Integrative Analysis of the
Caenorhabditis elegans
Genome by the modENCODE Project
Authors: Gerstein Mark B. , Lu Zhi John , Van Nostrand Eric L. , Cheng Chao , Arshinoff Bradley I. , Liu Tao , Yip Kevin Y. , Robilotto Rebecca , Rechtsteiner Andreas , Ikegami Kohta , Alves Pedro , Chateigner Aurelien , Perry Marc , Morris Mitzi , Auerbach Raymond K. , Feng Xin , Leng Jing , Vielle Anne , Niu Wei , Rhrissorrakrai Kahn , Agarwal Ashish , Alexander Roger P. , Barber Galt , Brdlik Cathleen M. , Brennan Jennifer , Brouillet Jeremy Jean , Carr Adrian , Cheung Ming-Sin , Clawson Hiram , Contrino Sergio , Dannenberg Luke O. , Dernburg Abby F. , Desai Arshad , Dick Lindsay , Dosé Andréa C. , Du Jiang , Egelhofer Thea , Ercan Sevinc , Euskirchen Ghia , Ewing Brent , Feingold Elise A. , Gassmann Reto , Good Peter J. , Green Phil , Gullier Francois , Gutwein Michelle , Guyer Mark S. , Habegger Lukas , Han Ting , Henikoff Jorja G. , Henz Stefan R. , Hinrichs Angie , Holster Heather , Hyman Tony , Iniguez A. Leo , Janette Judith , Jensen Morten , Kato Masaomi , Kent W. James , Kephart Ellen , Khivansara Vishal , Khurana Ekta , Kim John K. , Kolasinska-Zwierz Paulina , Lai Eric C. , Latorre Isabel , Leahey Amber , Lewis Suzanna , Lloyd Paul , Lochovsky Lucas , Lowdon Rebecca F. , Lubling Yaniv , Lyne Rachel , MacCoss Michael , Mackowiak Sebastian D. , Mangone Marco , McKay Sheldon , Mecenas Desirea , Merrihew Gennifer , Miller David M. , Muroyama Andrew , Murray John I. , Ooi Siew-Loon , Pham Hoang , Phippen Taryn , Preston Elicia A. , Rajewsky Nikolaus , Rätsch Gunnar , Rosenbaum Heidi , Rozowsky Joel , Rutherford Kim , Ruzanov Peter , Sarov Mihail , Sasidharan Rajkumar , Sboner Andrea , Scheid Paul , Segal Eran , Shin Hyunjin , Shou Chong , Slack Frank J. , Slightam Cindie , Smith Richard , Spencer William C. , Stinson E. O. , Taing Scott , Takasaki Teruaki , Vafeados Dionne , Voronina Ksenia , Wang Guilin , Washington Nicole L. , Whittle Christina M. , Wu Beijing , Yan Koon-Kiu , Zeller Georg , Zha Zheng , Zhong Mei , Zhou Xingliang ,   modENCODE Consortium, Ahringer Julie , Strome Susan , Gunsalus Kristin C. , Micklem Gos , Liu X. Shirley , Reinke Valerie , Kim Stuart K. , Hillier LaDeana W. , Henikoff Steven , Piano Fabio , Snyder Michael , Stein Lincoln , Lieb Jason D. , Waterston Robert H. 
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.