Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE-Reference-Cited by-同舟云学术

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Published:2010-12-24 Issue:6012 Volume:330 Page:1787-1797
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

,Roy Sushmita¹²,Ernst Jason¹²,Kharchenko Peter V.³,Kheradpour Pouya¹²,Negre Nicolas⁴,Eaton Matthew L.⁵,Landolin Jane M.⁶,Bristow Christopher A.¹²,Ma Lijia⁴,Lin Michael F.¹²,Washietl Stefan¹,Arshinoff Bradley I.⁷⁸,Ay Ferhat¹⁹,Meyer Patrick E.¹¹⁰,Robine Nicolas¹¹,Washington Nicole L.¹²,Di Stefano Luisa¹¹³,Berezikov Eugene¹⁴,Brown Christopher D.⁴,Candeias Rogerio¹,Carlson Joseph W.⁶,Carr Adrian¹⁵,Jungreis Irwin¹²,Marbach Daniel¹²,Sealfon Rachel¹²,Tolstorukov Michael Y.³,Will Sebastian¹,Alekseyenko Artyom A.¹⁶,Artieri Carlo¹⁷,Booth Benjamin W.⁶,Brooks Angela N.¹⁸,Dai Qi¹¹,Davis Carrie A.¹⁹,Duff Michael O.²⁰,Feng Xin¹⁹⁸²¹,Gorchakov Andrey A.¹⁶,Gu Tingting²²,Henikoff Jorja G.¹¹,Kapranov Philipp²³,Li Renhua²⁴,MacAlpine Heather K.⁵,Malone John¹⁷,Minoda Aki⁶,Nordman Jared²⁵,Okamura Katsutomo¹¹,Perry Marc⁸,Powell Sara K.⁵,Riddle Nicole C.²²,Sakai Akiko²⁶,Samsonova Anastasia²⁷,Sandler Jeremy E.⁶,Schwartz Yuri B.³,Sher Noa²⁵,Spokony Rebecca⁴,Sturgill David¹⁷,van Baren Marijke²⁸,Wan Kenneth H.⁶,Yang Li²⁰,Yu Charles⁶,Feingold Elise²⁴,Good Peter²⁴,Guyer Mark²⁴,Lowdon Rebecca²⁴,Ahmad Kami²⁶,Andrews Justen²⁹,Berger Bonnie¹²,Brenner Steven E.¹⁸³⁰,Brent Michael R.²⁸,Cherbas Lucy²⁹³¹,Elgin Sarah C. R.²²,Gingeras Thomas R.¹⁹²³,Grossman Robert⁴,Hoskins Roger A.⁶,Kaufman Thomas C.²⁹,Kent William³²,Kuroda Mitzi I.¹⁶,Orr-Weaver Terry²⁵,Perrimon Norbert²⁷,Pirrotta Vincenzo³³,Posakony James W.³⁴,Ren Bing³⁴,Russell Steven¹⁵,Cherbas Peter²⁹³¹,Graveley Brenton R.²⁰,Lewis Suzanna¹²,Micklem Gos¹⁵,Oliver Brian¹⁷,Park Peter J.³,Celniker Susan E.⁶,Henikoff Steven³⁵,Karpen Gary H.⁶¹⁸,Lai Eric C.¹¹,MacAlpine David M.⁵,Stein Lincoln D.⁸,White Kevin P.⁴,Kellis Manolis¹²,Acevedo David,Auburn Richard,Barber Galt,Bellen Hugo J.,Bishop Eric P.,Bryson Terri D.,Chateigner Aurelien,Chen Jia,Clawson Hiram,Comstock Charles L. G.,Contrino Sergio,DeNapoli Leyna C.,Ding Queying,Dobin Alex,Domanus Marc H.,Drenkow Jorg,Dudoit Sandrine,Dumais Jackie,Eng Thomas,Fagegaltier Delphine,Gadel Sarah E.,Ghosh Srinka,Guillier Francois,Hanley David,Hannon Gregory J.,Hansen Kasper D.,Heinz Elizabeth,Hinrichs Angie S.,Hirst Martin,Jha Sonali,Jiang Lichun,Jung Youngsook L.,Kashevsky Helena,Kennedy Cameron D.,Kephart Ellen T.,Langton Laura,Lee Ok-Kyung,Li Sharon,Li Zirong,Lin Wei,Linder-Basso Daniela,Lloyd Paul,Lyne Rachel,Marchetti Sarah E.,Marra Marco,Mattiuzzo Nicolas R.,McKay Sheldon,Meyer Folker,Miller David,Miller Steven W.,Moore Richard A.,Morrison Carolyn A.,Prinz Joseph A.,Rooks Michelle,Moore Richard,Rutherford Kim M.,Ruzanov Peter,Scheftner Douglas A.,Senderowicz Lionel,Shah Parantu K.,Shanower Gregory,Smith Richard,Stinson E. O.,Suchy Sarah,Tenney Aaron E.,Tian Feng,Venken Koen J. T.,Wang Huaien,White Robert,Wilkening Jared,Willingham Aarron T.,Zaleski Chris,Zha Zheng,Zhang Dayu,Zhao Yongjun,Zieba Jennifer

Affiliation:

1. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

2. Broad Institute of MIT and Harvard, Cambridge, MA 02140, USA.

3. Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA.

4. Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, IL 60637, USA.

5. Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

6. Department of Genome Dynamics, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Berkeley, CA 94720 USA.

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

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

9. Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA.

10. Machine Learning Group, Université Libre de Bruxelles, CP212, Brussels 1050, Belgium.

11. Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, NY 10065, USA.

12. Genome Sciences Division, LBNL, 1 Cyclotron Road, Berkeley, CA 94720, USA.

13. Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.

14. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, Netherlands.

15. Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.

16. Department of Medicine and Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

17. Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

18. Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

19. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

20. Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, 263 Farmington, CT 06030–6403, USA.

21. Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.

22. Department of Biology CB-1137, Washington University, Saint Louis, MO 63130, USA.

23. Affymetrix, Santa Clara, CA 95051, USA.

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

25. Whitehead Institute, Cambridge, MA 02142, USA.

26. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

27. Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

28. Center for Genome Sciences, Washington University, 4444 Forest Park Boulevard, Saint Louis, MO 63108, USA.

29. Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA.

30. Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

31. Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, IN 47405–7005, USA.

32. Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute (HHMI), University of California Santa Cruz, Santa Cruz, CA 95064, USA.

33. Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.

34. Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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

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

Reference70 articles.

1. www.genome.gov/10005107.

2. Unlocking the secrets of the genome

3. Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin

4. Compared to FlyBase release 5.12 (October 2008) available at http://fb2008_09.flybase.org/

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