Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

被引：735

作者：

Gerstein, Mark B. ^{[1
,2
,3
]}

Lu, Zhi John ^{[1
,2
]}

Van Nostrand, Eric L. ^{[4
]}

Cheng, Chao ^{[1
,2
]}

Arshinoff, Bradley I. ^{[5
,6
]}

Liu, Tao ^{[7
,8
]}

Yip, Kevin Y. ^{[1
,2
]}

Robilotto, Rebecca ^{[1
]}

Rechtsteiner, Andreas

Ikegami, Kohta ^{[9
,10
]}

Alves, Pedro ^{[1
]}

Chateigner, Aurelien ^{[11
,12
]}

Perry, Marc ^{[5
]}

Morris, Mitzi ^{[13
]}

Auerbach, Raymond K. ^{[1
]}

Feng, Xin ^{[5
,23
]}

Leng, Jing ^{[1
]}

Vielle, Anne ^{[14
]}

Niu, Wei ^{[15
,16
]}

Rhrissorrakrai, Kahn ^{[13
]}

Agarwal, Ashish ^{[2
,3
]}

Alexander, Roger P. ^{[1
,2
]}

Barber, Galt

Brdlik, Cathleen M. ^{[4
]}

Brennan, Jennifer ^{[9
,10
]}

Brouillet, Jeremy Jean ^{[4
]}

Carr, Adrian ^{[11
,12
]}

Cheung, Ming-Sin ^{[14
]}

Clawson, Hiram

Contrino, Sergio ^{[11
,12
]}

Dannenberg, Luke O. ^{[17
]}

Dernburg, Abby F. ^{[18
,19
]}

Desai, Arshad ^{[20
]}

Dick, Lindsay ^{[39
]}

Dose, Andrea C. ^{[18
,19
]}

Du, Jiang ^{[3
]}

Egelhofer, Thea

Ercan, Sevinc ^{[9
,10
]}

Euskirchen, Ghia ^{[15
]}

Ewing, Brent ^{[21
]}

Feingold, Elise A. ^{[22
]}

Gassmann, Reto ^{[20
]}

Good, Peter J. ^{[22
]}

Green, Phil ^{[21
]}

Gullier, Francois ^{[11
,12
]}

Gutwein, Michelle ^{[13
]}

Guyer, Mark S. ^{[22
]}

Habegger, Lukas ^{[1
]}

Han, Ting ^{[24
]}

Henikoff, Jorja G. ^{[25
]}

机构：

[1] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

[2] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[3] Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA

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

[5] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

[6] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada

[7] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[8] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[9] Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA

[10] Univ N Carolina, Carolina Ctr Genome Sci, Chapel Hill, NC 27599 USA

[11] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England

[12] Cambridge Syst Biol Ctr, Cambridge CB2 1QR, England

[13] NYU, Dept Biol, Ctr Genom & Syst Biol, New York, NY 10003 USA

[14] Univ Cambridge, Wellcome Trust Canc Res UK Gurdon Inst, Cambridge CB2 1QN, England

[15] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06824 USA

[16] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA

[17] Roche NimbleGen, Madison, WI 53719 USA

[18] Univ Calif Berkeley, Howard Hughes Med Inst, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[19] Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA

[20] Univ Calif San Diego, Ludwig Inst Canc Res, Dept Cellular & Mol Med, San Diego, CA 92093 USA

[21] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA

[22] NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA

[23] SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA

[24] Univ Michigan, Inst Life Sci, Dept Human Genet, Ann Arbor, MI 48109 USA

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

[26] Max Planck Gesell, Friedrich Miescher Lab, D-72076 Tubingen, Germany

[27] Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany

[28] Vanderbilt Univ, Dept Cell & Dev Biol, Nashville, TN 37232 USA

[29] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

[30] Max Planck Inst Dev Biol, D-72076 Tubingen, Germany

[31] Sloan Kettering Inst, New York, NY 10065 USA

[32] Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[33] Weizmann Inst Sci, Dept Comp Sci & Appl Math, IL-76100 Rehovot, Israel

[34] Max Delbruck Ctr Mol Med, Div Syst Biol, D-13125 Berlin, Germany

[35] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11542 USA

[36] Stanford Univ, Med Ctr, Dept Dev Biol, Stanford, CA 94305 USA

[37] European Mol Biol Lab, D-69117 Heidelberg, Germany

[38] NYU, Abu Dhabi, U Arab Emirates

[39] Rockefeller Univ, David Rockefeller Grad Program, New York, NY 10065 USA

来源：

SCIENCE | 2010年 / 330卷 / 6012期

基金：

英国惠康基金;

关键词：

TRANSCRIPTION; REVEALS; DNA; MOTIFS; ROLES; IDENTIFICATION; ORGANIZATION; EXPRESSION; LANDSCAPE; GERMLINE;

D O I：

10.1126/science.1196914

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：

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

引用

页码：1775 / 1787

页数：13

共 76 条

[1] Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays [J].

Agarwal, Ashish ;

Koppstein, David ;

Rozowsky, Joel ;

Sboner, Andrea ;

Habegger, Lukas ;

Hillier, LaDeana W. ;

Sasidharan, Rajkumar ;

Reinke, Valerie ;

Waterston, Robert H. ;

Gerstein, Mark .

BMC GENOMICS, 2010, 11

[2]

Albertson D., 1997, C ELEGANS, P47

[3] A global analysis of C. elegans trans-splicing [J].

Allen, Mary Ann ;

Hillier, LaDeana W. ;

Waterston, Robert H. ;

Blumenthal, Thomas .

GENOME RESEARCH, 2011, 21 (02) :255-264

[4] Network motifs: theory and experimental approaches [J].

Alon, Uri .

NATURE REVIEWS GENETICS, 2007, 8 (06) :450-461

[5]

[Anonymous], 2005, WORMBOOK, DOI DOI 10.1895/WORMBOOK.1.8.1

[6] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[7]

BARNES TM, 1995, GENETICS, V141, P159

[8] The complex language of chromatin regulation during transcription [J].

Berger, Shelley L. .

NATURE, 2007, 447 (7143) :407-412

[9]

Bickel P. J., 2010, ANN APPL STAT, V0, P1

[10] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

← 1 2 3 4 5 6 7 8 →