title: A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.
abstract: Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth factor A (VEGFA), a major regulator of angiogenesis, triggers changes in transcriptional activity of human umbilical vein endothelial cells (HUVECs). Here, we used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to measure genome-wide changes in histone H3 acetylation at lysine 27 (H3K27ac), a marker of active enhancers, in unstimulated HUVECs and HUVECs stimulated with VEGFA for 1, 4, and 12 h. We show that sites with the greatest H3K27ac change upon stimulation were associated tightly with EP300, a histone acetyltransferase. Using the variation of H3K27ac as a novel epigenetic signature, we identified transcriptional regulatory elements that are functionally linked to angiogenesis, participate in rapid VEGFA-stimulated changes in chromatin conformation, and mediate VEGFA-induced transcriptional responses. Dynamic H3K27ac deposition and associated changes in chromatin conformation required EP300 activity instead of altered nucleosome occupancy or changes in DNase I hypersensitivity. EP300 activity was also required for a subset of dynamic H3K27ac sites to loop into proximity of promoters. Our study identified thousands of endothelial, VEGFA-responsive enhancers, demonstrating that an epigenetic signature based on the variation of a chromatin feature is a productive approach to define signal-responsive genomic elements. Further, our study implicates global epigenetic modifications in rapid, signal-responsive transcriptional regulation.
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Day
authors.forename: Joshua W
authors.initials: JW
authors.lastname: Ho
authors.forename: Lingyun
authors.initials: L
authors.lastname: Song
authors.forename: Jingjing
authors.initials: J
authors.lastname: Cao
authors.forename: Danos
authors.initials: D
authors.lastname: Christodoulou
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Seidman
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.forename: William T
authors.initials: WT
authors.lastname: Pu
mesh_terms: D000107:Acetylation; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D016000:Cluster Analysis; D050881:E1A-Associated p300 Protein / Q000378:metabolism*; D042783:Endothelial Cells / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism*; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D059372:Nucleotide Motifs; D011485:Protein Binding; D020218:Response Elements; D014157:Transcription Factors / Q000378:metabolism; D042461:Vascular Endothelial Growth Factor A / Q000378:metabolism*
chemical_list: D002843:Chromatin; D006657:Histones; D014157:Transcription Factors; D042461:Vascular Endothelial Growth Factor A; D050881:E1A-Associated p300 Protein
references.citation: Circ Res. 2008 Mar 28;102(6):637-52
references.pmid: 18369162
references.citation: Thromb Haemost. 2009 Sep;102(3):544-54
references.pmid: 19718476
references.citation: Biochem Soc Trans. 2009 Dec;37(Pt 6):1248-53
references.pmid: 19909256
references.citation: Nature. 2010 Sep 23;467(7314):430-5
references.pmid: 20720539
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6
references.pmid: 21808000
references.citation: Nat Rev Mol Cell Biol. 2011 Mar;12(3):141-51
references.pmid: 21346730
references.citation: Nat Genet. 2012 Jan 08;44(2):148-56
references.pmid: 22231485
references.citation: Curr Protoc Mol Biol. 2011 Apr;Chapter 4:Unit4.12
references.pmid: 21472699
references.citation: Chem Biol. 2010 May 28;17(5):471-82
references.pmid: 20534345
references.citation: Genome Res. 2011 Aug;21(8):1273-83
references.pmid: 21632746
references.citation: Genome Res. 2012 May;22(5):860-9
references.pmid: 22300769
references.citation: Nat Genet. 2007 Mar;39(3):311-8
references.pmid: 17277777
references.citation: Nature. 2011 May 5;473(7345):43-9
references.pmid: 21441907
references.citation: Nature. 2009 Feb 12;457(7231):854-8
references.pmid: 19212405
references.citation: Science. 2002 Feb 15;295(5558):1306-11
references.pmid: 11847345
references.citation: Nat Protoc. 2007;2(7):1722-33
references.pmid: 17641637
references.citation: Cell. 2008 Jan 25;132(2):311-22
references.pmid: 18243105
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6
references.pmid: 21106759
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Cell. 1996 Nov 29;87(5):953-9
references.pmid: 8945521
references.citation: Bioinformatics. 2011 Jun 15;27(12):1653-9
references.pmid: 21543442
references.citation: Mol Cell. 2002 Dec;10(6):1453-65
references.pmid: 12504019
references.citation: Nat Biotechnol. 2008 Dec;26(12):1351-9
references.pmid: 19029915
references.citation: Nature. 2011 May 19;473(7347):298-307
references.pmid: 21593862
references.citation: Cell Adh Migr. 2007 Jul-Sep;1(3):133-6
references.pmid: 19262131
references.citation: Nature. 2011 Mar 24;471(7339):480-5
references.pmid: 21179089
references.citation: Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384
references.pmid: 20150147
references.citation: Nat Genet. 2010 Apr;42(4):343-7
references.pmid: 20208536
references.citation: Nature. 2011 Feb 10;470(7333):279-83
references.pmid: 21160473
references.citation: FASEB J. 2011 Apr;25(4):1188-97
references.pmid: 21169383
references.citation: Genome Res. 2012 Sep;22(9):1735-47
references.pmid: 22955985
references.citation: Nat Protoc. 2006;1(2):729-48
references.pmid: 17406303
references.citation: Nature. 2011 May 15;474(7351):390-4
references.pmid: 21572438
references.citation: Cell. 2008 Dec 12;135(6):1053-64
references.pmid: 19070576
references.citation: Nature. 2010 May 13;465(7295):182-7
references.pmid: 20393465
references.citation: Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6374-8
references.pmid: 7541539
references.citation: Genome Biol. 2007;8(2):R24
references.pmid: 17324271
references.citation: PLoS Genet. 2007 Aug;3(8):e136
references.pmid: 17708682