Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Mark B. Gerstein, Zhi John Lu, Eric L. Van Nostrand, Chao Cheng, Bradley I. Arshinoff, Tao Liu, Kevin Y. Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami, Pedro Alves, Aurelien Chateigner, Marc Perry, Mitzi Morris, Raymond K. Auerbach, Xin Feng, Jing Leng, Anne Vielle, Wei Niu, Kahn Rhrissorrakrai & 111 others Ashish Agarwal, Roger P. Alexander, Galt Barber, Cathleen M. Brdlik, Jennifer Brennan, Jeremy Jean Brouillet, Adrian Carr, Ming Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O. Dannenberg, Abby F. Dernburg, Arshad Desai, Lindsay Dick, Andréa C. Dosé, Jiang Du, Thea Egelhofer, Sevinc Ercan, Ghia Euskirchen, Brent Ewing, Elise A. Feingold, Reto Gassmann, Peter J. Good, Phil Green, Francois Gullier, Michelle Gutwein, Mark S. Guyer, Lukas Habegger, Ting Han, Jorja G. Henikoff, Stefan R. Henz, Angie Hinrichs, Heather Holster, Tony Hyman, A. Leo Iniguez, Judith Janette, Morten Jensen, Masaomi Kato, W. James Kent, Ellen Kephart, Vishal Khivansara, Ekta Khurana, John K. Kim, Paulina Kolasinska-Zwierz, Eric C. Lai, Isabel Latorre, Amber Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F. Lowdon, Yaniv Lubling, Rachel Lyne, Michael MacCoss, Sebastian D. Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer Merrihew, David M. Miller, Andrew Muroyama, John I. Murray, Siew Loon Ooi, Hoang Pham, Taryn Phippen, Elicia A. 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, Cindie Slightam, Richard Smith, William C. Spencer, E. O. Stinson, Scott Taing, Teruaki Takasaki, Dionne Vafeados, Ksenia 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, X. Shirley Liu, Valerie Reinke, Stuart K. Kim, Ladeana W. Hillier, Steven Henikoff, Fabio Piano, Michael Snyder, Lincoln Stein, Jason D. Lieb, Robert H. Waterston

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1775-1787
Number of pages13
JournalScience
Volume330
Issue number6012
DOIs
StatePublished - Dec 24 2010

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Caenorhabditis elegans
Transcription Factors
Genome
Chromatin
Histone Code
Untranslated RNA
X Chromosome
Gene Expression Profiling
Statistical Models
MicroRNAs
Chromosomes
Binding Sites
Gene Expression
Genes
Datasets

ASJC Scopus subject areas

  • General

Cite this

Gerstein, M. B., Lu, Z. J., Van Nostrand, E. L., Cheng, C., Arshinoff, B. I., Liu, T., ... Waterston, R. H. (2010). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science, 330(6012), 1775-1787. https://doi.org/10.1126/science.1196914

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. / Gerstein, Mark B.; 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 K.; 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 C.; 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, Tony; 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; 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.; Rajewsky, Nikolaus; Rätsch, Gunnar; Rosenbaum, Heidi; Rozowsky, Joel; Rutherford, Kim; Ruzanov, Peter; Sarov, Mihail; Sasidharan, Rajkumar; Sboner, Andrea; Scheid, Paul; Segal, Eran; Shin, Hyunjin; Shou, Chong; Slack, Frank J.; Slightam, 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; Yan, 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.

In: Science, Vol. 330, No. 6012, 24.12.2010, p. 1775-1787.

Research output: Contribution to journalArticle

Gerstein, MB, Lu, ZJ, Van Nostrand, EL, Cheng, C, Arshinoff, BI, Liu, T, Yip, KY, Robilotto, R, Rechtsteiner, A, Ikegami, K, Alves, P, Chateigner, A, Perry, M, Morris, M, Auerbach, RK, Feng, X, Leng, J, Vielle, A, Niu, W, Rhrissorrakrai, K, Agarwal, A, Alexander, RP, Barber, G, Brdlik, CM, Brennan, J, Brouillet, JJ, Carr, A, Cheung, MS, Clawson, H, Contrino, S, Dannenberg, LO, Dernburg, AF, Desai, A, Dick, L, Dosé, AC, Du, J, Egelhofer, T, Ercan, S, Euskirchen, G, Ewing, B, Feingold, EA, Gassmann, R, Good, PJ, Green, P, Gullier, F, Gutwein, M, Guyer, MS, Habegger, L, Han, T, Henikoff, JG, Henz, SR, Hinrichs, A, Holster, H, Hyman, T, Iniguez, AL, Janette, J, Jensen, M, Kato, M, Kent, WJ, Kephart, E, Khivansara, V, Khurana, E, Kim, JK, Kolasinska-Zwierz, P, Lai, EC, Latorre, I, Leahey, A, Lewis, S, Lloyd, P, Lochovsky, L, Lowdon, RF, Lubling, Y, Lyne, R, MacCoss, M, Mackowiak, SD, Mangone, M, McKay, S, Mecenas, D, Merrihew, G, Miller, DM, Muroyama, A, Murray, JI, Ooi, SL, Pham, H, Phippen, T, Preston, EA, Rajewsky, N, Rätsch, G, Rosenbaum, H, Rozowsky, J, Rutherford, K, Ruzanov, P, Sarov, M, Sasidharan, R, Sboner, A, Scheid, P, Segal, E, Shin, H, Shou, C, Slack, FJ, Slightam, C, Smith, R, Spencer, WC, Stinson, EO, Taing, S, Takasaki, T, Vafeados, D, Voronina, K, Wang, G, Washington, NL, Whittle, CM, Wu, B, Yan, KK, Zeller, G, Zha, Z, Zhong, M, Zhou, X, Ahringer, J, Strome, S, Gunsalus, KC, Micklem, G, Liu, XS, Reinke, V, Kim, SK, Hillier, LW, Henikoff, S, Piano, F, Snyder, M, Stein, L, Lieb, JD & Waterston, RH 2010, 'Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project', Science, vol. 330, no. 6012, pp. 1775-1787. https://doi.org/10.1126/science.1196914
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24;330(6012):1775-1787. https://doi.org/10.1126/science.1196914
Gerstein, Mark B. ; 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 K. ; 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 C. ; 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, Tony ; 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 ; 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. ; Rajewsky, Nikolaus ; Rätsch, Gunnar ; Rosenbaum, Heidi ; Rozowsky, Joel ; Rutherford, Kim ; Ruzanov, Peter ; Sarov, Mihail ; Sasidharan, Rajkumar ; Sboner, Andrea ; Scheid, Paul ; Segal, Eran ; Shin, Hyunjin ; Shou, Chong ; Slack, Frank J. ; Slightam, 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 ; Yan, 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. / Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. In: Science. 2010 ; Vol. 330, No. 6012. pp. 1775-1787.
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title = "Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project",
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.",
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TY - JOUR

