Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin

Xiying Fan, Dongmei Wang, Jeremy Evan Burgmaier, Yudong Teng, Rose Anne Romano, Satrajit Sinha, Rui Yi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


How embryonic progenitors coordinate cell fate specification and establish transcriptional and signaling competence is a fundamental question in developmental biology. Here, we show that transcription factor ΔNp63 profoundly changes the transcriptome and remodels thousands of open chromatin regions of Krt8+ progenitors during epidermal fate specification. ATAC-seq and single-cell RNA-seq reveal that ΔNp63-dependent programs govern epidermal lineage formation, and ΔNp63-independent programs, mediated by AP2 and AP1 transcription factors, promote epidermal differentiation and epithelial-to-mesenchymal transition. ΔNp63 promotes Wnt signaling by directly upregulating Wnt ligands, Frizzled receptors, and transcription factors. Deletion of β-catenin in Krt8+ progenitors delays their maturation into Krt5+ progenitors. The lack of epidermal Wnt production in the absence of ΔNp63 also incapacitates Wnt activation in the underlying dermal cells. These findings reveal the remarkable changes of the transcriptome, open chromatin, and signaling pathways at the onset of skin development and uncover the molecular cascade for epidermal lineage formation. Employing single-cell RNA-seq and ATAC-seq, Fan et al. examine transcriptional and chromatin changes occurring during epidermal fate specification in mice. They characterize a developmental program, dependent on the transcription factor ΔNp63, generating epidermal progenitors, and ΔNp63-independent programs promoting epidermal differentiation and epithelial-to-mesenchymal transition.

Original languageEnglish (US)
Pages (from-to)21-37.e5
JournalDevelopmental Cell
Issue number1
StatePublished - Oct 8 2018
Externally publishedYes


  • ATAC-seq
  • epidermal fate
  • single cell analysis
  • transcriptional network
  • Wnt signaling

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Developmental Biology
  • Cell Biology

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