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 language | English (US) |
|---|---|
| Pages (from-to) | 1787-1797 |
| Number of pages | 11 |
| Journal | Science |
| Volume | 330 |
| Issue number | 6012 |
| DOIs | |
| State | Published - Dec 24 2010 |
ASJC Scopus subject areas
- General
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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 journal › Article
}
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
C2 - 21177974
AN - SCOPUS:78650331647
VL - 330
SP - 1787
EP - 1797
JO - Science
JF - Science
SN - 0036-8075
IS - 6012
ER -