Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE (Science, 2010 Dec 22)

Science. 2010 Dec 22. [Epub ahead of print]
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.

The modENCODE Consortium, 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 SC, 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.
Collaborators (76)
Acevedo D, Auburn R, Barber G, Bellen HJ, Bishop EP, Bryson TD, Chateigner A, Chen J, Clawson H, Comstock CL, Contrino S, Denapoli LC, Ding Q, Dobin A, Domanus MH, Drenkow J, Dudoit S, Dumais J, Eng T, Fagegaltier D, Gadel SE, Ghosh S, Guillier F, Hanley D, Hannon GJ, Hansen KD, Heinz E, Hinrichs AS, Hirst M, Jha S, Jiang L, Jung YL, Kashevsky H, Kennedy CD, Kephart ET, Langton L, Lee OK, Li S, Li Z, Lin W, Linder-Basso D, Lloyd P, Lyne R, Marchetti SE, Marra M, Mattiuzzo NR, McKay S, Meyer F, Miller D, Miller SW, Moore RA, Morrison CA, Prinz JA, Rooks M, Moore R, Rutherford KM, Ruzanov P, Scheftner DA, Senderowicz L, Shah PK, Shanower G, Smith R, Stinson EO, Suchy S, Tenney AE, Tian F, Venken KJ, Wang H, White R, Wilkening J, Willingham AT, Zaleski C, Zha Z, Zhang D, Zhao Y, Zieba J.

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

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