Dynamic rewiring of cell identity transcriptional programs by loss of ERG in aortic endothelial cells [ATAC-Seq]

The ETS transcription factor ERG is a critical transcription factor that establishes and maintains an EC identity program. ERG is downregulated in several chronic vascular diseases, including atherosclerosis, and has been implicated in suppressing endothelial-to-mesenchymal transition (EndMT). However, the dynamic phenotypic and transcriptional consequences of ERG loss in the endothelium is poorly understood. We knocked down ERG using siRNA and compared this transient ERG loss over time to chronic deletion of ERG in a CRISPR/Cas9 deletion line in aortic ECs. RNA-sequencing and ATAC-sequencing revealed profound and dynamic rewiring of endothelial and mesenchymal transcriptional programs. While EC identity was rapidly lost (24 hours knock-down) at the transcriptional level, barrier dysfunction required longer-term knock- down (72 hours). A mesenchymal gene network and enhanced cell migration also required 72 hours to manifest. Loss of ERG was accompanied by a rapid loss of occupancy of ETS motifs and a gain in open chromatin containing AP1 motifs. Inhibition of AP1, washout of ERG siRNA or expression of ERG protein in ERG knock-out cells, demonstrated that EndMT was reversible. Finally, ERG-regulated genes and regulatory elements were associated with human disease, demonstrating that this transcription factor may be a valuable target of future therapies for vascular diseases.