis in up-regulated (Up; n = 2,976) or down-regulated (Down; n = 941) in tp63^−/− mutant compared to WT. c Bar plot with the mean expression of sox3 gene in WT vs. tp63^−/− embryos at 36 hpf as measured by RNA-seq (n = 3, for each condition). Error bars represent s.d. Individual values are shown as red dots. Non-corrected p-value from the differential expression analysis is shown. d Box plots showing the expression fold-change in tp63^−/− embryos of the transcripts associated to Up- (n = 222), Down-regulated (n = 75) and not changed (NC; n = 1,255) Sox3 BSs from (a) compared to the total de-regulated transcripts (n = 2,344) in that mutant. Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers. Statistical significance was assessed using the Wilcoxon’s rank sum test. For (c) and (d), source data are provided as a Source Data file. e Genome tracks of p63 ChIP-seq, Sox3 ChIP-seq, and RNA-seq in the indicated developmental stages showing signal intensities in a region of chromosome 8. An up-regulated Sox3 BS in tp63^−/− mutant and the associated up-regulated gene (cldn5a) are highlighted in light orange. The Genes track represents ENSEMBL annotated genes. See also Supplementary Fig. 3