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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

2010; American Association for the Advancement of Science; Volume: 330; Issue: 6012 Linguagem: Inglês

10.1126/science.1196914

1095-9203

Mark Gerstein, Zhi John Lu, Eric L. Van Nostrand, Chao Cheng, Bradley I. Arshinoff, Tao Liu, Kevin Y. Yip, R. Robilotto, Andreas Rechtsteiner, Kohta Ikegami, Pedro Alves, Aurélien Chateigner, Marc D. Perry, Mitzi Morris, Raymond K. Auerbach, Xin Feng, Jing Leng, Anne Vielle, Wei Niu, Kahn Rhrissorrakrai, Ashish Agarwal, Roger P. Alexander, Galt P Barber, Cathleen Brdlik, Jennifer Brennan, Jeremy Brouillet, Adrian R. Carr, Ming-Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O. Dannenberg, Abby F. Dernburg, Arshad Desai, Lindsay L. Dick, Andrea C. Dosé, Jiang Du, Thea A. Egelhofer, Sevinç Ercan, Ghia Euskirchen, Brent Ewing, Elise A. Feingold, Reto Gassmann, Peter J. Good, Phil Green, F. Gullier, Michelle Gutwein, Mark S. Guyer, Lukas Habegger, Ting Han, Jorja G. Henikoff, Stefan R. Henz, Angie S. Hinrichs, H. Holster, Anthony A. Hyman, Al Iniguez, J. Janette, Morten B. Jensen, Masaomi Kato, W. James Kent, Ellen T. Kephart, Vishal Khivansara, Ekta Khurana, John K. Kim, Paulina Kolasinska-Zwierz, Eric C. Lai, Isabel Latorre, A. Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F. Lowdon, Yaniv Lubling, Rachel Lyne, Michael J. MacCoss, Sebastian D. Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer E. Merrihew, David M. Miller, Andrew Muroyama, John I. Murray, Siew-Loon Ooi, Vu Pham, T. Phippen, Elicia Preston, Nikolaus Rajewsky, Gunnar Rätsch, Heidi Rosenbaum, Joel Rozowsky, Kim Rutherford, Peter Ruzanov, Mihail Sarov, Rajkumar Sasidharan, Andrea Sboner, Paul Scheid, Eran Segal, Hyunjin Shin, Chong Shou, Frank J. Slack, C. Slightam, Richard Smith, William C. Spencer, Eo Stinson, S. Taing, Teruaki Takasaki, Dionne Vafeados, K. Voronina, Guilin Wang, Nicole L. Washington, Christina M. Whittle, Beijing Wu, Koon-Kiu Yan, Georg Zeller, Zheng Zha, Mei Zhong, Xingliang Zhou, Julie Ahringer, Susan Strome, Kristin C. Gunsalus, Gos Micklem, Xuyuan Liu, V Reinke, Stuart K. Kim, LaDeana Hillier, Steven Henikoff, Fabio Piano, M Snyder, Lincoln Stein, Jason D. Lieb, R Waterston,

Bioinformatics and Genomic Networks

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.