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Miller Lab

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

AUTHORS

Gerstein MBMark B , Lu ZJ Zhi John , Van Nostrand EL Eric L , Cheng C Chao , Arshinoff BI Bradley I , Liu T Tao , Yip KY Kevin Y , Robilotto R Rebecca , Rechtsteiner A Andreas , Ikegami K Kohta , Alves P Pedro , Chateigner A Aurelien , Perry M Marc , Morris M Mitzi , Auerbach RK Raymond K , Feng X Xin , Leng J Jing , Vielle A Anne , Niu W Wei , Rhrissorrakrai K Kahn , Agarwal A Ashish , Alexander RP Roger P , Barber G Galt , Brdlik CM Cathleen M , Brennan J Jennifer , Brouillet JJ Jeremy Jean , Carr A Adrian , Cheung MS Ming-Sin , Clawson H Hiram , Contrino S Sergio , Dannenberg LO Luke O , Dernburg AF Abby F , Desai A Arshad , Dick L Lindsay , Dosé AC Andréa C , Du J Jiang , Egelhofer T Thea , Ercan S Sevinc , Euskirchen G Ghia , Ewing B Brent , Feingold EA Elise A , Gassmann R Reto , Good PJ Peter J , Green P Phil , Gullier F Francois , Gutwein M Michelle , Guyer MS Mark S , Habegger L Lukas , Han T Ting , Henikoff JG Jorja G , Henz SR Stefan R , Hinrichs A Angie , Holster H Heather , Hyman T Tony , Iniguez AL A Leo , Janette J Judith , Jensen M Morten , Kato M Masaomi , Kent WJ W James , Kephart E Ellen , Khivansara V Vishal , Khurana E Ekta , Kim JK John K , Kolasinska-Zwierz P Paulina , Lai EC Eric C , Latorre I Isabel , Leahey A Amber , Lewis S Suzanna , Lloyd P Paul , Lochovsky L Lucas , Lowdon RF Rebecca F , Lubling Y Yaniv , Lyne R Rachel , MacCoss M Michael , Mackowiak SD Sebastian D , Mangone M Marco , McKay S Sheldon , Mecenas D Desirea , Merrihew G Gennifer , Miller DM David M , Muroyama A Andrew , Murray JI John I , Ooi SL Siew-Loon , Pham H Hoang , Phippen T Taryn , Preston EA Elicia A , Rajewsky N Nikolaus , Rätsch G Gunnar , Rosenbaum H Heidi , Rozowsky J Joel , Rutherford K Kim , Ruzanov P Peter , Sarov M Mihail , Sasidharan R Rajkumar , Sboner A Andrea , Scheid P Paul , Segal E Eran , Shin H Hyunjin , Shou C Chong , Slack FJ Frank J , Slightam C Cindie , Smith R Richard , Spencer WC William C , Stinson EO E O , Taing S Scott , Takasaki T Teruaki , Vafeados D Dionne , Voronina K Ksenia , Wang G Guilin , Washington NL Nicole L , Whittle CM Christina M , Wu B Beijing , Yan KK Koon-Kiu , Zeller G Georg , Zha Z Zheng , Zhong M Mei , Zhou X Xingliang , , Ahringer J Julie , Strome S Susan , Gunsalus KC Kristin C , Micklem G Gos , Liu XS X Shirley , Reinke V Valerie , Kim SK Stuart K , Hillier LW LaDeana W , Henikoff S Steven , Piano F Fabio , Snyder M Michael , Stein L Lincoln , Lieb JD Jason D , Waterston RH Robert H . Science (New York, N.Y.). 2010 12 24; 330(6012). 1775-87

ABSTRACT

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.