Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation

Stem Cell Reports. 2016 Apr 12;6(4):618-632. doi: 10.1016/j.stemcr.2016.03.003. Epub 2016 Mar 31.


Human skin is maintained by the differentiation and maturation of interfollicular stem and progenitors cells. We used DeepCAGE, genome-wide profiling of histone modifications and retroviral integration analysis, to map transcripts, promoters, enhancers, and super-enhancers (SEs) in prospectively isolated keratinocytes and transit-amplifying progenitors, and retrospectively defined keratinocyte stem cells. We show that >95% of the active promoters are in common and differentially regulated in progenitors and differentiated keratinocytes, while approximately half of the enhancers and SEs are stage specific and account for most of the epigenetic changes occurring during differentiation. Transcription factor (TF) motif identification and correlation with TF binding site maps allowed the identification of TF circuitries acting on enhancers and SEs during differentiation. Overall, our study provides a broad, genome-wide description of chromatin dynamics and differential enhancer and promoter usage during epithelial differentiation, and describes a novel approach to identify active regulatory elements in rare stem cell populations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites / genetics
  • Cell Differentiation / genetics*
  • Cells, Cultured
  • Enhancer Elements, Genetic / genetics
  • Epidermal Cells
  • Epigenesis, Genetic*
  • Foreskin / cytology
  • Gene Expression Profiling / methods
  • Gene Ontology
  • Gene Regulatory Networks
  • Histones / metabolism
  • Humans
  • Keratinocytes / cytology
  • Keratinocytes / metabolism*
  • Male
  • Mice
  • Models, Genetic
  • NIH 3T3 Cells
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • Reverse Transcriptase Polymerase Chain Reaction
  • Stem Cells / cytology
  • Stem Cells / metabolism*
  • Transcription Factors / metabolism
  • Transcription, Genetic*


  • Histones
  • Transcription Factors