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Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Collaborators (173)

Roy S, Ernst J, Kheradpour P, Bristow CA, Lin MF, Washietl S, Ay F, Meyer PE, Di Stefano L, Candeias R, Jungreis I, Marbach D, Sealfon R, Kellis M, Landolin JM, Carlson JW, Booth B, Brooks AN, Davis CA, Duff MO, Kapranov P, Samsonova AA, Sandler JE, van Baren MJ, Wan KH, Yang L, Yu C, Andrews J, Brenner SE, Brent MR, Cherbas L, Gingeras TR, Hoskins RA, Kaufman TC, Perrimon N, Cherbas P, Graveley BR, Celniker SE, Comstock CL, 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, Kharchenko PV, Tolstorukov MY, Alekseyenko AA, Gorchakov AA, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Kuroda MI, Pirrotta V, Park PJ, Karpen GH, Acevedo D, Bishop EP, Gadel SE, Jung YL, Kennedy CD, Lee OK, Linder-Basso D, Marchetti SE, Shanower G, Nègre N, Ma L, Brown CD, Spokony R, Grossman RL, Posakony JW, Ren B, Russell S, White KP, 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 KJ, White R, Wilkening J, Zieba J, Eaton ML, MacAlpine HK, Nordman JT, Powell SK, Sher N, Orr-Weaver TL, MacAlpine DM, DeNapoli LC, Ding Q, Eng T, Kashevsky H, Li S, Prinz JA, Robine N, Berezikov E, Dai Q, Okamura K, Lai EC, Dai Q, Hannon GJ, Hirst M, Marra M, Rooks M, Zhao Y, Henikoff JG, Sakai A, Ahmad K, Henikoff S, Bryson TD, Arshinoff BI, Washington NL, Carr A, Feng X, Perry MD, Kent WJ, Lewis SE, Micklem G, Stein LD, 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, Li R, Malone JH, Sturgill D, Oliver B, Jiang L, Mattiuzzo N, Will S, Berger B, Feingold EA, Good PJ, Guyer MS, Lowdon RF.

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Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.


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.

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