A comparative encyclopedia of DNA elements in the mouse genome

被引：1243

作者：

Yue, Feng ^{[1
,2
,3
]}

Cheng, Yong ^{[4
]}

Breschi, Alessandra ^{[5
,6
]}

Vierstra, Jeff ^{[7
]}

Wu, Weisheng ^{[8
]}

Ryba, Tyrone ^{[9
]}

Sandstrom, Richard ^{[7
]}

Ma, Zhihai ^{[4
]}

Davis, Carrie ^{[10
]}

Pope, Benjamin D. ^{[9
]}

Shen, Yin ^{[1
,2
]}

Pervouchine, Dmitri D. ^{[5
,6
]}

Djebali, Sarah ^{[5
,6
]}

Thurman, Robert E. ^{[7
]}

Kaul, Rajinder ^{[7
]}

Rynes, Eric ^{[7
]}

Kirilusha, Anthony ^{[11
]}

Marinov, Georgi K. ^{[11
]}

Williams, Brian A. ^{[11
]}

Trout, Diane ^{[11
]}

Amrhein, Henry ^{[11
]}

Fisher-Aylor, Katherine ^{[11
]}

Antoshechkin, Igor ^{[11
]}

DeSalvo, Gilberto ^{[11
]}

See, Lei-Hoon ^{[10
]}

Fastuca, Meagan ^{[10
]}

Drenkow, Jorg ^{[10
]}

Zaleski, Chris ^{[10
]}

Dobin, Alex ^{[10
]}

Prieto, Pablo ^{[5
,6
]}

Lagarde, Julien ^{[5
,6
]}

Bussotti, Giovanni ^{[5
,6
]}

Tanzer, Andrea ^{[5
,6
,12
]}

Denas, Olgert ^{[13
,14
]}

Li, Kanwei ^{[13
,14
]}

Bender, M. A. ^{[15
,16
]}

Zhang, Miaohua ^{[17
]}

Byron, Rachel ^{[17
]}

Groudine, Mark T. ^{[17
,18
]}

McCleary, David ^{[1
,2
]}

Pham, Long ^{[1
,2
]}

Ye, Zhen ^{[1
,2
]}

Kuan, Samantha ^{[1
,2
]}

Edsall, Lee ^{[1
,2
]}

Wu, Yi-Chieh ^{[19
]}

Rasmussen, Matthew D. ^{[19
]}

Bansal, Mukul S. ^{[19
]}

Kellis, Manolis ^{[19
,20
]}

Keller, Cheryl A. ^{[8
]}

Morrissey, Christapher S. ^{[8
]}

机构：

[1] Ludwig Inst Canc Res, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Sch Med, La Jolla, CA 92093 USA

[3] Penn State Univ, Coll Med, Dept Biochem & Mol Biol, Hershey, PA 17033 USA

[4] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[5] Ctr Genom Regulat, Barcelona 08003, Catalonia, Spain

[6] UPF, Barcelona 08003, Catalonia, Spain

[7] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[8] Penn State Univ, Huck Inst,Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

[9] Florida State Univ, Dept Biol Sci, Tallahassee, FL 32306 USA

[10] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[11] CALTECH, Div Biol, Pasadena, CA 91125 USA

[12] Univ Vienna, Fac Chem, Dept Theoret Chem, A-1090 Vienna, Austria

[13] Emory Univ, O Wayne Rollins Res Ctr, Dept Biol, Atlanta, GA 30322 USA

[14] Emory Univ, O Wayne Rollins Res Ctr, Dept Math & Comp Sci, Atlanta, GA 30322 USA

[15] Univ Washington, Dept Pediat, Seattle, WA 98195 USA

[16] Fred Hutchinson Canc Res Ctr, Div Clin Res, Seattle, WA 98109 USA

[17] Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98109 USA

[18] Univ Washington, Dept Radiat Oncol, Seattle, WA 98195 USA

[19] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

[20] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[21] Univ Calif Irvine, Dept Dev & Cell Biol, Irvine, CA 92697 USA

[22] Univ Calif Santa Cruz, Sch Engn, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[23] Univ Calif San Francisco, Dept Obstet Gynecol, San Francisco, CA 94143 USA

[24] Univ Calif San Francisco, Dept Pathol, San Francisco, CA 94143 USA

[25] Univ Calif San Francisco, Ctr Reprod Sci, San Francisco, CA 94143 USA

[26] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[27] Yale Univ, Dept Genet, New Haven, CT 06520 USA

[28] Univ Florida, Gainesville, FL 32611 USA

[29] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

[30] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD 21205 USA

[31] UCL, UCL Canc Inst, Bill Lyons Informat Ctr, London WC1E 6DD, England

[32] Univ Washington, Dept Biol Struct, Seattle, WA 98195 USA

[33] Univ Oxford, MRC Mol Haemotol Unit, Oxford OX3 9DS, England

[34] Weill Cornell Med Coll, Dept Cell & Dev Biol, New York, NY 10065 USA

[35] Mem Sloan Kettering Canc Ctr, Program Immunol, HHMI & Ludwig Ctr, New York, NY 10065 USA

[36] Harvard Univ, Sch Med, Dana Farber Canc Inst, Cambridge, MA 02138 USA

[37] Univ Iowa, Carver Coll Med, Dept Internal Med, Iowa City, IA 52242 USA

[38] Univ Washington, Dept Med, Div Hematol, Seattle, WA 98195 USA

[39] Albert Einstein Coll Med, Dept Cell Biol, Bronx, NY 10461 USA

[40] Univ Washington, Dept Pathol, Seattle, WA 98195 USA

[41] Univ Washington, Dept Comparat Med, Seattle, WA 98195 USA

[42] Penn State Univ, Bioinformat & Genom Program, University Pk, PA 16802 USA

[43] St Jude Childrens Res Hosp, Dept Hematol, Memphis, TN 38105 USA

[44] Childrens Hosp Philadelphia, Div Hematol, Philadelphia, PA 19104 USA

[45] Univ Penn, Perelman Sch Med, Philadelphia, PA 19104 USA

[46] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[47] Washington Univ, Sch Med, Ctr Genome Sci & Syst Biol, Dept Genet, St Louis, MO 63108 USA

[48] NHGRI, NIH, Bethesda, MD 20892 USA

来源：

NATURE | 2014年 / 515卷 / 7527期

基金：

英国惠康基金; 美国国家卫生研究院; 美国国家科学基金会; 欧洲研究理事会;

关键词：

TRANSCRIPTION FACTOR-BINDING; EMBRYONIC STEM-CELLS; PERVASIVE TRANSCRIPTION; CHROMATIN INTERACTIONS; EVOLUTIONARY DYNAMICS; TRANSPOSABLE ELEMENTS; ENCODE DATA; LANDSCAPE; GENE; EXPRESSION;

D O I：

10.1038/nature13992

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：355 / +

页数：15

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