Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA-seq]. Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA-seq]

The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program, its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here, we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63-knock-out mutants that recapitulate human phenotypes and show down-regulated epidermal gene expression. Following p63-binding dynamics during development, we found two distinct functions clearly separated in space and time. During early development, p63 binds enhancers associated to neural genes, where it limits Sox3 binding and reduces the expression of these neural genes. Indeed, we show that p63 and Sox3 are co-expressed in the neural plate border. Later in development, p63 binds enhancers associated to epidermal genes and promotes their expression, acting as a pioneer factor, as it binds to non-accessible chromatin and is required for its opening. Therefore, our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification, promoting the epidermal fate and inhibiting the neural program. Overall design: RNA-seq assays in tp63 zebrafish mutants

转录因子p63是外胚层发育的主控调控因子，对表皮特化至关重要。尽管既往研究已阐明p63可激活表皮转录组程序，但其在发育胚胎的复杂环境中调控靶基因的精确机制仍不甚明晰。本研究以斑马鱼胚胎为模型，在体内分析p63在发育过程中如何调控其靶基因的表达。我们构建了可重现人类表型的tp63敲除突变体，该突变体的表皮基因表达显著下调。通过追踪发育进程中p63的结合动态，我们发现其存在两种时空上完全分离的独特功能。发育早期阶段，p63结合与神经基因相关的增强子，通过抑制Sox3的结合来降低此类神经基因的表达。本研究证实，p63与Sox3在神经板边界处共表达。发育后期，p63结合与表皮基因相关的增强子并促进其表达，作为先锋因子（pioneer factor）发挥作用：它可结合非开放染色质，并介导该染色质的开放。综上，本研究结果表明，p63是外胚层特化过程中细胞命运决定的重要调控因子，可促进表皮细胞命运定向，同时抑制神经程序的激活。研究整体设计：对tp63斑马鱼突变体开展RNA测序（RNA-seq）检测。