Identification of functional elements and regulatory circuits by Drosophila modENCODE

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio Candeias & 171 others Joseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C R Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis, Benjamin Booth, Anastasia A. Samsonova, Marijke van Baren, Thomas R. Gingeras, Roger A. Hoskins, Charles L G Comstock, Alex Dobin, Jorg Drenkow, Sandrine Dudoit, Jacqueline Dumais, Delphine Fagegaltier, Srinka Ghosh, Kasper D. Hansen, Sonali Jha, Laura Langton, Wei Lin, David Miller, Aaron E. Tenney, Huaien Wang, Aarron T. Willingham, Chris Zaleski, Dayu Zhang, David Acevedo, Eric P. Bishop, Sarah E. Gadel, Youngsook L. Jung, Cameron D. Kennedy, Ok Kyung Lee, Daniela Linder-Basso, Sarah E. Marchetti, Gregory Shanower, Nicolas Nègre, Robert L. Grossman, Richard Auburn, Hugo J. Bellen, Jia Chen, Marc H. Domanus, David Hanley, Elizabeth Heinz, Zirong Li, Folker Meyer, Steven W. Miller, Carolyn A. Morrison, Douglas A. Scheftner, Lionel Senderowicz, Parantu K. Shah, Sarah Suchy, Feng Tian, Koen J T Venken, Robert White, Jared Wilkening, Jennifer Zieba, Jared T. Nordman, Terry L. Orr-Weaver, Leyna C. DeNapoli, Queying Ding, Thomas Eng, Helena Kashevsky, Sharon Li, Joseph A. Prinz, Qi Dai, Gregory J. Hannon, Martin Hirst, Marco Marra, Michelle Rooks, Yongjun Zhao, Terri D. Bryson, Marc D. Perry, William J. Kent, Suzanna E. Lewis, Galt Barber, Aurelien Chateigner, Hiram Clawson, Sergio Contrino, Francois Guillier, Angie S. Hinrichs, Ellen T. Kephart, Paul Lloyd, Rachel Lyne, Sheldon McKay, Richard A. Moore, Chris Mungall, Kim M. Rutherford, Peter Ruzanov, Richard Smith, E. O. Stinson, Zheng Zha, Carlo G. Artieri, John H. Malone, Lichun Jiang, Nicolas Mattiuzzo, Elise A. Feingold, Peter J. Good, Mark S. Guyer, Rebecca F. Lowdon

Research output: Contribution to journalArticle

763 Citations (Scopus)

Abstract

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

Original languageEnglish (US)
Pages (from-to)1787-1797
Number of pages11
JournalScience
Volume330
Issue number6012
DOIs
StatePublished - Dec 24 2010

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Encyclopedias
Drosophila
DNA
Histone Code
Untranslated RNA
Proteins
Nucleosomes
Regulator Genes
Chromatin
Transcription Factors
Genome
Gene Expression
Cell Line
Genes

ASJC Scopus subject areas

  • General

Cite this

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., ... Lowdon, R. F. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330(6012), 1787-1797. https://doi.org/10.1126/science.1198374

