Empirical analysis of transcriptional activity in the Arabidopsis genome.
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.
Plant Gene Expression Center, Albany, CA 94710, USA.
Kayoko
K
Yamada
Jun
J
Lim
Joseph M
JM
Dale
Huaming
H
Chen
Paul
P
Shinn
Curtis J
CJ
Palm
Audrey M
AM
Southwick
Hank C
HC
Wu
Christopher
C
Kim
Michelle
M
Nguyen
Paul
P
Pham
Rosa
R
Cheuk
George
G
Karlin-Newmann
Shirley X
SX
Liu
Bao
B
Lam
Hitomi
H
Sakano
Troy
T
Wu
Guixia
G
Yu
Molly
M
Miranda
Hong L
HL
Quach
Matthew
M
Tripp
Charlie H
CH
Chang
Jeong M
JM
Lee
Mitsue
M
Toriumi
Marie M H
MM
Chan
Carolyn C
CC
Tang
Courtney S
CS
Onodera
Justine M
JM
Deng
Kenji
K
Akiyama
Yasser
Y
Ansari
Takahiro
T
Arakawa
Jenny
J
Banh
Fumika
F
Banno
Leah
L
Bowser
Shelise
S
Brooks
Piero
P
Carninci
Qimin
Q
Chao
Nathan
N
Choy
Akiko
A
Enju
Andrew D
AD
Goldsmith
Mani
M
Gurjal
Nancy F
NF
Hansen
Yoshihide
Y
Hayashizaki
Chanda
C
Johnson-Hopson
Vickie W
VW
Hsuan
Kei
K
Iida
Meagan
M
Karnes
Shehnaz
S
Khan
Eric
E
Koesema
Junko
J
Ishida
Paul X
PX
Jiang
Ted
T
Jones
Jun
J
Kawai
Asako
A
Kamiya
Cristina
C
Meyers
Maiko
M
Nakajima
Mari
M
Narusaka
Motoaki
M
Seki
Tetsuya
T
Sakurai
Masakazu
M
Satou
Racquel
R
Tamse
Maria
M
Vaysberg
Erika K
EK
Wallender
Cecilia
C
Wong
Yuki
Y
Yamamura
Shiaulou
S
Yuan
Kazuo
K
Shinozaki
Ronald W
RW
Davis
Athanasios
A
Theologis
Joseph R
JR
Ecker
D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D021901:DNA, Intergenic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
D018076:DNA, Complementary; D021901:DNA, Intergenic; D012333:RNA, Messenger; D018749:RNA, Plant