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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.
Vierstra, Jeff; Rynes, Eric; Sandstrom, Richard; Zhang, Miaohua; Canfield, Theresa; Hansen, R Scott; Stehling-Sun, Sandra; Sabo, Peter J; Byron, Rachel; Humbert, Richard; Thurman, Robert E; Johnson, Audra K; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Haugen, Eric; Dunn, Douglas; Wilken, Matthew S; Josefowicz, Steven; Samstein, Robert; Chang, Kai-Hsin; Eichler, Evan E; De Bruijn, Marella; Reh, Thomas A; Skoultchi, Arthur; Rudensky, Alexander; Orkin, Stuart H; Papayannopoulou, Thalia; Treuting, Piper M; Selleri, Licia; Kaul, Rajinder; Groudine, Mark; Bender, M A; Stamatoyannopoulos, John A.
Afiliação
  • Vierstra J; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Rynes E; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Sandstrom R; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Zhang M; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • Canfield T; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Hansen RS; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
  • Stehling-Sun S; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Sabo PJ; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Byron R; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • Humbert R; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Thurman RE; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Johnson AK; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Vong S; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Lee K; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Bates D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Neri F; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Diegel M; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Giste E; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Haugen E; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Dunn D; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Wilken MS; Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
  • Josefowicz S; Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute.
  • Samstein R; Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute.
  • Chang KH; Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
  • Eichler EE; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute.
  • De Bruijn M; Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK.
  • Reh TA; Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.
  • Skoultchi A; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
  • Rudensky A; Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Howard Hughes Medical Institute.
  • Orkin SH; Howard Hughes Medical Institute. Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.
  • Papayannopoulou T; Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
  • Treuting PM; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA.
  • Selleri L; Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY 10065, USA.
  • Kaul R; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
  • Groudine M; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Radiation Oncology, University of Washington, Seattle, WA 98109, USA.
  • Bender MA; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
  • Stamatoyannopoulos JA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Division of Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA. jstam@uw.edu.
Science ; 346(6212): 1007-12, 2014 Nov 21.
Article em En | MEDLINE | ID: mdl-25411453
ABSTRACT
To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.
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Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Fatores de Transcrição / DNA / Sequências Reguladoras de Ácido Nucleico / Sequência Conservada / Evolução Molecular Limite: Animals / Humans Idioma: En Revista: Science Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Bases de dados: MEDLINE Assunto principal: Fatores de Transcrição / DNA / Sequências Reguladoras de Ácido Nucleico / Sequência Conservada / Evolução Molecular Limite: Animals / Humans Idioma: En Revista: Science Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Estados Unidos