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Science 31 October 2003:
Vol. 302. no. 5646, pp. 842 - 846
DOI: 10.1126/science.1088305
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Research Articles

Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome

Kayoko Yamada,1* Jun Lim,2* Joseph M. Dale,1 Huaming Chen,2,3 Paul Shinn,2,3 Curtis J. Palm,4 Audrey M. Southwick,4 Hank C. Wu,1 Christopher Kim,2,3 Michelle Nguyen,4 Paul Pham,1 Rosa Cheuk,2,3 George Karlin-Newmann,4 Shirley X. Liu,1 Bao Lam,4 Hitomi Sakano,1 Troy Wu,4 Guixia Yu,1 Molly Miranda,4 Hong L. Quach,1 Matthew Tripp,4 Charlie H. Chang,1 Jeong M. Lee,1 Mitsue Toriumi,1 Marie M. H. Chan,1 Carolyn C. Tang,1 Courtney S. Onodera,1 Justine M. Deng,1 Kenji Akiyama,5 Yasser Ansari,2 Takahiro Arakawa,6 Jenny Banh,1 Fumika Banno,1 Leah Bowser,4 Shelise Brooks,3 Piero Carninci,6,7 Qimin Chao,3 Nathan Choy,2 Akiko Enju,5 Andrew D. Goldsmith,1 Mani Gurjal,4 Nancy F. Hansen,4 Yoshihide Hayashizaki,6,7 Chanda Johnson-Hopson,3 Vickie W. Hsuan,1 Kei Iida,5 Meagan Karnes,2 Shehnaz Khan,3 Eric Koesema,2 Junko Ishida,5 Paul X. Jiang,1 Ted Jones,4 Jun Kawai,6,7 Asako Kamiya,5 Cristina Meyers,2 Maiko Nakajima,5 Mari Narusaka,5 Motoaki Seki,5,8 Tetsuya Sakurai,5 Masakazu Satou,5 Racquel Tamse,4 Maria Vaysberg,1 Erika K. Wallender,1 Cecilia Wong,1 Yuki Yamamura,1 Shiaulou Yuan,1 Kazuo Shinozaki,5,8 Ronald W. Davis,4,9 Athanasios Theologis,1*{dagger} Joseph R. Ecker2,3*{dagger}

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of ~30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

1 Plant Gene Expression Center, Albany, CA 94710, USA.
2 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
3 The Arabidopsis thaliana Genome Center, Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
4 Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
5 Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Tsukuba 305-0074, Japan.
6 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Wako 351-0198, Japan.
7 Laboratory for Genome Exploration Research Group, RIKEN GSC, Yokohama Institute, Kanagawa 230-0045, Japan.
8 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan.
9 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.



* These authors contributed equally to this manuscript.

{dagger} To whom correspondence should be addressed. E-mail: theo{at}nature.berkeley.edu (A.T.) or ecker{at}salk.edu (J.R.E.)

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   Abstract »    Full Text »    PDF »
Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway..
M. P. Samanta, W. Tongprasit, H. Sethi, C.-S. Chin, and V. Stolc (2006)
PNAS 103, 4192-4197
   Abstract »    Full Text »    PDF »
SUGAR-DEPENDENT1 Encodes a Patatin Domain Triacylglycerol Lipase That Initiates Storage Oil Breakdown in Germinating Arabidopsis Seeds.
P. J. Eastmond (2006)
PLANT CELL 18, 665-675
   Abstract »    Full Text »    PDF »
TOPAAS, a Tomato and Potato Assembly Assistance System for Selection and Finishing of Bacterial Artificial Chromosomes.
S. A. Peters, J. C. van Haarst, T. P. Jesse, D. Woltinge, K. Jansen, T. Hesselink, M. J. van Staveren, M. H.C. Abma-Henkens, and R. M. Klein-Lankhorst (2006)
Plant Physiology 140, 805-817
   Abstract »    Full Text »    PDF »
Design optimization methods for genomic DNA tiling arrays.
P. Bertone, V. Trifonov, J. S. Rozowsky, F. Schubert, O. Emanuelsson, J. Karro, M.-Y. Kao, M. Snyder, and M. Gerstein (2006)
Genome Res. 16, 271-281
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Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression.
W. Deng, X. Zhu, G. Skogerbo, Y. Zhao, Z. Fu, Y. Wang, H. He, L. Cai, H. Sun, C. Liu, et al. (2006)
Genome Res. 16, 20-29
   Abstract »    Full Text »    PDF »
Whole-Genome Microarray in Arabidopsis Facilitates Global Analysis of Retained Introns.
H. Ner-Gaon and R. Fluhr (2006)
DNA Res 13, 111-121
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Whole-Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus.
P. Hu, E. L. Brodie, Y. Suzuki, H. H. McAdams, and G. L. Andersen (2005)
J. Bacteriol. 187, 8437-8449
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The Arabidopsis genome: A foundation for plant research.
M. Bevan and S. Walsh (2005)
Genome Res. 15, 1632-1642
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Identification and Functional Characterization of Arabidopsis PEROXIN4 and the Interacting Protein PEROXIN22.
B. K. Zolman, M. Monroe-Augustus, I. D. Silva, and B. Bartel (2005)
PLANT CELL 17, 3422-3435
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