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posted on 2024-02-01, 14:20 authored by Marco Napoli, Avani A. Deshpande, Deepavali Chakravarti, Kimal Rajapakshe, Preethi H. Gunaratne, Cristian Coarfa, Elsa R. Flores Endogenous ∆Np63 and TAp63 bind to distinct regions throughout the genome. A, Experimental outline. WT, ΔNp63−/−, and TAp63−/− epidermal cells were isolated from embryonic day 18.5 (E18.5) embryos. RNA extracted from these cells was used for expression profiling by RNA-seq, and chromatin was used for genome-wide analysis of p63 binding to DNA by ChIP-seq. The overlap in genes identified from these analyses revealed: (i) direct p63 target genes; (ii) direct ΔNp63-specific target genes; and (iii) direct TAp63-specific target genes. B, Table summarizing the total number of peaks found through the ChIP-sequencing analysis and the relative p63 isoform responsible for the binding. C, Distribution of the ΔNp63-specific (left), common (center), and TAp63-specific (right) ChIP-seq peaks with respect to genomic landmarks. D, Nucleotide distribution in the ∆Np63-specific (top) and TAp63-specific (bottom) DNA response elements identified in the ChIP-seq peaks.
Funding
HHS | NIH | National Cancer Institute (NCI)
Cancer Prevention and Research Institute of Texas (CPRIT)
HHS | National Institutes of Health (NIH)
HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)
History
ARTICLE ABSTRACT
The p53 family member TP63 encodes two sets of N-terminal isoforms, TAp63 and ΔNp63 isoforms. They each regulate diverse biological functions in epidermal morphogenesis and in cancer. In the skin, where their activities have been extensively characterized, TAp63 prevents premature aging by regulating the quiescence and genomic stability of stem cells required for wound healing and hair regeneration, while ΔNp63 controls maintenance and terminal differentiation of epidermal basal cells. This functional diversity is surprising given that these isoforms share a high degree of similarity, including an identical sequence for a DNA-binding domain. To understand the mechanisms of the transcriptional programs regulated by each p63 isoform and leading to diverse biological functions, we performed genome-wide analyses using p63 isoform-specific chromatin immunoprecipitation, RNA sequencing, and metabolomics of TAp63−/− and ΔNp63−/− mouse epidermal cells. Our data indicate that TAp63 and ΔNp63 physically and functionally interact with distinct transcription factors for the downstream regulation of their target genes, thus ultimately leading to the regulation of unique transcriptional programs and biological processes. Our findings unveil novel transcriptomes regulated by the p63 isoforms to control diverse biological functions, including the cooperation between TAp63 and NRF2 in the modulation of metabolic pathways and response to oxidative stress providing a mechanistic explanation for the TAp63 knock out phenotypes.
The p63 isoforms, TAp63 and ΔNp63, control epithelial morphogenesis and tumorigenesis through the interaction with distinct transcription factors and the subsequent regulation of unique transcriptional programs.
