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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.

SUBMITTER: modENCODE Consortium 

PROVIDER: S-EPMC3192495 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Roy Sushmita S   Ernst Jason J   Kharchenko Peter V PV   Kheradpour Pouya P   Negre Nicolas N   Eaton Matthew L ML   Landolin Jane M JM   Bristow Christopher A CA   Ma Lijia L   Lin Michael F MF   Washietl Stefan S   Arshinoff Bradley I BI   Ay Ferhat F   Meyer Patrick E PE   Robine Nicolas N   Washington Nicole L NL   Di Stefano Luisa L   Berezikov Eugene E   Brown Christopher D CD   Candeias Rogerio R   Carlson Joseph W JW   Carr Adrian A   Jungreis Irwin I   Marbach Daniel D   Sealfon Rachel R   Tolstorukov Michael Y MY   Will Sebastian S   Alekseyenko Artyom A AA   Artieri Carlo C   Booth Benjamin W BW   Brooks Angela N AN   Dai Qi Q   Davis Carrie A CA   Duff Michael O MO   Feng Xin X   Gorchakov Andrey A AA   Gu Tingting T   Henikoff Jorja G JG   Kapranov Philipp P   Li Renhua R   MacAlpine Heather K HK   Malone John J   Minoda Aki A   Nordman Jared J   Okamura Katsutomo K   Perry Marc M   Powell Sara K SK   Riddle Nicole C NC   Sakai Akiko A   Samsonova Anastasia A   Sandler Jeremy E JE   Schwartz Yuri B YB   Sher Noa N   Spokony Rebecca R   Sturgill David D   van Baren Marijke M   Wan Kenneth H KH   Yang Li L   Yu Charles C   Feingold Elise E   Good Peter P   Guyer Mark M   Lowdon Rebecca R   Ahmad Kami K   Andrews Justen J   Berger Bonnie B   Brenner Steven E SE   Brent Michael R MR   Cherbas Lucy L   Elgin Sarah C R SC   Gingeras Thomas R TR   Grossman Robert R   Hoskins Roger A RA   Kaufman Thomas C TC   Kent William W   Kuroda Mitzi I MI   Orr-Weaver Terry T   Perrimon Norbert N   Pirrotta Vincenzo V   Posakony James W JW   Ren Bing B   Russell Steven S   Cherbas Peter P   Graveley Brenton R BR   Lewis Suzanna S   Micklem Gos G   Oliver Brian B   Park Peter J PJ   Celniker Susan E SE   Henikoff Steven S   Karpen Gary H GH   Lai Eric C EC   MacAlpine David M DM   Stein Lincoln D LD   White Kevin P KP   Kellis Manolis M  

Science (New York, N.Y.) 20101222 6012


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,  ...[more]

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