Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project-Reference-Cited by-同舟云学术

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Published:2010-12-24 Issue:6012 Volume:330 Page:1775-1787
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Gerstein Mark B.¹²³,Lu Zhi John¹²,Van Nostrand Eric L.⁴,Cheng Chao¹²,Arshinoff Bradley I.⁵⁶,Liu Tao⁷⁸,Yip Kevin Y.¹²,Robilotto Rebecca¹,Rechtsteiner Andreas⁹,Ikegami Kohta¹⁰,Alves Pedro¹,Chateigner Aurelien¹¹,Perry Marc⁵,Morris Mitzi¹²,Auerbach Raymond K.¹,Feng Xin⁵¹³,Leng Jing¹,Vielle Anne¹⁴,Niu Wei¹⁵¹⁶,Rhrissorrakrai Kahn¹²,Agarwal Ashish²³,Alexander Roger P.¹²,Barber Galt¹⁷,Brdlik Cathleen M.⁴,Brennan Jennifer¹⁰,Brouillet Jeremy Jean⁴,Carr Adrian¹¹,Cheung Ming-Sin¹⁴,Clawson Hiram¹⁷,Contrino Sergio¹¹,Dannenberg Luke O.¹⁸,Dernburg Abby F.¹⁹,Desai Arshad²⁰,Dick Lindsay²¹,Dosé Andréa C.¹⁹,Du Jiang³,Egelhofer Thea⁹,Ercan Sevinc¹⁰,Euskirchen Ghia¹⁵,Ewing Brent²²,Feingold Elise A.²³,Gassmann Reto²⁰,Good Peter J.²³,Green Phil²²,Gullier Francois¹¹,Gutwein Michelle¹²,Guyer Mark S.²³,Habegger Lukas¹,Han Ting²⁴,Henikoff Jorja G.²⁵,Henz Stefan R.²⁶,Hinrichs Angie¹⁷,Holster Heather¹⁸,Hyman Tony²⁷,Iniguez A. Leo¹⁸,Janette Judith¹⁶,Jensen Morten¹⁰,Kato Masaomi²⁸,Kent W. James¹⁷,Kephart Ellen⁵,Khivansara Vishal²⁴,Khurana Ekta¹²,Kim John K.²⁴,Kolasinska-Zwierz Paulina¹⁴,Lai Eric C.²⁹,Latorre Isabel¹⁴,Leahey Amber²²,Lewis Suzanna³⁰,Lloyd Paul⁵,Lochovsky Lucas¹,Lowdon Rebecca F.²³,Lubling Yaniv³¹,Lyne Rachel¹¹,MacCoss Michael²²,Mackowiak Sebastian D.³²,Mangone Marco¹²,McKay Sheldon³³,Mecenas Desirea¹²,Merrihew Gennifer²²,Miller David M.³⁴,Muroyama Andrew²⁰,Murray John I.²²,Ooi Siew-Loon²⁵,Pham Hoang¹⁹,Phippen Taryn⁹,Preston Elicia A.²²,Rajewsky Nikolaus³²,Rätsch Gunnar³⁵,Rosenbaum Heidi¹⁸,Rozowsky Joel¹²,Rutherford Kim¹¹,Ruzanov Peter⁵,Sarov Mihail²⁷,Sasidharan Rajkumar²,Sboner Andrea¹²,Scheid Paul¹²,Segal Eran³¹,Shin Hyunjin⁷⁸,Shou Chong¹,Slack Frank J.²⁸,Slightam Cindie³⁶,Smith Richard¹¹,Spencer William C.³⁴,Stinson E. O.³⁰,Taing Scott⁷,Takasaki Teruaki⁹,Vafeados Dionne²²,Voronina Ksenia²⁰,Wang Guilin¹⁶,Washington Nicole L.³⁰,Whittle Christina M.¹⁰,Wu Beijing³⁶,Yan Koon-Kiu¹²,Zeller Georg³⁵³⁷,Zha Zheng⁵,Zhong Mei¹⁵,Zhou Xingliang¹⁰,Ahringer Julie¹⁴,Strome Susan⁹,Gunsalus Kristin C.¹²³⁸,Micklem Gos¹¹,Liu X. Shirley⁷⁸,Reinke Valerie¹⁶,Kim Stuart K.⁴³⁶,Hillier LaDeana W.²²,Henikoff Steven²⁵,Piano Fabio¹²³⁸,Snyder Michael⁴¹⁵,Stein Lincoln⁵⁶³³,Lieb Jason D.¹⁰,Waterston Robert H.²²,

Affiliation:

1. Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

2. Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

3. Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA.

4. Department of Genetics, Stanford University Medical Center, Stanford, CA 94305, USA.

5. Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada.

6. Department of Molecular Genetics, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1, Canada.

7. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.

8. Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.

9. Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

10. Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

11. Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK, and Cambridge Systems Biology Centre, Tennis Court Road, Cambridge CB2 1QR, UK.

12. Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA.

13. Department of Biomedical Engineering, State University of New York at Stonybrook, Stonybrook, NY 11794, USA.

14. Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.

15. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06824, USA.

16. Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA.

17. Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064 USA.

18. Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA.

19. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA, and Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

20. Ludwig Institute Cancer Research/Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0653, USA.

21. David Rockefeller Graduate Program, Rockefeller University, 1230 York Avenue New York, NY 10065, USA.

22. Department of Genome Sciences, University of Washington School of Medicine, William H. Foege Building S350D, 1705 NE Pacific Street, Post Office Box 355065, Seattle, WA 98195–5065, USA.

23. Division of Extramural Research, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, Bethesda, MD 20892–9305, USA.

24. Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA.

25. Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

26. Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076 Tübingen, Germany.

27. Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.

28. Department of Molecular, Cellular and Developmental Biology, Post Office Box 208103, Yale University, New Haven, CT 06520, USA.

29. Sloan-Kettering Institute, 1275 York Avenue, Post Office Box 252, New York, NY 10065, USA.

30. Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720 USA.

31. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel.

32. Max-Delbrück-Centrum für Molekulare Medizin, Division of Systems Biology, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.

33. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11542 USA.

34. Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37232–8240, USA.

35. Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.

36. Department of Developmental Biology, Stanford University Medical Center, 279 Campus Drive, Stanford, CA 94305–5329, USA.

37. European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

38. New York University, Abu Dhabi, United Arab Emirates.

Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by

Blaxter

). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference76 articles.

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

2. Unlocking the secrets of the genome

3. The embryonic cell lineage of the nematode Caenorhabditis elegans

4. The structure of the nervous system of the nematodeCaenorhabditis elegans

5. Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology

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