Empirical Analysis of Transcriptional Activity in the <i>Arabidopsis</i> Genome
Kayoko Yamada(Salk Institute for Biological Studies), Jun Lim(Salk Institute for Biological Studies), Joseph M. Dale(Salk Institute for Biological Studies), Huaming Chen(Salk Institute for Biological Studies), Paul Shinn(Salk Institute for Biological Studies), Curtis Palm(Salk Institute for Biological Studies), Audrey M. Southwick(Salk Institute for Biological Studies), Hank Wu(Salk Institute for Biological Studies), Christopher Kim(Salk Institute for Biological Studies), Michelle Nguyen(Salk Institute for Biological Studies), Paul K. Pham(Salk Institute for Biological Studies), Rosa Cheuk(Salk Institute for Biological Studies), George Karlin-Newmann(Salk Institute for Biological Studies), Shirley X. Liu(Salk Institute for Biological Studies), Bao Lam(Salk Institute for Biological Studies), Hitomi Sakano(Salk Institute for Biological Studies), Troy Wu(Salk Institute for Biological Studies), Guixia Yu(Salk Institute for Biological Studies), Molly Miranda(Salk Institute for Biological Studies), Hong Quach(Salk Institute for Biological Studies), Matthew L. Tripp(Salk Institute for Biological Studies), Charlie H. Chang(Salk Institute for Biological Studies), Jeong Min Lee(Salk Institute for Biological Studies), Mitsue J. Toriumi(Salk Institute for Biological Studies), Marie M. H. Chan(Salk Institute for Biological Studies), Carolyn C. Tang(Salk Institute for Biological Studies), Courtney Onodera(Salk Institute for Biological Studies), Justine M. Deng(Salk Institute for Biological Studies), Kenji Akiyama(Salk Institute for Biological Studies), Yasser Ansari(Salk Institute for Biological Studies), Takahiro Arakawa(Wako University), Jenny Banh(Salk Institute for Biological Studies), Fumika Banno(Salk Institute for Biological Studies), Leah Bowser(Salk Institute for Biological Studies), Shelise Brooks(Salk Institute for Biological Studies), Piero Carninci(Wako University), Qimin Chao(Salk Institute for Biological Studies), Nathan Choy(Salk Institute for Biological Studies), Akiko Enju(Salk Institute for Biological Studies), Andrew D. Goldsmith(Salk Institute for Biological Studies), Mani Gurjal(Salk Institute for Biological Studies), Nancy F. Hansen(Salk Institute for Biological Studies), Yoshihide Hayashizaki(Wako University), Chanda Johnson-Hopson(Salk Institute for Biological Studies), Vickie Hsuan(Salk Institute for Biological Studies), Kei Iida(Salk Institute for Biological Studies), Meagan Karnes(Salk Institute for Biological Studies), Shehnaz Khan(Salk Institute for Biological Studies), Eric Koesema(Salk Institute for Biological Studies), Junko Ishida(Salk Institute for Biological Studies), Paul X. Jiang(Salk Institute for Biological Studies), Ted Jones(Salk Institute for Biological Studies), Jun Kawai(Wako University), Asako Kamiya(Salk Institute for Biological Studies), Cristina C. Meyers(Salk Institute for Biological Studies), Maiko Nakajima(Salk Institute for Biological Studies), Mari Narusaka(Salk Institute for Biological Studies), Motoaki Seki(Salk Institute for Biological Studies), Tetsuya Sakurai(Salk Institute for Biological Studies), Masakazu Satou(Salk Institute for Biological Studies), Racquel Tamse(Salk Institute for Biological Studies), Maria Vaysberg(Salk Institute for Biological Studies), Erika K. Wallender(Salk Institute for Biological Studies), Cecilia Wong(Salk Institute for Biological Studies), Yuki Yamamura(Salk Institute for Biological Studies), Shiaulou Yuan(Salk Institute for Biological Studies), Kazuo Shinozaki(Salk Institute for Biological Studies), Ronald W. Davis(Salk Institute for Biological Studies), Athanasios Theologis(Salk Institute for Biological Studies), Joseph R. Ecker(Salk Institute for Biological Studies)
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Abstract
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 approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.