Identification of functional elements and regulatory circuits by Drosophila modENCODE. / Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V.; Kheradpour, Pouya; Negre, Nicolas; Eaton, Matthew L.; Landolin, Jane M.; Bristow, Christopher A.; Ma, Lijia; Lin, Michael F.; Washietl, Stefan; Arshinoff, Bradley I.; Ay, Ferhat; Meyer, Patrick E.; Robine, Nicolas; Washington, Nicole L.; Di Stefano, Luisa; Berezikov, Eugene; Brown, Christopher D.; Candeias, Rogerio; Carlson, Joseph W.; Carr, Adrian; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Tolstorukov, Michael Y.; Will, Sebastian; Alekseyenko, Artyom A.; Artieri, Carlo; Booth, Benjamin W.; Brooks, Angela N.; Dai, Qi; Davis, Carrie A.; Duff, Michael O.; Feng, Xin; Gorchakov, Andrey A.; Gu, Tingting; Henikoff, Jorja G.; Kapranov, Philipp; Li, Renhua; MacAlpine, Heather K.; Malone, John; Minoda, Aki; Nordman, Jared; Okamura, Katsutomo; Perry, Marc; Powell, Sara K.; Riddle, Nicole C.; Sakai, Akiko; Samsonova, Anastasia; Sandler, Jeremy E.; Schwartz, Yuri B.; Sher, Noa; Spokony, Rebecca; Sturgill, David; van Baren, Marijke; Wan, Kenneth H.; Yang, Li; Yu, Charles; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca; Ahmad, Kami; Andrews, Justen; Berger, Bonnie; Brenner, Steven E.; Brent, Michael R.; Cherbas, Lucy; Elgin, Sarah C R; Gingeras, Thomas R.; Grossman, Robert; Hoskins, Roger A.; Kaufman, Thomas C.; Kent, William; Kuroda, Mitzi I.; Orr-Weaver, Terry; Perrimon, Norbert; Pirrotta, Vincenzo; Posakony, James W.; Ren, Bing; Russell, Steven; Cherbas, Peter; Graveley, Brenton R.; Lewis, Suzanna; Micklem, Gos; Oliver, Brian; Park, Peter J.; Celniker, Susan E.; Henikoff, Steven; Karpen, Gary H.; Lai, Eric C.; MacAlpine, David M.; Stein, Lincoln D.; White, Kevin P.; Kellis, Manolis; Booth, Benjamin; Samsonova, Anastasia A.; van Baren, Marijke; Gingeras, Thomas R.; Hoskins, Roger A.; Comstock, Charles L G; Dobin, Alex; Drenkow, Jorg; Dudoit, Sandrine; Dumais, Jacqueline; Fagegaltier, Delphine; Ghosh, Srinka; Hansen, Kasper D.; Jha, Sonali; Langton, Laura; Lin, Wei; Miller, David; Tenney, Aaron E.; Wang, Huaien; Willingham, Aarron T.; Zaleski, Chris; Zhang, Dayu; Acevedo, David; Bishop, Eric P.; Gadel, Sarah E.; Jung, Youngsook L.; Kennedy, Cameron D.; Lee, Ok Kyung; Linder-Basso, Daniela; Marchetti, Sarah E.; Shanower, Gregory; Nègre, Nicolas; Grossman, Robert L.; Auburn, Richard; Bellen, Hugo J.; Chen, Jia; Domanus, Marc H.; Hanley, David; Heinz, Elizabeth; Li, Zirong; Meyer, Folker; Miller, Steven W.; Morrison, Carolyn A.; Scheftner, Douglas A.; Senderowicz, Lionel; Shah, Parantu K.; Suchy, Sarah; Tian, Feng; Venken, Koen J T; White, Robert; Wilkening, Jared; Zieba, Jennifer; Nordman, Jared T.; Orr-Weaver, Terry L.; DeNapoli, Leyna C.; Ding, Queying; Eng, Thomas; Kashevsky, Helena; Li, Sharon; Prinz, Joseph A.; Dai, Qi; Hannon, Gregory J.; Hirst, Martin; Marra, Marco; Rooks, Michelle; Zhao, Yongjun; Bryson, Terri D.; Perry, Marc D.; Kent, William J.; Lewis, Suzanna E.; Barber, Galt; Chateigner, Aurelien; Clawson, Hiram; Contrino, Sergio; Guillier, Francois; Hinrichs, Angie S.; Kephart, Ellen T.; Lloyd, Paul; Lyne, Rachel; McKay, Sheldon; Moore, Richard A.; Mungall, Chris; Rutherford, Kim M.; Ruzanov, Peter; Smith, Richard; Stinson, E. O.; Zha, Zheng; Artieri, Carlo G.; Malone, John H.; Jiang, Lichun; Mattiuzzo, Nicolas; Feingold, Elise A.; Good, Peter J.; Guyer, Mark S.; Lowdon, Rebecca F.

In: Science, Vol. 330, No. 6012, 24.12.2010, p. 1787-1797.

