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Genome Res. 2019 Feb;29(2):193-207. doi: 10.1101/gr.239053.118. Epub 2019 Jan 22.

A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA.

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Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Xin Hua Hospital, Shanghai Jiao Tong University, Shanghai 200240, China.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.
School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
Department for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
Renji-Med Clinical Stem Cell Research Center, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China.
Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas 78229, USA.
Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.
Contributed equally


Cell behaviors are dictated by epigenetic and transcriptional programs. Little is known about how extracellular stimuli modulate these programs to reshape gene expression and control cell behavioral responses. Here, we interrogated the epigenetic and transcriptional response of endothelial cells to VEGFA treatment and found rapid chromatin changes that mediate broad transcriptomic alterations. VEGFA-responsive genes were associated with active promoters, but changes in promoter histone marks were not tightly linked to gene expression changes. VEGFA altered transcription factor occupancy and the distal epigenetic landscape, which profoundly contributed to VEGFA-dependent changes in gene expression. Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network, which revealed that the small MAF transcription factors are master regulators of the VEGFA transcriptional program and angiogenesis. Collectively these results revealed that extracellular stimuli rapidly reconfigure the chromatin landscape to coordinately regulate biological responses.

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