Epigenetic modulation of epithelial-mesenchymal plasticity through chromatin modifiers KDM6A and CTCF.

Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of EMT, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that KDM6A and CTCF are suppressed and re-expressed, coincident with dynamic H3K27me3 and broad alterations in chromatin accessibility, during EMT/MET. These two factors are also lower in triple-negative breast cancer cell lines with EMT features. Through analysis of chromatin accessibility we identify that early EMT is characterized by enrichment for AP-1 family member binding motifs but also by diminished enrichment for CTCF binding motifs. Through loss-of-function analysis we demonstrate that suppression of CTCF strengthens the epithelial phenotype via upregulation of epithelial markers E-cadherin/CDH1, and downregulation of N-cadherin/CDH2. Conversely, upregulation of CTCF leads to upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal gene expression