Research output: Contribution to journalArticle

Roy, S, Ernst, J, Kharchenko, PV, Kheradpour, P, Negre, N, Eaton, ML, Landolin, JM, Bristow, CA, Ma, L, Lin, MF, Washietl, S, Arshinoff, BI, Ay, F, Meyer, PE, Robine, N, Washington, NL, Di Stefano, L, Berezikov, E, Brown, CD, Candeias, R, Carlson, JW, Carr, A, Jungreis, I, Marbach, D, Sealfon, R, Tolstorukov, MY, Will, S, Alekseyenko, AA, Artieri, C, Booth, BW, Brooks, AN, Dai, Q, Davis, CA, Duff, MO, Feng, X, Gorchakov, AA, Gu, T, Henikoff, JG, Kapranov, P, Li, R, MacAlpine, HK, Malone, J, Minoda, A, Nordman, J, Okamura, K, Perry, M, Powell, SK, Riddle, NC, Sakai, A, Samsonova, A, Sandler, JE, Schwartz, YB, Sher, N, Spokony, R, Sturgill, D, van Baren, M, Wan, KH, Yang, L, Yu, C, Feingold, E, Good, P, Guyer, M, Lowdon, R, Ahmad, K, Andrews, J, Berger, B, Brenner, SE, Brent, MR, Cherbas, L, Elgin, SCR, Gingeras, TR, Grossman, R, Hoskins, RA, Kaufman, TC, Kent, W, Kuroda, MI, Orr-Weaver, T, Perrimon, N, Pirrotta, V, Posakony, JW, Ren, B, Russell, S, Cherbas, P, Graveley, BR, Lewis, S, Micklem, G, Oliver, B, Park, PJ, Celniker, SE, Henikoff, S, Karpen, GH, Lai, EC, MacAlpine, DM, Stein, LD, White, KP, Kellis, M, Booth, B, Samsonova, AA, van Baren, M, Gingeras, TR, Hoskins, RA, Comstock, CLG, Dobin, A, Drenkow, J, Dudoit, S, Dumais, J, Fagegaltier, D, Ghosh, S, Hansen, KD, Jha, S, Langton, L, Lin, W, Miller, D, Tenney, AE, Wang, H, Willingham, AT, Zaleski, C, Zhang, D, Acevedo, D, Bishop, EP, Gadel, SE, Jung, YL, Kennedy, CD, Lee, OK, Linder-Basso, D, Marchetti, SE, Shanower, G, Nègre, N, Grossman, RL, Auburn, R, Bellen, HJ, Chen, J, Domanus, MH, Hanley, D, Heinz, E, Li, Z, Meyer, F, Miller, SW, Morrison, CA, Scheftner, DA, Senderowicz, L, Shah, PK, Suchy, S, Tian, F, Venken, KJT, White, R, Wilkening, J, Zieba, J, Nordman, JT, Orr-Weaver, TL, DeNapoli, LC, Ding, Q, Eng, T, Kashevsky, H, Li, S, Prinz, JA, Dai, Q, Hannon, GJ, Hirst, M, Marra, M, Rooks, M, Zhao, Y, Bryson, TD, Perry, MD, Kent, WJ, Lewis, SE, Barber, G, Chateigner, A, Clawson, H, Contrino, S, Guillier, F, Hinrichs, AS, Kephart, ET, Lloyd, P, Lyne, R, McKay, S, Moore, RA, Mungall, C, Rutherford, KM, Ruzanov, P, Smith, R, Stinson, EO, Zha, Z, Artieri, CG, Malone, JH, Jiang, L, Mattiuzzo, N, Feingold, EA, Good, PJ, Guyer, MS & Lowdon, RF 2010, 'Identification of functional elements and regulatory circuits by Drosophila modENCODE', Science, vol. 330, no. 6012, pp. 1787-1797. https://doi.org/10.1126/science.1198374
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-1797. https://doi.org/10.1126/science.1198374
Roy, Sushmita ; Ernst, Jason ; Kharchenko, Peter V. ; Kheradpour, Pouya ; Negre, Nicolas ; Eaton, Matthew L. ; Landolin, Jane M. ; Bristow, Christopher A. ; Ma, Lijia ; Lin, Michael F. ; Washietl, Stefan ; Arshinoff, Bradley I. ; Ay, Ferhat ; Meyer, Patrick E. ; Robine, Nicolas ; Washington, Nicole L. ; Di Stefano, Luisa ; Berezikov, Eugene ; Brown, Christopher D. ; Candeias, Rogerio ; Carlson, Joseph W. ; Carr, Adrian ; Jungreis, Irwin ; Marbach, Daniel ; Sealfon, Rachel ; Tolstorukov, Michael Y. ; Will, Sebastian ; Alekseyenko, Artyom A. ; Artieri, Carlo ; Booth, Benjamin W. ; Brooks, Angela N. ; Dai, Qi ; Davis, Carrie A. ; Duff, Michael O. ; Feng, Xin ; Gorchakov, Andrey A. ; Gu, Tingting ; Henikoff, Jorja G. ; Kapranov, Philipp ; Li, Renhua ; MacAlpine, Heather K. ; Malone, John ; Minoda, Aki ; Nordman, Jared ; Okamura, Katsutomo ; Perry, Marc ; Powell, Sara K. ; Riddle, Nicole C. ; Sakai, Akiko ; Samsonova, Anastasia ; Sandler, Jeremy