(2019) UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47:D506-D515. https://doi.org/10.1093/nar/gky1049

Abbas N, Perbellini F, Thum T (2020) Non-coding RNAs: emerging players in cardiomyocyte proliferation and cardiac regeneration. Basic Res Cardiol 115:52. https://doi.org/10.1007/s00395-020-0816-0

Article  CAS  Google Scholar 

Allhoff M, Seré K, Pires FJ, Zenke M, Costa GI (2016) Differential peak calling of ChIP-seq signals with replicates with THOR. Nucleic Acids Res 44:e153. https://doi.org/10.1093/nar/gkw680

Article  CAS  Google Scholar 

Andrews S. (2010) FastQC: a quality control tool for high throughput sequence data

Baumgarten N, Hecker D, Karunanithi S, Schmidt F, List M, Schulz MH (2020) EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res 48:W193–W199. https://doi.org/10.1093/nar/gkaa382

Article  CAS  Google Scholar 

Bibli S-I, Hu J, Looso M, Weigert A, Ratiu C, Wittig J, Drekolia MK, Tombor L, Randriamboavonjy V, Leisegang MS, Goymann P, Delgado Lagos F, Fisslthaler B, Zukunft S, Kyselova A, Justo AFO, Heidler J, Tsilimigras D, Brandes RP, Dimmeler S, Papapetropoulos A, Knapp S, Offermanns S, Wittig I, Nishimura SL, Sigala F, Fleming I (2021) Mapping the endothelial cell S-sulfhydrome highlights the crucial role of integrin sulfhydration in vascular function. Circulation 143:935–948. https://doi.org/10.1161/CIRCULATIONAHA.120.051877

Article  CAS  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  Google Scholar 

Broad Institute (2019) Picard toolkit

Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol. https://doi.org/10.1002/0471142727.Mb2129s109

Article  Google Scholar 

Bultman S, Gebuhr T, Yee D, La Mantia C, Nicholson J, Gilliam A, Randazzo F, Metzger D, Chambon P, Crabtree G, Magnuson T (2000) A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol Cell 6:1287–1295. https://doi.org/10.1016/s1097-2765(00)00127-1

Article  CAS  Google Scholar 

Cairns BR (2007) Chromatin remodeling: insights and intrigue from single-molecule studies. Nat Struct Mol Biol 14:989–996. https://doi.org/10.1038/nsmb1333

Article  CAS  Google Scholar 

Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR, Kingston RE, Kohtz JD (2015) Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 142:2641–2652. https://doi.org/10.1242/dev.126318

Article  CAS  Google Scholar 

Calandrelli R, Xu L, Luo Y, Wu W, Fan X, Nguyen T, Chen C-J, Sriram K, Tang X, Burns AB, Natarajan R, Chen ZB, Zhong S (2020) Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Nat Commun 11:5211. https://doi.org/10.1038/s41467-020-18957-w

Article  CAS  Google Scholar 

Deanfield JE, Halcox JP, Rabelink TJ (2007) Endothelial function and dysfunction: testing and clinical relevance. Circulation 115:1285–1295. https://doi.org/10.1161/CIRCULATIONAHA.106.652859

Article  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

Article  CAS  Google Scholar 

Ertürk A, Becker K, Jährling N, Mauch CP, Hojer CD, Egen JG, Hellal F, Bradke F, Sheng M, Dodt H-U (2012) Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nat Protoc 7:1983–1995. https://doi.org/10.1038/nprot.2012.119

Article  CAS  Google Scholar 

Krueger F, James F, Ewels P, Afyounian E, Schuster-Boeckler B (2021) FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo. Zenodo

Feng J, Liu T, Qin B, Zhang Y, Liu XS (2012) Identifying ChIP-seq enrichment using MACS. Nat Protoc 7:1728–1740. https://doi.org/10.1038/nprot.2012.101

Article  CAS  Google Scholar 

Ferrara N, Mass RD, Campa C, Kim R (2007) Targeting VEGF-A to treat cancer and age-related macular degeneration. Annu Rev Med 58:491–504. https://doi.org/10.1146/annurev.med.58.061705.145635

Article  CAS  Google Scholar 

Fiedler J, Breckwoldt K, Remmele CW, Hartmann D, Dittrich M, Pfanne A, Just A, Xiao K, Kunz M, Müller T, Hansen A, Geffers R, Dandekar T, Eschenhagen T, Thum T (2015) Development of long noncoding RNA-based strategies to modulate tissue vascularization. J Am Coll Cardiol 66:2005–2015. https://doi.org/10.1016/j.jacc.2015.07.081

