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.
Yamada
Kayoko
K
Plant Gene Expression Center, Albany, CA 94710, USA.
Lim
Jun
J
Dale
Joseph M
JM
Chen
Huaming
H
Shinn
Paul
P
Palm
Curtis J
CJ
Southwick
Audrey M
AM
Wu
Hank C
HC
Kim
Christopher
C
Nguyen
Michelle
M
Pham
Paul
P
Cheuk
Rosa
R
Karlin-Newmann
George
G
Liu
Shirley X
SX
Lam
Bao
B
Sakano
Hitomi
H
Wu
Troy
T
Yu
Guixia
G
Miranda
Molly
M
Quach
Hong L
HL
Tripp
Matthew
M
Chang
Charlie H
CH
Lee
Jeong M
JM
Toriumi
Mitsue
M
Chan
Marie M H
MM
Tang
Carolyn C
CC
Onodera
Courtney S
CS
Deng
Justine M
JM
Akiyama
Kenji
K
Ansari
Yasser
Y
Arakawa
Takahiro
T
Banh
Jenny
J
Banno
Fumika
F
Bowser
Leah
L
Brooks
Shelise
S
Carninci
Piero
P
Chao
Qimin
Q
Choy
Nathan
N
Enju
Akiko
A
Goldsmith
Andrew D
AD
Gurjal
Mani
M
Hansen
Nancy F
NF
Hayashizaki
Yoshihide
Y
Johnson-Hopson
Chanda
C
Hsuan
Vickie W
VW
Iida
Kei
K
Karnes
Meagan
M
Khan
Shehnaz
S
Koesema
Eric
E
Ishida
Junko
J
Jiang
Paul X
PX
Jones
Ted
T
Kawai
Jun
J
Kamiya
Asako
A
Meyers
Cristina
C
Nakajima
Maiko
M
Narusaka
Mari
M
Seki
Motoaki
M
Sakurai
Tetsuya
T
Satou
Masakazu
M
Tamse
Racquel
R
Vaysberg
Maria
M
Wallender
Erika K
EK
Wong
Cecilia
C
Yamamura
Yuki
Y
Yuan
Shiaulou
S
Shinozaki
Kazuo
K
Davis
Ronald W
RW
Theologis
Athanasios
A
Ecker
Joseph R
JR
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