A comparative encyclopedia of DNA elements in the mouse genome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-11-19

AUTHORS

Feng Yue, Yong Cheng, Alessandra Breschi, Jeff Vierstra, Weisheng Wu, Tyrone Ryba, Richard Sandstrom, Zhihai Ma, Carrie Davis, Benjamin D. Pope, Yin Shen, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman, Rajinder Kaul, Eric Rynes, Anthony Kirilusha, Georgi K. Marinov, Brian A. Williams, Diane Trout, Henry Amrhein, Katherine Fisher-Aylor, Igor Antoshechkin, Gilberto DeSalvo, Lei-Hoon See, Meagan Fastuca, Jorg Drenkow, Chris Zaleski, Alex Dobin, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer, Olgert Denas, Kanwei Li, M. A. Bender, Miaohua Zhang, Rachel Byron, Mark T. Groudine, David McCleary, Long Pham, Zhen Ye, Samantha Kuan, Lee Edsall, Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis, Cheryl A. Keller, Christapher S. Morrissey, Tejaswini Mishra, Deepti Jain, Nergiz Dogan, Robert S. Harris, Philip Cayting, Trupti Kawli, Alan P. Boyle, Ghia Euskirchen, Anshul Kundaje, Shin Lin, Yiing Lin, Camden Jansen, Venkat S. Malladi, Melissa S. Cline, Drew T. Erickson, Vanessa M. Kirkup, Katrina Learned, Cricket A. Sloan, Kate R. Rosenbloom, Beatriz Lacerda de Sousa, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian, Tamer Kahveci, Dongwon Lee, W. James Kent, Miguel Ramalho Santos, Javier Herrero, Cedric Notredame, Audra Johnson, Shinny Vong, Kristen Lee, Daniel Bates, Fidencio Neri, Morgan Diegel, Theresa Canfield, Peter J. Sabo, Matthew S. Wilken, Thomas A. Reh, Erika Giste, Anthony Shafer, Tanya Kutyavin, Eric Haugen, Douglas Dunn, Alex P. Reynolds, Shane Neph, Richard Humbert, R. Scott Hansen, Marella De Bruijn, Licia Selleri, Alexander Rudensky, Steven Josefowicz, Robert Samstein, Evan E. Eichler, Stuart H. Orkin, Dana Levasseur, Thalia Papayannopoulou, Kai-Hsin Chang, Arthur Skoultchi, Srikanta Gosh, Christine Disteche, Piper Treuting, Yanli Wang, Mitchell J. Weiss, Gerd A. Blobel, Xiaoyi Cao, Sheng Zhong, Ting Wang, Peter J. Good, Rebecca F. Lowdon, Leslie B. Adams, Xiao-Qiao Zhou, Michael J. Pazin, Elise A. Feingold, Barbara Wold, James Taylor, Ali Mortazavi, Sherman M. Weissman, John A. Stamatoyannopoulos, Michael P. Snyder, Roderic Guigo, Thomas R. Gingeras, David M. Gilbert, Ross C. Hardison, Michael A. Beer, Bing Ren

ABSTRACT

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases. More... »

PAGES

355-364

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  • Journal

    TITLE

    Nature

    ISSUE

    7527

    VOLUME

    515

    Author Affiliations

  • Present Address: Present addresses: Department of Biochemistry and Molecular Biology, School of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA (F.Y.); BRCF Bioinformatics Core, University of Michigan, Ann Arbor, Michigan 48105, USA (W.W.); Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, USA (T.R.); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA (A.P.B.); Washington University in St Louis, St Louis, Missouri 63108, USA (R.L.); University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599, USA (L.B.A.),
  • Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.,
  • Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.,
  • Department of Genome Sciences, University of Washington, Seattle, 98195 Washington USA
  • Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.,
  • Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, 32306-4295 Florida USA
  • Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.,
  • Division of Biology, California Institute of Technology, Pasadena, 91125 California USA
  • Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria.,
  • Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.,
  • Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, 98109 Washington USA
  • Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, 98109 Washington USA
  • Department of Radiation Oncology, University of Washington, Seattle, 98195 Washington USA
  • Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, 02139 Massachusetts USA
  • Broad Institute of MIT and Harvard, Cambridge, 02142 Massachusetts USA
  • Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, 16802 Pennsylvania USA
  • Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.,
  • Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, 95064 California USA
  • Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, 94143 California USA
  • European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,
  • Department of Genetics, Yale University, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.,
  • Computer & Information Sciences & Engineering, University of Florida, Gainesville, 32611 Florida USA
  • McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.,
  • Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK.,
  • Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.,
  • MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK.,
  • Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, 10065 New York USA
  • HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, 10065 New York USA
  • Dana Farber Cancer Institute, Harvard Medical School, Cambridge, 02138 Massachusetts USA
  • Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, 52242 Iowa USA
  • Division of Hematology, Department of Medicine, University of Washington, Seattle, 98195 Washington USA
  • Department of Cell Biology, Albert Einstein College of Medicine, Bronx, 10461 New York USA
  • Department of Pathology, University of Washington, Seattle, 98195 Washington USA
  • Department of Comparative Medicine, University of Washington, Seattle, 98195 Washington USA
  • Bioinformatics and Genomics program, The Pennsylvania State University, University Park, 16802 Pennsylvania USA
  • Department of Hematology, St Jude Children’s Research Hospital, Memphis, 38105 Tennessee USA
  • Perelman School of Medicine at the University of Pennsylvania, Philadelphia, 19104 Pennsylvania USA
  • Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.,
  • Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, 63108 Missouri USA
  • NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.,
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature13992

    DOI

    http://dx.doi.org/10.1038/nature13992

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1036662703

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25409824


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