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Plant and Cell Physiology Advance Access originally published online on July 13, 2008
Plant and Cell Physiology 2008 49(8):1135-1149; doi:10.1093/pcp/pcn101
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Rapid paper

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

Akihiro Matsui1, Junko Ishida1, Taeko Morosawa1, Yoshiki Mochizuki2, Eli Kaminuma2, Takaho A. Endo2, Masanori Okamoto1, Eiji Nambara3, Maiko Nakajima1, Makiko Kawashima1, Masakazu Satou1, Jong-Myong Kim1, Norio Kobayashi2, Tetsuro Toyoda2, Kazuo Shinozaki4 and Motoaki Seki1,5,*

1Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
2Bioinformatics and Systems Engineering Division, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
3Dormancy and Adaptation Research Team, Growth Regulation Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
4Gene Discovery Research Team, Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan
5Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan

*Corresponding author: E-mail, mseki{at}psc.riken.jp; Fax, +81-45-503-9586.


  Abstract

Plants respond and adapt to drought, cold and high-salinity stresses in order to survive. In this study, we applied Arabidopsis Affymetrix tiling arrays to study the whole genome transcriptome under drought, cold, high-salinity and ABA treatment conditions. The bioinformatic analysis using the tiling array data showed that 7,719 non-AGI transcriptional units (TUs) exist in the unannotated "intergenic" regions of Arabidopsis genome. These include 1,275 and 181 TUs that are induced and downregulated, respectively, by the stress or ABA treatments. Most of the non-AGI TUs are hypothetical non-protein-coding RNAs. About 80% of the non-AGI TUs belong to pairs of the fully overlapping sense-antisense transcripts (fSATs). Significant linear correlation between the expression ratios (treated/untreated) of the sense TUs and the ratios of the antisense TUs was observed in the SATs of AGI code/non-AGI TU. We studied the biogenesis mechanisms of the stress- or ABA-inducible antisense RNAs and found that the expression of sense TUs is necessary for the stress- or ABA-inducible expression of the antisense TUs in the fSATs (AGI code/non-AGI TU).

Keywords: Abiotic stress - Antisense RNA - Arabidopsis - Non-protein-coding RNA - Tiling array

Abbreviations: ARTADE, Arabidopsis tiling array-based detection of exons; fSAT, fully-overlapping sense-antisense transcript; HLE, Hodges-Lehmann estimator; PASR, promoter-associated short RNA; pSAT, partially-overlapping sense-antisense transcript; RD, responsive to dehydration; SAT, sense-antisense transcript; TAIR, the Arabidopsis information resource; TASR, termini-associated short RNA; TU, transcriptional unit.

(Received June 24, 2008; Accepted July 8, 2008)
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