Identification of Functional Elements and Regulatory Circuits by
Drosophila
modENCODE
Authors:   The modENCODE Consortium, 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 , Acevedo David , Auburn Richard , Barber Galt , Bellen Hugo J. , Bishop Eric P. , Bryson Terri D. , Chateigner Aurelien , Chen Jia , Clawson Hiram , Comstock Charles L. G. , Contrino Sergio , DeNapoli Leyna C. , Ding Queying , Dobin Alex , Domanus Marc H. , Drenkow Jorg , Dudoit Sandrine , Dumais Jackie , Eng Thomas , Fagegaltier Delphine , Gadel Sarah E. , Ghosh Srinka , Guillier Francois , Hanley David , Hannon Gregory J. , Hansen Kasper D. , Heinz Elizabeth , Hinrichs Angie S. , Hirst Martin , Jha Sonali , Jiang Lichun , Jung Youngsook L. , Kashevsky Helena , Kennedy Cameron D. , Kephart Ellen T. , Langton Laura , Lee Ok-Kyung , Li Sharon , Li Zirong , Lin Wei , Linder-Basso Daniela , Lloyd Paul , Lyne Rachel , Marchetti Sarah E. , Marra Marco , Mattiuzzo Nicolas R. , McKay Sheldon , Meyer Folker , Miller David , Miller Steven W. , Moore Richard A. , Morrison Carolyn A. , Prinz Joseph A. , Rooks Michelle , Moore Richard , Rutherford Kim M. , Ruzanov Peter , Scheftner Douglas A. , Senderowicz Lionel , Shah Parantu K. , Shanower Gregory , Smith Richard , Stinson E. O. , Suchy Sarah , Tenney Aaron E. , Tian Feng , Venken Koen J. T. , Wang Huaien , White Robert , Wilkening Jared , Willingham Aarron T. , Zaleski Chris , Zha Zheng , Zhang Dayu , Zhao Yongjun , Zieba Jennifer 
Published: December 2010

From Genome to Regulatory Networks

For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by

Blaxter

). In this vein,

Gerstein
et al.

(p.
1775
) summarize for the
Caenorhabditis elegans
genome, and
The modENCODE Consortium
(p.
1787
) summarize for the
Drosophila melanogaster
genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.