Antisense transcripts with rice full-length cDNAs.
BACKGROUND
Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs.


RESULTS
We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86%) had coding potential.


CONCLUSIONS
The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts.
Osato
Naoki
N
Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045.
Yamada
Hitomi
H
Satoh
Kouji
K
Ooka
Hisako
H
Yamamoto
Makoto
M
Suzuki
Kohji
K
Kawai
Jun
J
Carninci
Piero
P
Ohtomo
Yasuhiro
Y
Murakami
Kazuo
K
Matsubara
Kenichi
K
Kikuchi
Shoshi
S
Hayashizaki
Yoshihide
Y
D016373:DNA, Antisense / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D018076:DNA, Complementary / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000145:classification / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012275:Oryza / Q000235:genetics*; D034622:RNA Interference / Q000502:physiology; D016372:RNA, Antisense / Q000145:classification / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000145:classification / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry / Q000145:classification / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic / Q000502:physiology
D016373:DNA, Antisense; D018076:DNA, Complementary; D018744:DNA, Plant; D016372:RNA, Antisense; D012333:RNA, Messenger; D018749:RNA, Plant