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.

DOI: 10.1126/science.1198374

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@article{Roy2010IdentificationOF, title={Identification of functional elements and regulatory circuits by Drosophila modENCODE.}, author={Sushmita Roy and Jason Ernst and Peter V. Kharchenko and Pouya Kheradpour and Nicolas N. Negre and Matthew L. Eaton and Jane M . Landolin and Christopher Aaron Bristow and Lijia Ma and Michael F. Lin and Stefan Washietl and Bradley I. Arshinoff and Ferhat Ay and Patrick Meyer and Nicolas Robine and Nicole L. Washington and Luisa Di Stefano and Eugene Berezikov and Christopher D Brown and Rogerio Candeias and Joseph W. Carlson and Adrian Carr and Irwin Jungreis and Daniel Marbach and Rachel S. G. Sealfon and Michael Y. Tolstorukov and Sebastian Will and Artyom A. Alekseyenko and Carlo G. Artieri and Benjamin W . Booth and Angela N. Brooks and Qi Dai and Carrie A. Davis and Michael O . Duff and Xin Feng and Andrey A . Gorchakov and Tingting Gu and Jorja G. Henikoff and Philipp Kapranov and Renhua Li and Heather K. MacAlpine and John H. Malone and Aki Minoda and Jared T. Nordman and Katsutomo Okamura and Marc D. Perry and Sara K . Powell and Nicole C. Riddle and Akiko Sakai and Anastasia Samsonova and Jeremy E . Sandler and Yuri B. Schwartz and Noa Sher and Rebecca Spokony and David Sturgill and Marijke J. van Baren and Kenneth H . Wan and Li Yang and Charles Yu and Elise A. Feingold and Peter J. Good and Mark Guyer and Rebecca F. Lowdon and Kami Ahmad and Justen Andrews and Bonnie Berger and Steven E. Brenner and Michael R. Brent and Lucy Cherbas and Sarah C. R. Elgin and Thomas R. Gingeras and Robert Grossman and Roger A . Hoskins and Thomas C Kaufman and William Kent and Mitzi I. Kuroda and Terry L Orr-Weaver and Norbert Perrimon and Vincenzo Pirrotta and James W Posakony and Bing Ren and Steven Russell and Peter Cherbas and Brenton R . Graveley and Suzanna Lewis and Gos Micklem and Brian Oliver and Peter J. Park and Susan E. Celniker and Steven Henikoff and Gary H. Karpen and Eric C. Lai and David M. MacAlpine and Lincoln Stein and Kevin P. White and Manolis Kellis}, journal={Science}, year={2010}, volume={330 6012}, pages={1787-97} }