Control of VEGF-A trancriptional programs by pausing and genomic compartmentalization

Vascular endothelial growth factor A (VEGF-A) is a master regulator of vascular development and function. Consequently, VEGF-A regulated gene expression programs have been under heavy research. In this study we study the transcriptional regulation of VEGF-A-responsive genes in primary aortic endothelial cells (HAEC) and vein endothelial cells (HUVEC) using genome wide global run-on sequencing (GRO-Seq). We show that half of VEGF-A induced genes display a paused phenotype under basal conditions and are thus poised for rapid gene activation. Promoters of paused genes are distinguished from those of non-paused by higher basal enrichment for active histone marks H3K4me3, H3K9ac and H3K27ac. We also show that nearly 100% of the VEGF-upregulated genes are induced at the level of elongation, whereas 38-53% are also induced at the level of initiation. We also report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and identify chromatin compartments enriched for VEGF-regulated genes. Cell-type specific transcriptional activity was also shown to reflect boundaries of chromatin interactions within the HOXA cluster. Collectively, these findings provide new insight into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells. ChIP-Seq (H3K4me2), GRO-Seq and HiC profiling was performed in HUVECs and HAECs.