E. ; Schwartz, Yuri B. ; Sher, Noa ; Spokony, Rebecca ; Sturgill, David ; van Baren, Marijke ; Wan, Kenneth H. ; Yang, Li ; Yu, Charles ; Feingold, Elise ; Good, Peter ; Guyer, Mark ; Lowdon, Rebecca ; Ahmad, Kami ; Andrews, Justen ; Berger, Bonnie ; Brenner, Steven E. ; Brent, Michael R. ; Cherbas, Lucy ; Elgin, Sarah C R ; Gingeras, Thomas R. ; Grossman, Robert ; Hoskins, Roger A. ; Kaufman, Thomas C. ; Kent, William ; Kuroda, Mitzi I. ; Orr-Weaver, Terry ; Perrimon, Norbert ; Pirrotta, Vincenzo ; Posakony, James W. ; Ren, Bing ; Russell, Steven ; Cherbas, Peter ; Graveley, Brenton R. ; Lewis, Suzanna ; Micklem, Gos ; Oliver, Brian ; Park, Peter J. ; Celniker, Susan E. ; Henikoff, Steven ; Karpen, Gary H. ; Lai, Eric C. ; MacAlpine, David M. ; Stein, Lincoln D. ; White, Kevin P. ; Kellis, Manolis ; Booth, Benjamin ; Samsonova, Anastasia A. ; van Baren, Marijke ; Gingeras, Thomas R. ; Hoskins, Roger A. ; Comstock, Charles L G ; Dobin, Alex ; Drenkow, Jorg ; Dudoit, Sandrine ; Dumais, Jacqueline ; Fagegaltier, Delphine ; Ghosh, Srinka ; Hansen, Kasper D. ; Jha, Sonali ; Langton, Laura ; Lin, Wei ; Miller, David ; Tenney, Aaron E. ; Wang, Huaien ; Willingham, Aarron T. ; Zaleski, Chris ; Zhang, Dayu ; Acevedo, David ; Bishop, Eric P. ; Gadel, Sarah E. ; Jung, Youngsook L. ; Kennedy, Cameron D. ; Lee, Ok Kyung ; Linder-Basso, Daniela ; Marchetti, Sarah E. ; Shanower, Gregory ; Nègre, Nicolas ; Grossman, Robert L. ; Auburn, Richard ; Bellen, Hugo J. ; Chen, Jia ; Domanus, Marc H. ; Hanley, David ; Heinz, Elizabeth ; Li, Zirong ; Meyer, Folker ; Miller, Steven W. ; Morrison, Carolyn A. ; Scheftner, Douglas A. ; Senderowicz, Lionel ; Shah, Parantu K. ; Suchy, Sarah ; Tian, Feng ; Venken, Koen J T ; White, Robert ; Wilkening, Jared ; Zieba, Jennifer ; Nordman, Jared T. ; Orr-Weaver, Terry L. ; DeNapoli, Leyna C. ; Ding, Queying ; Eng, Thomas ; Kashevsky, Helena ; Li, Sharon ; Prinz, Joseph A. ; Dai, Qi ; Hannon, Gregory J. ; Hirst, Martin ; Marra, Marco ; Rooks, Michelle ; Zhao, Yongjun ; Bryson, Terri D. ; Perry, Marc D. ; Kent, William J. ; Lewis, Suzanna E. ; Barber, Galt ; Chateigner, Aurelien ; Clawson, Hiram ; Contrino, Sergio ; Guillier, Francois ; Hinrichs, Angie S. ; Kephart, Ellen T. ; Lloyd, Paul ; Lyne, Rachel ; McKay, Sheldon ; Moore, Richard A. ; Mungall, Chris ; Rutherford, Kim M. ; Ruzanov, Peter ; Smith, Richard ; Stinson, E. O. ; Zha, Zheng ; Artieri, Carlo G. ; Malone, John H. ; Jiang, Lichun ; Mattiuzzo, Nicolas ; Feingold, Elise A. ; Good, Peter J. ; Guyer, Mark S. ; Lowdon, Rebecca F. / Identification of functional elements and regulatory circuits by Drosophila modENCODE. In: Science. 2010 ; Vol. 330, No. 6012. pp. 1787-1797.
@article{b3a1170e8b4e4926a4be0be7a9012e9e,
title = "Identification of functional elements and regulatory circuits by Drosophila modENCODE",
abstract = "To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.",
author = "Sushmita Roy and Jason Ernst and Kharchenko, {Peter V.} and Pouya Kheradpour and Nicolas Negre and Eaton, {Matthew L.} and Landolin, {Jane M.} and Bristow, {Christopher A.} and Lijia Ma and Lin, {Michael F.} and Stefan Washietl and Arshinoff, {Bradley I.} and Ferhat Ay and Meyer, {Patrick E.} and Nicolas Robine and Washington, {Nicole L.} and {Di Stefano}, Luisa and Eugene Berezikov and Brown, {Christopher D.} and Rogerio Candeias and Carlson, {Joseph W.} and Adrian Carr and Irwin Jungreis and Daniel Marbach and Rachel Sealfon and Tolstorukov, {Michael Y.} and Sebastian Will and Alekseyenko, {Artyom A.