A comparative encyclopedia of DNA elements in the mouse genome

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 () and Bing Ren ()
Additional contact information
Feng Yue: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Yong Cheng: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Alessandra Breschi: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Jeff Vierstra: University of Washington
Weisheng Wu: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Tyrone Ryba: 319 Stadium Drive, Florida State University
Richard Sandstrom: University of Washington
Zhihai Ma: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Carrie Davis: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Benjamin D. Pope: 319 Stadium Drive, Florida State University
Yin Shen: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Dmitri D. Pervouchine: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Sarah Djebali: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Robert E. Thurman: University of Washington
Rajinder Kaul: University of Washington
Eric Rynes: University of Washington
Anthony Kirilusha: California Institute of Technology
Georgi K. Marinov: California Institute of Technology
Brian A. Williams: California Institute of Technology
Diane Trout: California Institute of Technology
Henry Amrhein: California Institute of Technology
Katherine Fisher-Aylor: California Institute of Technology
Igor Antoshechkin: California Institute of Technology
Gilberto DeSalvo: California Institute of Technology
Lei-Hoon See: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Meagan Fastuca: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Jorg Drenkow: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Chris Zaleski: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Alex Dobin: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Pablo Prieto: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Julien Lagarde: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Giovanni Bussotti: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Andrea Tanzer: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Olgert Denas: Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
Kanwei Li: Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
M. A. Bender: University of Washington
Miaohua Zhang: Fred Hutchinson Cancer Research Center
Rachel Byron: Fred Hutchinson Cancer Research Center
Mark T. Groudine: Fred Hutchinson Cancer Research Center
David McCleary: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Long Pham: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Zhen Ye: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Samantha Kuan: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Lee Edsall: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
Yi-Chieh Wu: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)
Matthew D. Rasmussen: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)
Mukul S. Bansal: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)
Manolis Kellis: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT)
Cheryl A. Keller: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Christapher S. Morrissey: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Tejaswini Mishra: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Deepti Jain: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Nergiz Dogan: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Robert S. Harris: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Philip Cayting: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Trupti Kawli: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Alan P. Boyle: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Ghia Euskirchen: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Anshul Kundaje: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Shin Lin: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Yiing Lin: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Camden Jansen: University of California, Irvine, Irvine, California 92697, USA.
Venkat S. Malladi: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Melissa S. Cline: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC)
Drew T. Erickson: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Vanessa M. Kirkup: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC)
Katrina Learned: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC)
Cricket A. Sloan: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Kate R. Rosenbloom: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC)
Beatriz Lacerda de Sousa: and Center for Reproductive Sciences, University of California San Francisco
Kathryn Beal: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Miguel Pignatelli: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Paul Flicek: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Jin Lian: Yale University, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.
Tamer Kahveci: Computer & Information Sciences & Engineering, University of Florida
Dongwon Lee: Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
W. James Kent: Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC)
Miguel Ramalho Santos: and Center for Reproductive Sciences, University of California San Francisco
Javier Herrero: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Cedric Notredame: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Audra Johnson: University of Washington
Shinny Vong: University of Washington
Kristen Lee: University of Washington
Daniel Bates: University of Washington
Fidencio Neri: University of Washington
Morgan Diegel: University of Washington
Theresa Canfield: University of Washington
Peter J. Sabo: University of Washington
Matthew S. Wilken: University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.
Thomas A. Reh: University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.
Erika Giste: University of Washington
Anthony Shafer: University of Washington
Tanya Kutyavin: University of Washington
Eric Haugen: University of Washington
Douglas Dunn: University of Washington
Alex P. Reynolds: University of Washington
Shane Neph: University of Washington
Richard Humbert: University of Washington
R. Scott Hansen: University of Washington
Marella De Bruijn: MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK.
Licia Selleri: Weill Cornell Medical College
Alexander Rudensky: HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter
Steven Josefowicz: HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter
Robert Samstein: HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter
Evan E. Eichler: University of Washington
Stuart H. Orkin: Dana Farber Cancer Institute, Harvard Medical School
Dana Levasseur: University of Iowa Carver College of Medicine
Thalia Papayannopoulou: University of Washington
Kai-Hsin Chang: University of Iowa Carver College of Medicine
Arthur Skoultchi: Albert Einstein College of Medicine
Srikanta Gosh: Albert Einstein College of Medicine
Christine Disteche: University of Washington
Piper Treuting: University of Washington
Yanli Wang: Bioinformatics and Genomics program, The Pennsylvania State University, University Park
Mitchell J. Weiss: St Jude Children’s Research Hospital, Memphis
Gerd A. Blobel: The Children’s Hospital of Philadelphia
Xiaoyi Cao: University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
Sheng Zhong: University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
Ting Wang: Center for Genome Sciences and Systems Biology, Washington University School of Medicine
Peter J. Good: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Rebecca F. Lowdon: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Leslie B. Adams: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Xiao-Qiao Zhou: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Michael J. Pazin: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Elise A. Feingold: NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA.
Barbara Wold: California Institute of Technology
James Taylor: Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
Ali Mortazavi: University of California, Irvine, Irvine, California 92697, USA.
Sherman M. Weissman: Yale University, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.
John A. Stamatoyannopoulos: University of Washington
Michael P. Snyder: Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
Roderic Guigo: Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
Thomas R. Gingeras: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
David M. Gilbert: 319 Stadium Drive, Florida State University
Ross C. Hardison: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park
Michael A. Beer: Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
Bing Ren: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

Nature, 2014, vol. 515, issue 7527, 355-364

Abstract: 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.

Date: 2014
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DOI: 10.1038/nature13992

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