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    Nature. 2014 Nov 21. pii: nature13992. doi: 10.1038/nature13992. pmc: PMC4266106. mid: NIHMS638072
    A comparative encyclopedia of DNA elements in the mouse genome.
    Yue F1,  Cheng Y2,  Breschi A3,  Vierstra J4,  Wu W5,  Ryba T6,  Sandstrom R7,  Ma Z8,  Davis C9,  Pope BD10,  Shen Y11,  Pervouchine DD12,  Djebali S13,  Thurman RE14,  Kaul R15,  Rynes E16,  Kirilusha A17,  Marinov GK18,  Williams BA19,  Trout D20,  Amrhein H21,  Fisher-Aylor K22,  Antoshechkin I23,  DeSalvo G24,  See LH25,  Fastuca M26,  Drenkow J27,  Zaleski C28,  Dobin A29,  Prieto P30,  Lagarde J31,  Bussotti G32,  Tanzer A33,  Denas O34,  Li K35,  Bender MA36,  Zhang M37,  Byron R38,  Groudine MT39,  McCleary D40,  Pham L41,  Ye Z42,  Kuan S43,  Edsall L44,  Wu YC45,  Rasmussen MD46,  Bansal MS47,  Kellis M48,  Keller CA49,  Morrissey CS50,  Mishra T51,  Jain D52,  Dogan N53,  Harris RS54,  Cayting P55,  Kawli T56,  Boyle AP57,  Euskirchen G58,  Kundaje A59,  Lin S60,  Lin Y61,  Jansen C62,  Malladi VS63,  Cline MS64,  Erickson DT65,  Kirkup VM66,  Learned K67,  Sloan CA68,  Rosenbloom KR69,  Lacerda de Sousa B70,  Beal K71,  Pignatelli M72,  Flicek P73,  Lian J74,  Kahveci T75,  Lee D76,  Kent WJ77,  Ramalho Santos M78,  Herrero J79,  Notredame C80,  Johnson A81,  Vong S82,  Lee K83,  Bates D84,  Neri F85,  Diegel M86,  Canfield T87,  Sabo PJ88,  Wilken MS89,  Reh TA90,  Giste E91,  Shafer A92,  Kutyavin T93,  Haugen E94,  Dunn D95,  Reynolds AP96,  Neph S97,  Humbert R98,  Hansen RS99,  De Bruijn M100,  Selleri L101,  Rudensky A102,  Josefowicz S103,  Samstein R104,  Eichler EE105,  Orkin SH106,  Levasseur D107,  Papayannopoulou T108,  Chang KH109,  Skoultchi A110,  Gosh S111,  Disteche C112,  Treuting P113,  Wang Y114,  Weiss MJ115,  Blobel GA116,  Cao X117,  Zhong S118,  Wang T119,  Good PJ120,  Lowdon RF121,  Adams LB122,  Zhou XQ123,  Pazin MJ124,  Feingold EA125,  Wold B126,  Taylor J127,  Mortazavi A128,  Weissman SM129,  Stamatoyannopoulos JA130,  Snyder MP131,  Guigo R132,  Gingeras TR133,  Gilbert DM134,  Hardison RC135,  Beer MA136,  Ren B137
    Author information
    11] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
    2Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    3Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    4Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    5Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    6Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA.
    7Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    8Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    9Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    10Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA.
    11Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    12Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    13Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    14Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    15Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    16Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    17Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    18Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    19Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    20Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    21Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    22Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    23Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    24Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    25Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    26Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    27Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    28Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    29Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    30Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    31Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    32Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    331] Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain. [2] Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17/3/303, A-1090 Vienna, Austria.
    34Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
    35Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
    361] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA. [2] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
    37Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
    38Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
    391] Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [2] Department of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA.
    40Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    41Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    42Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    43Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    44Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    45Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
    46Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
    47Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
    481] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
    49Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    50Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    51Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    52Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    53Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    54Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    55Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    56Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    57Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    58Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    59Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    60Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    61Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    62Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.
    63Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    64Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
    65Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    66Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
    67Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
    68Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    69Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
    70Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA.
    71European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
    72European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
    73European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
    74Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.
    75Computer &Information Sciences &Engineering, University of Florida, Gainesville, Florida 32611, USA.
    76McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
    77Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
    78Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA.
    791] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. [2] Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK.
    80Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    81Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    82Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    83Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    84Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    85Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    86Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    87Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    88Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    89Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.
    90Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.
    91Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    92Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    93Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    94Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    95Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    96Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    97Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    98Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    99Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    100MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK.
    101Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA.
    102HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA.
    103HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA.
    104HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA.
    105Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    106Dana Farber Cancer Institute, Harvard Medical School, Cambridge, Massachusetts 02138, USA.
    107University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA.
    108Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.
    109University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA.
    110Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
    111Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
    112Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
    113Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA.
    114Bioinformatics and Genomics program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    115Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
    1161] Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. [2] Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
    117Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
    118Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
    119Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
    120NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    121NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    122NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    123NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    124NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    125NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
    126Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
    127Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
    128Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.
    129Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.
    130Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
    131Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
    132Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
    133Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
    134Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA.
    135Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
    136McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
    137Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
    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.


    Publikations ID: 25409824
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