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; 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

doi:10.1126/science.1196914

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 RhrissorrakraiAshish 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 journal › Article › peer-review

755 Scopus citations

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 language	English (US)
Pages (from-to)	1775-1787
Number of pages	13
Journal	Science
Volume	330
Issue number	6012
DOIs	https://doi.org/10.1126/science.1196914
State	Published - Dec 24 2010
Externally published	Yes

ASJC Scopus subject areas

General

Access to Document

10.1126/science.1196914

Cite this

Gerstein, M. B., Lu, Z. J., Van Nostrand, E. L., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y., Robilotto, R., Rechtsteiner, A., Ikegami, K., Alves, P., Chateigner, A., Perry, M., Morris, M., Auerbach, R. K., Feng, X., Leng, J., Vielle, A., Niu, W., ... 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

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

@article{3407971faa7540419d57a43b586252bb,

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.",

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

year = "2010",

month = dec,

day = "24",

doi = "10.1126/science.1196914",

language = "English (US)",

volume = "330",

pages = "1775--1787",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6012",

}

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.

UR - http://www.scopus.com/inward/record.url?scp=78650410139&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650410139&partnerID=8YFLogxK

U2 - 10.1126/science.1196914

DO - 10.1126/science.1196914

M3 - Article

C2 - 21177976

AN - SCOPUS:78650410139

SN - 0036-8075

VL - 330

SP - 1775

EP - 1787

JO - Science

JF - Science

IS - 6012

ER -

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this