Integrative analysis of the Caenorhabditis elegans genome by the modENCODE 
project

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

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Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

MPS-Authors

Van Nostrand, Eric L.
Max Planck Society;

Cheng, Chao
Max Planck Society;

Arshinoff, Bradley I.
Max Planck Society;

/persons/resource/persons219396

Liu, Tao
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

Yip, Kevin Y.
Max Planck Society;

Robilotto, Rebecca
Max Planck Society;

Rechtsteiner, Andreas
Max Planck Society;

Ikegami, Kohta
Max Planck Society;

Chateigner, Aurelien
Max Planck Society;

Perry, Marc
Max Planck Society;

Morris, Mitzi
Max Planck Society;

Feng, Xin
Max Planck Society;

Leng, Jing
Max Planck Society;

Vielle, Anne
Max Planck Society;

Rhrissorrakrai, Kahn
Max Planck Society;

Alexander, Roger P.
Max Planck Society;

Barber, Galt
Max Planck Society;

Brennan, Jennifer
Max Planck Society;

Brouillet, Jeremy Jean
Max Planck Society;

Carr, Adrian
Max Planck Society;

Cheung, Ming-Sin
Max Planck Society;

Clawson, Hiram
Max Planck Society;

Contrino, Sergio
Max Planck Society;

Dannenberg, Luke O.
Max Planck Society;

Dernburg, Abby F.
Max Planck Society;

/persons/resource/persons219103

Desai, Arshad
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

Dick, Lindsay
Max Planck Society;

Dosé, Andréa
Max Planck Society;

Du, Jiang
Max Planck Society;

Egelhofer, Thea
Max Planck Society;

Ercan, Sevinc
Max Planck Society;

Euskirchen, Ghia
Max Planck Society;

Ewing, Brent
Max Planck Society;

Feingold, Elise A.
Max Planck Society;

Gassmann, Reto
Max Planck Society;

Good, Peter J.
Max Planck Society;

Green, Phil
Max Planck Society;

Gullier, Francois
Max Planck Society;

Gutwein, Michelle
Max Planck Society;

Guyer, Mark S.
Max Planck Society;

Habegger, Lukas
Max Planck Society;

Han, Ting
Max Planck Society;

Henikoff, Jorja G.
Max Planck Society;

Henz, Stefan R.
Max Planck Society;

Hinrichs, Angie
Max Planck Society;

Holster, Heather
Max Planck Society;

/persons/resource/persons219253

Hyman, Anthony A.
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

Iniguez, A. Leo
Max Planck Society;

Jensen, Morten
Max Planck Society;

Kato, Masaomi
Max Planck Society;

Kent, W. James
Max Planck Society;

Kephart, Ellen
Max Planck Society;

Khivansara, Vishal
Max Planck Society;

Khurana, Ekta
Max Planck Society;

Kim, John K.
Max Planck Society;

Kolasinska-Zwierz, Paulina
Max Planck Society;

Latorre, Isabel
Max Planck Society;

Leahey, Amber
Max Planck Society;

Lloyd, Paul
Max Planck Society;

Lochovsky, Lucas
Max Planck Society;

Lowdon, Rebecca F.
Max Planck Society;

Lubling, Yaniv
Max Planck Society;

Lyne, Rachel
Max Planck Society;

MacCoss, Michael
Max Planck Society;

Mackowiak, Sebastian D.
Max Planck Society;

Mangone, Marco
Max Planck Society;

McKay, Sheldon
Max Planck Society;

Mecenas, Desirea
Max Planck Society;

Merrihew, Gennifer
Max Planck Society;

Miller, David M.
Max Planck Society;

Muroyama, Andrew
Max Planck Society;

Murray, John I.
Max Planck Society;

Ooi, Siew-Loon
Max Planck Society;

Pham, Hoang
Max Planck Society;

Phippen, Taryn
Max Planck Society;

Preston, Elicia A.
Max Planck Society;

Rajewski, Nikolaus
Max Planck Society;

Rätsch, Gunnar
Max Planck Society;

Rosenbaum, Heidi
Max Planck Society;

Rozowksy, Joel
Max Planck Society;

Rutherford, Kim
Max Planck Society;

Ruzanov, Peter
Max Planck Society;

/persons/resource/persons219618

Sarov, Mihail
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

Sasidharan, Rajkumar
Max Planck Society;

Sboner, Andrea
Max Planck Society;

Scheid, Paul
Max Planck Society;

Segal, Eran
Max Planck Society;

Shin, Hyunjin
Max Planck Society;

Shou, Chong
Max Planck Society;

Slack, Frank J.
Max Planck Society;

Smith, Richard
Max Planck Society;

Spencer, William C.
Max Planck Society;

Stinson, E. O.
Max Planck Society;

Taing, Scott
Max Planck Society;

Takasaki, Teruaki
Max Planck Society;

Vafeados, Dionne
Max Planck Society;

Voronina, Ksenia
Max Planck Society;

Wang, Guilin
Max Planck Society;

Washington, Nicole L.
Max Planck Society;

Whittle, Christina M.
Max Planck Society;

Wu, Beijing
Max Planck Society;

Yang, Koon-Kiu
Max Planck Society;

Zeller, Georg
Max Planck Society;

Zha, Zheng
Max Planck Society;

Zhong, Mei
Max Planck Society;

Zhou, Xingliang
Max Planck Society;

Strome, Susan
Max Planck Society;

Gunsalus, Kristin C.
Max Planck Society;

Micklem, Gos
Max Planck Society;

Liu, X. Shirley
Max Planck Society;

Henikoff, Steven
Max Planck Society;

Piano, Fabio
Max Planck Society;

Stein, Lincoln
Max Planck Society;

Lieb, Jason D.
Max Planck Society;

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Citation

Gerstein, M., Lu, Z. J., Van Nostrand, E. L., Cheng, C., Arshinoff, B. I., Liu, T., et al. (2010). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.), 330(6012), 1775-1787.

Cite as: https://hdl.handle.net/21.11116/0000-0001-0B92-E

Abstract

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.