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Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Moore, Jill E; Purcaro, Michael J; Pratt, Henry E; Epstein, Charles B; Shoresh, Noam; Adrian, Jessika; Kawli, Trupti; Davis, Carrie A; Dobin, Alexander; Kaul, Rajinder; Halow, Jessica; Van Nostrand, Eric L; Freese, Peter; Gorkin, David U; Shen, Yin; He, Yupeng; Mackiewicz, Mark; Pauli-Behn, Florencia; Williams, Brian A; Mortazavi, Ali; Keller, Cheryl A; Zhang, Xiao-Ou; Elhajjajy, Shaimae I; Huey, Jack; Dickel, Diane E; Snetkova, Valentina; Wei, Xintao; Wang, Xiaofeng; Rivera-Mulia, Juan Carlos; Rozowsky, Joel; Zhang, Jing; Chhetri, Surya B; Zhang, Jialing; Victorsen, Alec; White, Kevin P; Visel, Axel; Yeo, Gene W; Burge, Christopher B; Lécuyer, Eric; Gilbert, David M; Dekker, Job; Rinn, John; Mendenhall, Eric M; Ecker, Joseph R; Kellis, Manolis; Klein, Robert J; Noble, William S; Kundaje, Anshul; Guigó, Roderic; Farnham, Peggy J.
Afiliación
  • Moore JE; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Purcaro MJ; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Pratt HE; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Epstein CB; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Shoresh N; The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Adrian J; Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
  • Kawli T; Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
  • Davis CA; Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
  • Dobin A; Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
  • Kaul R; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
  • Halow J; Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
  • Van Nostrand EL; Altius Institute for Biomedical Sciences, Seattle, WA, USA.
  • Freese P; Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
  • Gorkin DU; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Shen Y; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
  • He Y; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
  • Mackiewicz M; Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
  • Pauli-Behn F; Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
  • Williams BA; Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
  • Mortazavi A; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Keller CA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Zhang XO; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Elhajjajy SI; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
  • Huey J; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
  • Dickel DE; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Snetkova V; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Wei X; University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
  • Wang X; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Rivera-Mulia JC; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Rozowsky J; Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
  • Zhang J; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.
  • Chhetri SB; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
  • Zhang J; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada.
  • Victorsen A; Department of Biological Science, Florida State University, Tallahassee, FL, USA.
  • White KP; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
  • Visel A; Yale University, New Haven, CT, USA.
  • Yeo GW; Yale University, New Haven, CT, USA.
  • Burge CB; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
  • Lécuyer E; Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
  • Gilbert DM; Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA.
  • Dekker J; Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
  • Rinn J; Tempus Labs, Chicago, IL, USA.
  • Mendenhall EM; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Ecker JR; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Kellis M; School of Natural Sciences, University of California, Merced, Merced, CA, USA.
  • Klein RJ; Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
  • Noble WS; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Kundaje A; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.
  • Guigó R; Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
  • Farnham PJ; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada.
Nature ; 583(7818): 699-710, 2020 07.
Article en En | MEDLINE | ID: mdl-32728249
ABSTRACT
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https//www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http//screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Sistema de Registros / Secuencias Reguladoras de Ácidos Nucleicos / Genoma / Genómica / Bases de Datos Genéticas / Anotación de Secuencia Molecular Límite: Animals / Humans Idioma: En Revista: Nature Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Sistema de Registros / Secuencias Reguladoras de Ácidos Nucleicos / Genoma / Genómica / Bases de Datos Genéticas / Anotación de Secuencia Molecular Límite: Animals / Humans Idioma: En Revista: Nature Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos