Epigenetic priming during the Epithelial-mesenchymal transition

Cells respond and adapt to environmental stimuli by stably retaining epigenetic marks of prior transcriptional activation, altering cellular responses to the same stimulus when encountered in the future. We developed a cell culture model to study this transcriptional memory during the epithelial to mesenchymal transition (EMT), a cell state change central to both development and disease states. To do this, we used an epithelial mouse mammary gland cell line that reversibly undergoes EMT in response to transforming growth factor beta (TGF?). We show that TGF? stimulation establishes transcriptional memory, leading to altered transcriptional responses of a subset of genes upon re-stimulation. In our model, the memory response was inherited through ~22 cell divisions and led to increased migratory capacity upon re-stimulation with TGF?. We performed genome-wide characterization of this model, including histone modifications (CUT&RUN), nascent RNA (PRO-seq), chromatin accessibility (ATAC-seq) and DNA methylation analyses (Nanopore). We found that the memory response was selective, as only 25% of all TGF? responsive genes demonstrate an elevated response, while another 25% shows a refractory response, to re-stimulation. Mechanistically, DNA methylation, cell signaling, and paused Pol II do not appear to play a role in establishing this transcriptional memory. However, we found that enhancer histone modifications H3K4Me1 and H3K27Ac bookmark the TGF-? primed genes and enhancer elements. Our data suggest that enhancer-promoter contacts might be involved in establishing and retaining the transcriptional memory response.