} and Carlo Artieri and Booth, {Benjamin W.} and Brooks, {Angela N.} and Qi Dai and Davis, {Carrie A.} and Duff, {Michael O.} and Xin Feng and Gorchakov, {Andrey A.} and Tingting Gu and Henikoff, {Jorja G.} and Philipp Kapranov and Renhua Li and MacAlpine, {Heather K.} and John Malone and Aki Minoda and Jared Nordman and Katsutomo Okamura and Marc Perry and Powell, {Sara K.} and Riddle, {Nicole C.} and Akiko Sakai and Anastasia Samsonova and Sandler, {Jeremy E.} and Schwartz, {Yuri B.} and Noa Sher and Rebecca Spokony and David Sturgill and {van Baren}, Marijke and Wan, {Kenneth H.} and Li Yang and Charles Yu and Elise Feingold and Peter Good and Mark Guyer and Rebecca Lowdon and Kami Ahmad and Justen Andrews and Bonnie Berger and Brenner, {Steven E.} and Brent, {Michael R.} and Lucy Cherbas and Elgin, {Sarah C R} and Gingeras, {Thomas R.} and Robert Grossman and Hoskins, {Roger A.} and Kaufman, {Thomas C.} and William Kent and Kuroda, {Mitzi I.} and Terry Orr-Weaver and Norbert Perrimon and Vincenzo Pirrotta and Posakony, {James W.} and Bing Ren and Steven Russell and Peter Cherbas and Graveley, {Brenton R.} and Suzanna Lewis and Gos Micklem and Brian Oliver and Park, {Peter J.} and Celniker, {Susan E.} and Steven Henikoff and Karpen, {Gary H.} and Lai, {Eric C.} and MacAlpine, {David M.} and Stein, {Lincoln D.} and White, {Kevin P.} and Manolis Kellis and Benjamin Booth and Samsonova, {Anastasia A.} and {van Baren}, Marijke and Gingeras, {Thomas R.} and Hoskins, {Roger A.} and Comstock, {Charles L G} and Alex Dobin and Jorg Drenkow and Sandrine Dudoit and Jacqueline Dumais and Delphine Fagegaltier and Srinka Ghosh and Hansen, {Kasper D.} and Sonali Jha and Laura Langton and Wei Lin and David Miller and Tenney, {Aaron E.} and Huaien Wang and Willingham, {Aarron T.} and Chris Zaleski and Dayu Zhang and David Acevedo and Bishop, {Eric P.} and Gadel, {Sarah E.} and Jung, {Youngsook L.} and Kennedy, {Cameron D.} and Lee, {Ok Kyung} and Daniela Linder-Basso and Marchetti, {Sarah E.} and Gregory Shanower and Nicolas N{\`e}gre and Grossman, {Robert L.} and Richard Auburn and Bellen, {Hugo J.} and Jia Chen and Domanus, {Marc H.} and David Hanley and Elizabeth Heinz and Zirong Li and Folker Meyer and Miller, {Steven W.} and Morrison, {Carolyn A.} and Scheftner, {Douglas A.} and Lionel Senderowicz and Shah, {Parantu K.} and Sarah Suchy and Feng Tian and Venken, {Koen J T} and Robert White and Jared Wilkening and Jennifer Zieba and Nordman, {Jared T.} and Orr-Weaver, {Terry L.} and DeNapoli, {Leyna C.} and Queying Ding and Thomas Eng and Helena Kashevsky and Sharon Li and Prinz, {Joseph A.} and Qi Dai and Hannon, {Gregory J.} and Martin Hirst and Marco Marra and Michelle Rooks and Yongjun Zhao and Bryson, {Terri D.} and Perry, {Marc D.} and Kent, {William J.} and Lewis, {Suzanna E.} and Galt Barber and Aurelien Chateigner and Hiram Clawson and Sergio Contrino and Francois Guillier and Hinrichs, {Angie S.} and Kephart, {Ellen T.} and Paul Lloyd and Rachel Lyne and Sheldon McKay and Moore, {Richard A.} and Chris Mungall and Rutherford, {Kim M.} and Peter Ruzanov and Richard Smith and Stinson, {E. O.} and Zheng Zha and Artieri, {Carlo G.} and Malone, {John H.} and Lichun Jiang and Nicolas Mattiuzzo and Feingold, {Elise A.} and Good, {Peter J.} and Guyer, {Mark S.} and Lowdon, {Rebecca F.}",
year = "2010",
month = "12",
day = "24",
doi = "10.1126/science.1198374",
language = "English (US)",
volume = "330",
pages = "1787--1797",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6012",

