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Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F1, Cheng Y2, Breschi A3, Vierstra J4, Wu W5, Ryba T6, Sandstrom R4, Ma Z2, Davis C7, Pope BD6, Shen Y8, Pervouchine DD3, Djebali S3, Thurman RE4, Kaul R4, Rynes E4, Kirilusha A9, Marinov GK9, Williams BA9, Trout D9, Amrhein H9, Fisher-Aylor K9, Antoshechkin I9, DeSalvo G9, See LH7, Fastuca M7, Drenkow J7, Zaleski C7, Dobin A7, Prieto P3, Lagarde J3, Bussotti G3, Tanzer A10, Denas O11, Li K11, Bender MA12, Zhang M13, Byron R13, Groudine MT14, McCleary D8, Pham L8, Ye Z8, Kuan S8, Edsall L8, Wu YC15, Rasmussen MD15, Bansal MS15, Kellis M16, Keller CA5, Morrissey CS5, Mishra T5, Jain D5, Dogan N5, Harris RS5, Cayting P2, Kawli T2, Boyle AP2, Euskirchen G2, Kundaje A2, Lin S2, Lin Y2, Jansen C17, Malladi VS2, Cline MS18, Erickson DT2, Kirkup VM18, Learned K18, Sloan CA2, Rosenbloom KR18, Lacerda de Sousa B19, Beal K20, Pignatelli M20, Flicek P20, Lian J21, Kahveci T22, Lee D23, Kent WJ18, Ramalho Santos M19, Herrero J24, Notredame C3, Johnson A4, Vong S4, Lee K4, Bates D4, Neri F4, Diegel M4, Canfield T4, Sabo PJ4, Wilken MS25, Reh TA25, Giste E4, Shafer A4, Kutyavin T4, Haugen E4, Dunn D4, Reynolds AP4, Neph S4, Humbert R4, Hansen RS4, De Bruijn M26, Selleri L27, Rudensky A28, Josefowicz S28, Samstein R28, Eichler EE4, Orkin SH29, Levasseur D30, Papayannopoulou T31, Chang KH30, Skoultchi A32, Gosh S32, Disteche C33, Treuting P34, Wang Y35, Weiss MJ36, Blobel GA37, Cao X38, Zhong S38, Wang T39, Good PJ40, Lowdon RF40, Adams LB40, Zhou XQ40, Pazin MJ40, Feingold EA40, Wold B9, Taylor J11, Mortazavi A17, Weissman SM21, Stamatoyannopoulos JA4, Snyder MP2, Guigo R3, Gingeras TR7, Gilbert DM6, Hardison RC5, Beer MA23, Ren B8; Mouse ENCODE Consortium.

Author information

1
1] 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.
2
Department of Genetics, Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA.
3
Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88, 08003 Barcelona, Catalonia, Spain.
4
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
5
Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
6
Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA.
7
Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
8
Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
9
Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
10
1] 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.
11
Departments of Biology and Mathematics and Computer Science, Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA.
12
1] Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA. [2] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
13
Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
14
1] Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [2] Department of Radiation Oncology, University of Washington, Seattle, Washington 98195, USA.
15
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
16
1] 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.
17
Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.
18
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California 95064, USA.
19
Departments of Obstetrics/Gynecology and Pathology, and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA.
20
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
21
Yale University, Department of Genetics, PO Box 208005, 333 Cedar Street, New Haven, Connecticut 06520-8005, USA.
22
Computer &Information Sciences &Engineering, University of Florida, Gainesville, Florida 32611, USA.
23
McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
24
1] 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.
25
Department of Biological Structure, University of Washington, HSB I-516, 1959 NE Pacific Street, Seattle, Washington 98195, USA.
26
MRC Molecular Haemotology Unit, University of Oxford, Oxford OX3 9DS, UK.
27
Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10065, USA.
28
HHMI and Ludwig Center at Memorial Sloan Kettering Cancer Center, Immunology Program, Memorial Sloan Kettering Cancer Canter, New York, New York 10065, USA.
29
Dana Farber Cancer Institute, Harvard Medical School, Cambridge, Massachusetts 02138, USA.
30
University of Iowa Carver College of Medicine, Department of Internal Medicine, Iowa City, Iowa 52242, USA.
31
Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.
32
Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
33
Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
34
Department of Comparative Medicine, University of Washington, Seattle, Washington 98195, USA.
35
Bioinformatics and Genomics program, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
36
Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
37
1] 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.
38
Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
39
Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
40
NHGRI, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, 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.

PMID:
25409824
PMCID:
PMC4266106
DOI:
10.1038/nature13992
[Indexed for MEDLINE]
Free PMC Article

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