Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators

Area of Science:

• Developmental Biology
• Molecular Biology
• Genomics

Background:

• Keratinocyte differentiation is crucial for skin structure and function.
• This process involves complex, coordinated gene expression changes over time and space.
• Understanding the regulatory mechanisms is key to comprehending skin development and homeostasis.

Purpose of the Study:

• To reconstruct the transcriptional regulation of genes during human keratinocyte differentiation.
• To identify key transcription factors (TFs) coordinating gene expression modules.
• To investigate the role of specific TFs and gene expression patterns in maintaining keratinocyte states.

Main Methods:

• Utilized single-cell RNA sequencing (scRNA-seq) on 22,338 human foreskin keratinocytes.
• Organized gene expression data by differentiation stage and TF-associated modules.
• Employed computational methods to predict TF binding enrichment in super-enhancers.

Main Results:

• Identified groups of TFs with coordinated expression changes during keratinocyte differentiation.
• Found concordant TF binding enrichment in dynamic super-enhancers.
• Experimental depletion of ZBED2 and ETV4 induced keratinocyte differentiation.
• Discovered preferential expression of antioxidant genes in the basal state.

Conclusions:

• Identified a core set of TFs as master coordinators of keratinocyte differentiation.
• Demonstrated the role of ZBED2 and ETV4 in maintaining the basal keratinocyte state.
• Highlighted the active suppression of reactive oxygen species in undifferentiated keratinocytes.
• Showcased computational approaches for studying dynamic gene regulation in development.