}

TY - JOUR

T1 - Identification of functional elements and regulatory circuits by Drosophila modENCODE

AU - Roy, Sushmita

AU - Ernst, Jason

AU - Kharchenko, Peter V.

AU - Kheradpour, Pouya

AU - Negre, Nicolas

AU - Eaton, Matthew L.

AU - Landolin, Jane M.

AU - Bristow, Christopher A.

AU - Ma, Lijia

AU - Lin, Michael F.

AU - Washietl, Stefan

AU - Arshinoff, Bradley I.

AU - Ay, Ferhat

AU - Meyer, Patrick E.

AU - Robine, Nicolas

AU - Washington, Nicole L.

AU - Di Stefano, Luisa

AU - Berezikov, Eugene

AU - Brown, Christopher D.

AU - Candeias, Rogerio

AU - Carlson, Joseph W.

AU - Carr, Adrian

AU - Jungreis, Irwin

AU - Marbach, Daniel

AU - Sealfon, Rachel

AU - Tolstorukov, Michael Y.

AU - Will, Sebastian

AU - Alekseyenko, Artyom A.

AU - Artieri, Carlo

AU - Booth, Benjamin W.

AU - Brooks, Angela N.

AU - Dai, Qi

AU - Davis, Carrie A.

AU - Duff, Michael O.

AU - Feng, Xin

AU - Gorchakov, Andrey A.

AU - Gu, Tingting

AU - Henikoff, Jorja G.

AU - Kapranov, Philipp

AU - Li, Renhua

AU - MacAlpine, Heather K.

AU - Malone, John

AU - Minoda, Aki

AU - Nordman, Jared

AU - Okamura, Katsutomo

AU - Perry, Marc

AU - Powell, Sara K.

AU - Riddle, Nicole C.

AU - Sakai, Akiko

AU - Samsonova, Anastasia

AU - Sandler, Jeremy E.

AU - Schwartz, Yuri B.

AU - Sher, Noa

AU - Spokony, Rebecca

AU - Sturgill, David

AU - van Baren, Marijke

AU - Wan, Kenneth H.

AU - Yang, Li

AU - Yu, Charles

AU - Feingold, Elise

AU - Good, Peter

AU - Guyer, Mark

AU - Lowdon, Rebecca

AU - Ahmad, Kami

AU - Andrews, Justen

AU - Berger, Bonnie

AU - Brenner, Steven E.

AU - Brent, Michael R.

AU - Cherbas, Lucy

AU - Elgin, Sarah C R

AU - Gingeras, Thomas R.

AU - Grossman, Robert

AU - Hoskins, Roger A.

AU - Kaufman, Thomas C.

AU - Kent, William

AU - Kuroda, Mitzi I.

