Decoding the Spatial and Epigenetic Logic of Early Skin Development

Abstract

The embryonic epidermis originates from a simple single-layered ectoderm that undergoes precise transcriptional and morphological transitions to generate a self-replenishing, multi-layered epidermis. A key early milestone is the emergence of the periderm; a transient, protective layer whose disruption underlies a series of devastating human congenital disorders. Despite its importance, the gene regulatory networks that drive periderm formation remain poorly defined. Here, we integrate single-cell multiome profiling with high-resolution spatial transcriptomics analysis in wild-type and transcription factor p63 mutant (Trp63-/-) embryos to dissect the transcriptional and epigenetic programs driving epidermal lineage diversification. We resolve the cellular repertoire of early embryonic skin, define epithelial subpopulations and reconstruct the transcriptional dynamics underlying the periderm emergence. We show that p63 sits at the core of a multilayered enhancer-gene regulatory network, demonstrate how this network is perturbed in vivo, and functionally validate key targets using comparative cellular models. Together, these findings delineate the gene regulatory architecture of early skin development and establish a framework for understanding epithelial-associated congenital disorders.