Article  CAS  Google Scholar 

Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JAC, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge ASB, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J-I, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JFJ, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R-I, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima-Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JGD, Rackham OJL, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, Hoen PAC, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y (2014) A promoter-level mammalian expression atlas. Nature 507:462–470. https://doi.org/10.1038/nature13182

Article  CAS  Google Scholar 

Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud J-B, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly J-S, Concordet J-P (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148. https://doi.org/10.1186/s13059-016-1012-2

Article  CAS  Google Scholar 

Han P, Li W, Lin C-H, Yang J, Shang C, Nuernberg ST, Jin KK, Xu W, Lin C-Y, Lin C-J, Xiong Y, Chien H, Zhou B, Ashley E, Bernstein D, Chen P-S, Chen H-SV, Quertermous T, Chang C-P (2014) A long noncoding RNA protects the heart from pathological hypertrophy. Nature 514:102–106. https://doi.org/10.1038/nature13596

Article  CAS  Google Scholar 

Hathaway CA, Heistad DD, Piegors DJ, Miller FJ (2002) Regression of atherosclerosis in monkeys reduces vascular superoxide levels. Circ Res 90:277–283. https://doi.org/10.1161/hh0302.104724

Article  CAS  Google Scholar 

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589. https://doi.org/10.1016/j.molcel.2010.05.004

Article  CAS  Google Scholar 

Iurlaro M, Stadler MB, Masoni F, Jagani Z, Galli GG, Schübeler D (2021) Mammalian SWI/SNF continuously restores local accessibility to chromatin. Nat Genet 53:279–287. https://doi.org/10.1038/s41588-020-00768-w

Article  CAS  Google Scholar 

Jaakkola P, Mole DR, Tian YM, Wilson MI, Gielbert J, Gaskell SJ, von Kriegsheim A, Hebestreit HF, Mukherji M, Schofield CJ, Maxwell PH, Pugh CW, Ratcliffe PJ (2001) Targeting of HIF-alpha to the von Hippel–Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292:468–472. https://doi.org/10.1126/science.1059796

Article  CAS  Google Scholar 

Jégu T, Blum R, Cochrane JC, Yang L, Wang C-Y, Gilles M-E, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT (2019) Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol 26:96–109. https://doi.org/10.1038/s41594-018-0176-8

Article  CAS  Google Scholar 

Johnson KE, Wilgus TA (2014) Vascular endothelial growth factor and angiogenesis in the regulation of cutaneous wound repair. Adv Wound Care (New Rochelle) 3:647–661. https://doi.org/10.1089/wound.2013.0517

Article  Google Scholar 

Kadam S, Emerson BM (2003) Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol Cell 11:377–389. https://doi.org/10.1016/S1097-2765(03)00034-0

Article  CAS  Google Scholar 

Kalna V, Yang Y, Peghaire CR, Frudd K, Hannah R, Shah AV, Osuna Almagro L, Boyle JJ, Göttgens B, Ferrer J, Randi AM, Birdsey GM (2019) The transcription factor ERG regulates super-enhancers associated with an endothelial-specific gene expression program. Circ Res 124:1337–1349. https://doi.org/10.1161/CIRCRESAHA.118.313788

Article  CAS  Google Scholar 

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D (2010) BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26:2204–2207. https://doi.org/10.1093/bioinformatics/btq351

Article  CAS  Google Scholar 

Korff T, Augustin HG (1998) Integration of endothelial cells in multicellular spheroids prevents apoptosis and induces differentiation. J Cell Biol 143:1341–1352. https://doi.org/10.1083/jcb.143.5.1341

Article  CAS  Google Scholar 

Kovacic JC, Dimmeler S, Harvey RP, Finkel T, Aikawa E, Krenning G, Baker AH (2019) Endothelial to mesenchymal transition in cardiovascular disease: JACC state-of-the-art review. J Am Coll Cardiol 73:190–209. https://doi.org/10.1016/j.jacc.2018.09.089

Article  Google Scholar 

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, Medvedeva YA, Magana-Mora A, Bajic VB, Papatsenko DA, Kolpakov FA, Makeev VJ (2018) HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res 46:D252–D259. https://doi.org/10.1093/nar/gkx1106

Article  CAS  Google Scholar 

Laib AM, Bartol A, Alajati A, Korff T, Weber H, Augustin HG (2009) Spheroid-based human endothelial cell microvessel formation in vivo. Nat Protoc 4:1202–1215. https://doi.org/10.1038/nprot.2009.96

Article  CAS  Google Scholar 

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923

Article  CAS