AU - Orr-Weaver, Terry

AU - Perrimon, Norbert

AU - Pirrotta, Vincenzo

AU - Posakony, James W.

AU - Ren, Bing

AU - Russell, Steven

AU - Cherbas, Peter

AU - Graveley, Brenton R.

AU - Lewis, Suzanna

AU - Micklem, Gos

AU - Oliver, Brian

AU - Park, Peter J.

AU - Celniker, Susan E.

AU - Henikoff, Steven

AU - Karpen, Gary H.

AU - Lai, Eric C.

AU - MacAlpine, David M.

AU - Stein, Lincoln D.

AU - White, Kevin P.

AU - Kellis, Manolis

AU - Booth, Benjamin

AU - Samsonova, Anastasia A.

AU - van Baren, Marijke

AU - Gingeras, Thomas R.

AU - Hoskins, Roger A.

AU - Comstock, Charles L G

AU - Dobin, Alex

AU - Drenkow, Jorg

AU - Dudoit, Sandrine

AU - Dumais, Jacqueline

AU - Fagegaltier, Delphine

AU - Ghosh, Srinka

AU - Hansen, Kasper D.

AU - Jha, Sonali

AU - Langton, Laura

AU - Lin, Wei

AU - Miller, David

AU - Tenney, Aaron E.

AU - Wang, Huaien

AU - Willingham, Aarron T.

AU - Zaleski, Chris

AU - Zhang, Dayu

AU - Acevedo, David

AU - Bishop, Eric P.

AU - Gadel, Sarah E.

AU - Jung, Youngsook L.

AU - Kennedy, Cameron D.

AU - Lee, Ok Kyung

AU - Linder-Basso, Daniela

AU - Marchetti, Sarah E.

AU - Shanower, Gregory

AU - Nègre, Nicolas

AU - Grossman, Robert L.

AU - Auburn, Richard

AU - Bellen, Hugo J.

AU - Chen, Jia

AU - Domanus, Marc H.

AU - Hanley, David

AU - Heinz, Elizabeth

AU - Li, Zirong

AU - Meyer, Folker

AU - Miller, Steven W.

AU - Morrison, Carolyn A.

AU - Scheftner, Douglas A.

AU - Senderowicz, Lionel

AU - Shah, Parantu K.

AU - Suchy, Sarah

AU - Tian, Feng

AU - Venken, Koen J T

AU - White, Robert

AU - Wilkening, Jared

AU - Zieba, Jennifer

AU - Nordman, Jared T.

AU - Orr-Weaver, Terry L.

AU - DeNapoli, Leyna C.

AU - Ding, Queying

AU - Eng, Thomas

AU - Kashevsky, Helena

AU - Li, Sharon

AU - Prinz, Joseph A.

AU - Dai, Qi

AU - Hannon, Gregory J.

AU - Hirst, Martin

AU - Marra, Marco

AU - Rooks, Michelle

AU - Zhao, Yongjun

AU - Bryson, Terri D.

AU - Perry, Marc D.

AU - Kent, William J.

AU - Lewis, Suzanna E.

AU - Barber, Galt

AU - Chateigner, Aurelien

AU - Clawson, Hiram

AU - Contrino, Sergio

AU - Guillier, Francois

AU - Hinrichs, Angie S.

AU - Kephart, Ellen T.

AU - Lloyd, Paul

AU - Lyne, Rachel

AU - McKay, Sheldon

AU - Moore, Richard A.

AU - Mungall, Chris

AU - Rutherford, Kim M.

AU - Ruzanov, Peter

AU - Smith, Richard

AU - Stinson, E. O.

AU - Zha, Zheng

AU - Artieri, Carlo G.

AU - Malone, John H.

AU - Jiang, Lichun

AU - Mattiuzzo, Nicolas

AU - Feingold, Elise A.

AU - Good, Peter J.

AU - Guyer, Mark S.

AU - Lowdon, Rebecca F.

PY - 2010/12/24

Y1 - 2010/12/24

N2 - To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

AB - To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

UR - http://www.scopus.com/inward/record.url?scp=78650331647&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650331647&partnerID=8YFLogxK

U2 - 10.1126/science.1198374

DO - 10.1126/science.1198374

M3 - Article

VL - 330

SP - 1787

EP - 1797

JO - Science

JF - Science

SN - 0036-8075

IS - 6012

ER -