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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #159460
Title: EMPIRICAL ANALYSIS OF TRANSCRIPTIONAL ACTIVITY IN THE ARABIDOPSIS GENOME

Author
item YAMADA, KAYOKO - ARS-UCB PLNT GENE EXP CTR
item LIM, JUN - SALK INST LA JOLLA CA
item DALE, JOSEPH - ARS-UCB PLNT GENE EXP CTR
item CHEN, HUAMING - SALK INST CA/U PA PHILA
item SHINN, PAUL - SALK INST CA/U PA PHILA
item PALM, CURTIS - STANFORD UNIV CA
item SOUTHWICK, AUDREY - STANFORD UNIV CA
item WU, HANK - ARS-UCB PLNT GENE EXP CTR
item KIM, CHRISTOPHER - SALK INST CA/U PA PHILA
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 CHANG, CHARLIE - ARS-UCB PLNT GENE EXP CTR
item LEE, JEONG - ARS-UCB PLNT GEN EXP CTR
item TORIUMI, MITSUE - ARS-UCB PLNT GENE EXP CTR
item CHAN, MARIE M H - ARS-UCB PLNT GENE EXP CTR
item TANG, CAROLYN - ARS-UCB PLNT GENE EXP CTR
item ONODERA, COURTNEY - ARS-UCB PLNT GENE EXP CTR
item DENG, JUSTINE - ARS-UCB PLNT GENE EXP CTR
item SHINOZAKI, KAZUO - RIKEN TSUKUBA JAPAN
item DAVIS, RONALD - STANDFORD UNIV CA
item Theologis, Athanasios
item ECKER, JOSEPH - SALK INST CA/U PA PHILA

Submitted to: Science Magazine
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2003
Publication Date: 8/1/2004
Citation: YAMADA, K., LIM, J., DALE, J.M., CHEN, H., SHINN, P., PALM, C.J., SOUTHWICK, A.M., WU, H.C., KIM, C., PHAM, P., LIU, S.X., SAKANO, H., YU, G., QUACH, H.L., CHANG, C.H., LEE, J.M., TORIUMI, M., CHAN, M., TANG, C.C., ONODERA, C.S., DENG, J.M., SHINOZAKI, K., DAVIS, R.W., THEOLOGIS, A., ECKER, J.R. EMPIRICAL ANALYSIS OF TRANSCRIPTIONAL ACTIVITY IN THE ARABIDOPSIS GENOME. SCIENCE MAGAZINE. 2003.YAMADA, K., LIM, J., DALE, J.M., CHEN, H., SHINN, P., PALM, C.J., SOUTHWICK, A.M., WU, H.C., KIM, C., LIU, S.X., SAKANO, H., YU, G., QUACH, H.L., CHANG, C.H., LEE, J.M., TORIUMI, M., CHAN, M., TANG, C.C., ONODERA, C.S., DENG, J.M.YAMADA, K., LIM, J., DALE, J.M., CHEN, H., SHINN, P., PALM, C.J., SOUTHWICK, A.M., WU, H.C., KIM, C., LIU, S.X., SHINOZAKI, K., DAVIS, R.W., THEOLOGIS, A., ECKER, J.R. EMPIRICAL ANALYSIS OF TRANSCRIPTIONAL ACTIVITY IN THE ARABIDOPSIS GENOME. SCIENCE MAGAZINE. 2004. V. 302, 5646:942-846.

Interpretive Summary: Functional analysis of a genome rquires 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.

Technical Abstract: Functional analysis of a genome rquires 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.