Journal Article

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

Akihiro Matsui, Junko Ishida, Taeko Morosawa, Yoshiki Mochizuki, Eli Kaminuma, Takaho A. Endo, Masanori Okamoto, Eiji Nambara, Maiko Nakajima, Makiko Kawashima, Masakazu Satou, Jong-Myong Kim, Norio Kobayashi, Tetsuro Toyoda, Kazuo Shinozaki and Motoaki Seki

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 49, issue 8, pages 1135-1149
Published in print August 2008 | ISSN: 0032-0781
Published online July 2008 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcn101
Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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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

Journal Article.  9059 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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