GRHL3 regulates the chromatin state during epidermal differentiation

The process of differentiation is tightly controlled, and such complex coordination of gene expression requires many layers of regulation. One such mechanism of regulation occurs through distal genomic regions called enhancers, which are believed to act as concentrating sites for transcription factors, like GRHL3, and other regulators, forming loops to contact promoters and enhance transcription. Active enhancers have been shown to have high levels of H3K4me1 and H3K27ac modified nucleosomes, with low levels of H3K4me3, while poised developmental enhancers have been shown to have H3K27me3 in place of H3K27ac. Additionally, in each cell type, a select few enhancers have been found to be unusually long (more than 12.5kb) and show high intensity of transcription factor binding and chromatin enhancer signature marks. These regions, termed super enhancers, are frequently tissue-specific and are thought to regulate the unique gene expression programs in each tissue. ChIP-Seq analysis revealed GRHL3 binding to be strongly enriched within enhancers and super enhancers in differentiating keratinocytes, however the effect of GRHL3 binding on enhancer and super enhancer activity and function is not known. ChIP-Seq with antibodies to H3K27ac, H3K4me3, and H3K4me1, and an Input control were performed on 24 hour differentiated primary epidermal keratinocytes (NHEK) after siRNA knockdown of GRHL3 (or scramble control). Duplicates of each ChIP were sequenced on Illumina Hi-Seq 2000.