Epigenome regulation during epidermal lineage commitment [RNA-seq]

Recent advances in human pluripotent stem cell (hPSC) technology provide a unique resource for skin tissue replacement, but the detailed understanding of regulatory mechanisms limits standardization and broad clinical application. Here, we interrogate chromatin accessibility and transcriptome dynamics during hPSC-derived epidermal differentiation, and discover two critical transition periods: surface ectoderm initiation and keratinocyte maturation. Using inference network modeling, we develop a computational framework for each transition, and identify TFAP2 and TP63 and their cofactors as key regulators. Surprisingly, functional studies demonstrate the sufficiency of TFAP2C to initiate surface ectoderm differentiation by activating the early TF network and its chromatin landscape changes, while loss of TFAP2C inhibits early commitment. TFAP2Cinitiated cells are competent to further differentiate into functional keratinocytes in selective media, accompanied by activation of the keratinocyte maturation network and decline of the early network. Mechanistically, TFAP2C activates the expression and increases binding site accessibility and positive autoregulation of the master regulator P63, while loss of P63 results in failure to close TFAP2-initiated early program and leads to maturation and survival defects, revealing a positive-negative feedback loop that ensures complete transition from progenitor to maturation tissue. Our work reveals the logic underlying dynamic epigenome-transcription factor interactions during human epidermal lineage commitment that will facilitate improved tissue engineering and regenerative medicine.

Dataset features

Information

Specifications

Dataset type:	Expression profiling by high throughput sequencing
Number of samples:	12
Release date:	Jan 28 2019
Last update date:	Feb 16 2019
Access:	Public
Dataset link	Epigenome regulation during epidermal lineage commitment [RNA-seq]

Experimental Protocol

chromatin accessibility and gene expression profile in epidermal differention from normal hESC, and hESCs containing inducible expression of TFAP2C or p63 KO were generated by ATAC-seq and RNA-seq, in two replicates at each stage, using illunia Hiseq 2000 and Nextseq 500.

Repositories

GEO

GSE122383

ENA

SRP168371

BioProject

PRJNA504858

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Contact

Anthony Oro