DNA methylation profiling of proliferating and differentiating keratinocytes

The epidermal compartment of the skin is regenerated constantly by proliferation of epidermal keratinocytes. Differentiation of a subset of these keratinocytes allows the epidermis to retain its barrier properties. Regulation of keratinocyte fate – whether to remain proliferative or terminally differentiate – is complex and not fully understood. The objective of our study was to assess if DNA methylation changes contribute to the regulation of keratinocyte fate. We employed genome-wide MethylationEPIC beadchip array measuring approximately 850,000 probes combined with RNA sequencing of in vitro cultured nondifferentiated and terminally differentiated adult human primary keratinocytes. We did not observe a correlation between methylation status and transcriptome changes and only two differentially methylated probes were detected, of which one was located in the TRIM29 gene. TRIM29 knockdown resulted in significantly lower expression levels of terminal differentiation genes as a group, although differences for individual genes were considered minor (<2 fold). From these results we conclude that it is unlikely that DNA methylation has a main regulatory role in terminal keratinocyte differentiation regulation in vitro. Primary keratinocytes of 5 different skin cell donors were cultured and DNA was harvested during proliferation and after terminal differentiation.