Large-scale discovery of enhancers from human heart tissue (original) (raw)

• Hoffman, J.I., Kaplan, S. & Liberthson, R.R. Prevalence of congenital heart disease. Am. Heart J. 147, 425–439 (2004).
  Article Google Scholar
• Lloyd-Jones, D. et al. Heart disease and stroke statistics—2010 update: a report from the American Heart Association. Circulation 121, e46–e215 (2010).
  Google Scholar
• Bentham, J. & Bhattacharya, S. Genetic mechanisms controlling cardiovascular development. Ann. NY Acad. Sci. 1123, 10–19 (2008).
  Article CAS Google Scholar
• Bruneau, B.G. The developmental genetics of congenital heart disease. Nature 451, 943–948 (2008).
  Article CAS Google Scholar
• Pierpont, M.E. et al. Genetic basis for congenital heart defects: current knowledge: a scientific statement from the American Heart Association Congenital Cardiac Defects Committee, Council on Cardiovascular Disease in the Young: endorsed by the American Academy of Pediatrics. Circulation 115, 3015–3038 (2007).
  Article Google Scholar
• Helgadottir, A. et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316, 1491–1493 (2007).
  Article CAS Google Scholar
• McPherson, R. et al. A common allele on chromosome 9 associated with coronary heart disease. Science 316, 1488–1491 (2007).
  Article CAS Google Scholar
• Schunkert, H. et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet. 43, 333–338 (2011).
  Article CAS Google Scholar
• Visel, A., Rubin, E.M. & Pennacchio, L.A. Genomic views of distant-acting enhancers. Nature 461, 199–205 (2009).
  Article CAS Google Scholar
• Visel, A. et al. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464, 409–412 (2010).
  Article CAS Google Scholar
• Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008).
  Article CAS Google Scholar
• Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311–318 (2007).
  Article CAS Google Scholar
• Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009).
  Article CAS Google Scholar
• Xi, H. et al. Identification and characterization of cell type–specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3, e136 (2007).
  Article Google Scholar
• Blow, M.J. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806–810 (2010).
  Article CAS Google Scholar
• Arany, Z., Sellers, W.R., Livingston, D.M. & Eckner, R. E1A-associated p300 and CREB-associated CBP belong to a conserved family of coactivators. Cell 77, 799–800 (1994).
  Article CAS Google Scholar
• Eckner, R. et al. Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. Genes Dev. 8, 869–884 (1994).
  Article CAS Google Scholar
• Ogryzko, V.V., Schiltz, R.L., Russanova, V., Howard, B.H. & Nakatani, Y. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87, 953–959 (1996).
  Article CAS Google Scholar
• Capaldi, A.P. et al. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet. 40, 1300–1306 (2008).
  Article CAS Google Scholar
• McLean, C.Y. et al. GREAT improves functional interpretation of _cis_-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).
  Article CAS Google Scholar
• Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).
  Article CAS Google Scholar
• Dimas, A.S. et al. Common regulatory variation impacts gene expression in a cell type–dependent manner. Science 325, 1246–1250 (2009).
  Article CAS Google Scholar
• Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).
  Article CAS Google Scholar
• Narlikar, L. et al. Genome-wide discovery of human heart enhancers. Genome Res. 20, 381–392 (2010).
  Article CAS Google Scholar
• Henderson, D.J. & Anderson, R.H. The development and structure of the ventricles in the human heart. Pediatr. Cardiol. 30, 588–596 (2009).
  Article Google Scholar
• Coppen, S.R. et al. Comparison of connexin expression patterns in the developing mouse heart and human foetal heart. Mol. Cell. Biochem. 242, 121–127 (2003).
  Article CAS Google Scholar
• Kothary, R. et al. A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube. Nature 335, 435–437 (1988).
  Article CAS Google Scholar
• Pennacchio, L.A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499–502 (2006).
  Article CAS Google Scholar
• Blake, J.A., Bult, C.J., Eppig, J.T., Kadin, J.A. & Richardson, J.E. The Mouse Genome Database genotypes:phenotypes. Nucleic Acids Res. 37, D712–D719 (2009).
  Article CAS Google Scholar
• Morimoto, T., Sunagawa, Y., Fujita, M. & Hasegawa, K. Novel heart failure therapy targeting transcriptional pathway in cardiomyocytes by a natural compound, curcumin. Circ. J. 74, 1059–1066 (2010).
  Article CAS Google Scholar
• Thompson, P.R. et al. Regulation of the p300 HAT domain via a novel activation loop. Nat. Struct. Mol. Biol. 11, 308–315 (2004).
  Article CAS Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS Google Scholar
• Kuhn, R.M. et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 37, D755–D761 (2009).
  Article CAS Google Scholar
• Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).
  Article CAS Google Scholar
• Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).
  Article CAS Google Scholar
• Conti, A. et al. Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy. BMC Genomics 8, 268 (2007).
  Article Google Scholar
• Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. Chapter 19, Unit 19.10.1–19.10.21 (Wiley, 2010).
• Goecks, J., Nekrutenko, A. & Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
  Article Google Scholar
• Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
  Article CAS Google Scholar
• Hinrichs, A.S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).
  Article CAS Google Scholar
• Nobrega, M.A., Ovcharenko, I., Afzal, V. & Rubin, E.M. Scanning human gene deserts for long-range enhancers. Science 302, 413 (2003).
  Article CAS Google Scholar
• Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L.A. VISTA Enhancer Browser—a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88–D92 (2007).
  Article CAS Google Scholar