title: Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization.
abstract: Vascular endothelial growth factor A (VEGF-A) is a master regulator of angiogenesis, vascular development and function. In this study we investigated the transcriptional regulation of VEGF-A-responsive genes in primary human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs) using genome-wide global run-on sequencing (GRO-Seq). We demonstrate that half of VEGF-A-regulated gene promoters are characterized by a transcriptionally competent paused RNA polymerase II (Pol II). We show that transition into productive elongation is a major mechanism of gene activation of virtually all VEGF-regulated genes, whereas only ∼40% of the genes are induced at the level of initiation. In addition, we 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 cell type-specific transcriptional activity reflects the boundaries of chromatin interactions. Furthermore, we identify large chromatin compartments with a tendency to be coordinately transcribed upon VEGF-A stimulation. We provide evidence that these compartments are enriched for clusters of regulatory regions such as super-enhancers and for disease-associated single nucleotide polymorphisms (SNPs). Collectively, these findings provide new insights into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells.
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland minna.kaikkonen@uef.fi.
authors.forename: Minna U
authors.initials: MU
authors.lastname: Kaikkonen
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland.
authors.forename: Henri
authors.initials: H
authors.lastname: Niskanen
authors.affiliation: Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
authors.forename: Casey E
authors.initials: CE
authors.lastname: Romanoski
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland.
authors.forename: Emilia
authors.initials: E
authors.lastname: Kansanen
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland.
authors.forename: Annukka M
authors.initials: AM
authors.lastname: Kivelä
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland.
authors.forename: Jarkko
authors.initials: J
authors.lastname: Laitalainen
authors.affiliation: Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
authors.forename: Sven
authors.initials: S
authors.lastname: Heinz
authors.affiliation: Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Benner
authors.affiliation: Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Glass
authors.affiliation: A.I. Virtanen Institute for Molecular Sciences, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland Science Service Center and Gene Therapy Unit, Kuopio University Hospital, Finland.
authors.forename: Seppo
authors.initials: S
authors.lastname: Ylä-Herttuala
mesh_terms: D002451:Cell Compartmentation; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D015894:Genome, Human; D006801:Humans; D010641:Phenotype; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects; D015533:Transcriptional Activation; D042461:Vascular Endothelial Growth Factor A / Q000494:pharmacology*
chemical_list: D002843:Chromatin; D014157:Transcription Factors; D042461:Vascular Endothelial Growth Factor A