Mutant p63 Affects Epidermal Cell Identity through Rewiring the Enhancer Landscape

Summary: Transcription factor p63 is a key regulator of epidermal keratinocyte proliferation and differentiation. Mutations in the p63 DNA-binding domain are associated with ectrodactyly, ectodermal dysplasia, and cleft lip/palate (EEC) syndrome. However, the underlying molecular mechanism of these mutations remains unclear. Here, we characterized the transcriptome and epigenome of p63 mutant keratinocytes derived from EEC patients. The transcriptome of p63 mutant keratinocytes deviated from the normal epidermal cell identity. Epigenomic analyses showed an altered enhancer landscape in p63 mutant keratinocytes contributed by loss of p63-bound active enhancers and unexpected gain of enhancers. The gained enhancers were frequently bound by deregulated transcription factors such as RUNX1. Reversing RUNX1 overexpression partially rescued deregulated gene expression and the altered enhancer landscape. Our findings identify a disease mechanism whereby mutant p63 rewires the enhancer landscape and affects epidermal cell identity, consolidating the pivotal role of p63 in controlling the enhancer landscape of epidermal keratinocytes. : Using transcriptomics and epigenomics, Qu et al. elucidate how mutant p63 associated with EEC syndrome alters the enhancer landscape in skin keratinocytes. The genome-wide redistribution of enhancers leads to the downregulation of epidermal genes and upregulation of non-epidermal genes and affects the cell identity of skin keratinocytes. Keywords: p63, enhancer, cell identity, transcriptional regulation, EEC syndrome, epidermal keratinocyte