Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment

Abstract

Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine 1 – 3 , yet conversion into transplantable tissues remains poorly understood. Using our keratinocyte differentiation system, we employ a multi-dimensional genomics approach to interrogate the contributions of inductive morphogens retinoic acid (RA) and bone morphogenetic protein 4 (BMP4) and the epidermal master regulator p63 4 , 5 during surface ectoderm commitment. In contrast to other master regulators 6 – 9 , p63 effects major transcriptional changes only after morphogens alter chromatin accessibility, establishing an epigenetic landscape for p63 to modify. p63 distally closes chromatin accessibility and promotes accumulation of H3K27me3 modifications. Cohesin HiChIP 10 visualizations of chromosome conformation reveal that p63 and the morphogens contribute to dynamic long-range chromatin interactions, as illustrated with TFAP2C regulation 11 . Our study demonstrates the unexpected dependency of p63 on morphogenetic signaling and provides novel insights into how a master regulator can specify diverse transcriptional programs based on the chromatin landscape induced by specific morphogen exposure.

Epidermal Stem Cells in Wound Healing and Regeneration

“…The nucleoprotein p63 is widely and selectively expressed in a variety of human tissues, especially in proliferating epithelial tissues [42]. Studies have shown an important role of p63 in skin development, maintenance of an undifferentiated state of stem cells, and stem cell proliferation [43].…”

TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development

“…These opposite interpretations may indicate that other lineage-determining factors could compensate for p63 function in a p63-null context, whereas mutant p63 in iPSCs abrogates the function of the normal p63. Although p63 is dispensable to drive human embryonic stem cells (hESCs) to differentiate to surface ectoderm progenitor cells, it is required for further differentiation toward functional keratinocytes upon RA/BMP4 treatment [ 60 ]. It has been shown that genes expressed at an early differentiation stage are not under the control of p63.…”

“…Interestingly, ΔNp63 (−/−) epidermal cells express a number of transcripts associated with embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) and display compromised epithelial identity [ 69 ], suggesting that ΔNp63 exerts repressive role on genes expressed at the early differentiation stage once surface ectoderm progenitor cells enter maturation stage. Mechanistically, p63 reduces chromatin accessibility at morphogen-dependent accessible sites through promoting deposition of H3K27me3 at these sites during the maturation stage [ 60 ]. These studies consistently highlight that p63 exerts intrinsic pioneer factor activity, to open inaccessible chromatin, and it cooperates with specific TFs during keratinocyte maturation.…”

Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics

“…These molecular characteristics are suggestive of a relatively quiescent, primitive stem/progenitor cell state, a notion supported by its placement as the initial state in the epidermal lineage (this study), and its high expression of Col17a1, which encodes a marker of long-term epidermal stem cells that can outcompete other cells (Liu et al, 2019). The Col17a1 Hi state is enriched for genes such as Trp63, a master regulator of various aspects of epidermal development, including the initial specification from simple epithelia, promotion of stratification, proliferation, as well as terminal differentiation (Li et al, 2019;Mills et al, 1999;Pattison et al, 2018;Truong et al, 2006;Yang et al, 1999). The reduction of basal cells in the Col17a1 Hi state during wound re-epithelization implicates their mobilization in the case of increased demands for cellular outputs.…”