T1 - Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

AU - Gerstein, Mark B.

AU - Lu, Zhi John

AU - Van Nostrand, Eric L.

AU - Cheng, Chao

AU - Arshinoff, Bradley I.

AU - Liu, Tao

AU - Yip, Kevin Y.

AU - Robilotto, Rebecca

AU - Rechtsteiner, Andreas

AU - Ikegami, Kohta

AU - Alves, Pedro

AU - Chateigner, Aurelien

AU - Perry, Marc

AU - Morris, Mitzi

AU - Auerbach, Raymond K.

AU - Feng, Xin

AU - Leng, Jing

AU - Vielle, Anne

AU - Niu, Wei

AU - Rhrissorrakrai, Kahn

AU - Agarwal, Ashish

AU - Alexander, Roger P.

AU - Barber, Galt

AU - Brdlik, Cathleen M.

AU - Brennan, Jennifer

AU - Brouillet, Jeremy Jean

AU - Carr, Adrian

AU - Cheung, Ming Sin

AU - Clawson, Hiram

AU - Contrino, Sergio

AU - Dannenberg, Luke O.

AU - Dernburg, Abby F.

AU - Desai, Arshad

AU - Dick, Lindsay

AU - Dosé, Andréa C.

AU - Du, Jiang

AU - Egelhofer, Thea

AU - Ercan, Sevinc

AU - Euskirchen, Ghia

AU - Ewing, Brent

AU - Feingold, Elise A.

AU - Gassmann, Reto

AU - Good, Peter J.

AU - Green, Phil

AU - Gullier, Francois

AU - Gutwein, Michelle

AU - Guyer, Mark S.

AU - Habegger, Lukas

AU - Han, Ting

AU - Henikoff, Jorja G.

AU - Henz, Stefan R.

AU - Hinrichs, Angie

AU - Holster, Heather

AU - Hyman, Tony

AU - Iniguez, A. Leo

AU - Janette, Judith

AU - Jensen, Morten

AU - Kato, Masaomi

AU - Kent, W. James

AU - Kephart, Ellen

AU - Khivansara, Vishal

AU - Khurana, Ekta

AU - Kim, John K.

AU - Kolasinska-Zwierz, Paulina

AU - Lai, Eric C.

AU - Latorre, Isabel

AU - Leahey, Amber

AU - Lewis, Suzanna

AU - Lloyd, Paul

AU - Lochovsky, Lucas

AU - Lowdon, Rebecca F.

AU - Lubling, Yaniv

AU - Lyne, Rachel

AU - MacCoss, Michael

AU - Mackowiak, Sebastian D.

AU - Mangone, Marco

AU - McKay, Sheldon

AU - Mecenas, Desirea

AU - Merrihew, Gennifer

AU - Miller, David M.

AU - Muroyama, Andrew

AU - Murray, John I.

AU - Ooi, Siew Loon

AU - Pham, Hoang

AU - Phippen, Taryn

AU - Preston, Elicia A.

AU - Rajewsky, Nikolaus

AU - Rätsch, Gunnar

AU - Rosenbaum, Heidi

AU - Rozowsky, Joel

AU - Rutherford, Kim

AU - Ruzanov, Peter

AU - Sarov, Mihail

AU - Sasidharan, Rajkumar

AU - Sboner, Andrea

AU - Scheid, Paul

AU - Segal, Eran

AU - Shin, Hyunjin

AU - Shou, Chong

AU - Slack, Frank J.

AU - Slightam, Cindie

AU - Smith, Richard

AU - Spencer, William C.

AU - Stinson, E. O.

AU - Taing, Scott

AU - Takasaki, Teruaki

AU - Vafeados, Dionne

AU - Voronina, Ksenia

AU - Wang, Guilin

AU - Washington, Nicole L.

AU - Whittle, Christina M.

AU - Wu, Beijing

AU - Yan, Koon Kiu

AU - Zeller, Georg

AU - Zha, Zheng

AU - Zhong, Mei

AU - Zhou, Xingliang

AU - Ahringer, Julie

AU - Strome, Susan

AU - Gunsalus, Kristin C.

AU - Micklem, Gos

AU - Liu, X. Shirley

AU - Reinke, Valerie

AU - Kim, Stuart K.

AU - Hillier, Ladeana W.

AU - Henikoff, Steven

AU - Piano, Fabio

AU - Snyder, Michael

AU - Stein, Lincoln

AU - Lieb, Jason D.

AU - Waterston, Robert H.

PY - 2010/12/24

Y1 - 2010/12/24

N2 - 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.

AB - 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.

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