Identification of Functional Elements and Regulatory Circuits by
Drosophila
modENCODE
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/
Cited by
1048 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献
|
|