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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #157757
Title: EMPIRICAL ANALYSIS OF TRANSCIRPTIONAL ACTIVITY IN THE ARABIDOPSIS GENOME

Author
item YAMADA, KAYOKO - ARS-UCB PLNT GENE EXP CTR
item LIM, JUN - SALK INSTITUTE BIOL
item DALE, JOSEPH - ARS-UCB PLNT GENE EXP CTR
item CHEN, HAUMING - SALK INST/UNIV PA
item SHINN, PAUL - SALK INST/UNIV PA
item PALM, CURTIS - STANFORD GENOME TECH
item WU, HANK - ARS-UCB PLNT GENE EXP CTR
item PHAM, PAUL - ARS-UCB PLNT GENE EXP CTR
item LIU, SHIRLEY - ARS-UCB PLNT GENE EXP CTR
item SAKANO, HITOMI - ARS-UCB PLNT GENE EXP CTR
item YU, GUIXIA - ARS-UCB PLNT GENE EXP CTR
item QUACH, HONG - ARS-UCB PLNT GENE EXP CTR
item AKIYAMA, KENJI - RIKEN TSUKUBA JAPAN
item ARAKAWA, TAKAHIRO - RIKEN KANAGAWA JAPAN
item CARNINCI, PEIRO - RIKEN WAKO/KANAGAWA
item SEKI, MOTOAKI - RIKEN TSUKUBA JAPAN
item DAVIS, RONALD - STANFORD UNIV
item Theologis, Athanasios
item ECKER, JOSEPH - SALK INST/UNIV PA

Submitted to: Science Magazine
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2003
Publication Date: 10/31/2003
Citation: YAMADA, K., LIM, J., DALE, J., CHEN, H., SHINN, P., PALM, C.J., WU, H.C., PHAM, P., LIU, S.X., SAKANO, H., YU, G., QUACH, H.L., AKIYAMA, K., ARAKAWA, T., CARNINCI, P., SEKI, M., DAVIS, R.W., THEOLOGIS, A., ECKER, J.R. EMPIRICAL ANALYSIS OF TRANSCIRPTIONAL ACTIVITY IN THE ARABIDOPSIS GENOME. SCIENCE MAGAZINE. 2003. 302(5646):842-6.

Interpretive Summary: Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. 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.

Technical 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.