title: Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array.
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).
authors.affiliation: Plant 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.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsui
authors.forename: Junko
authors.initials: J
authors.lastname: Ishida
authors.forename: Taeko
authors.initials: T
authors.lastname: Morosawa
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Eli
authors.initials: E
authors.lastname: Kaminuma
authors.forename: Takaho A
authors.initials: TA
authors.lastname: Endo
authors.forename: Masanori
authors.initials: M
authors.lastname: Okamoto
authors.forename: Eiji
authors.initials: E
authors.lastname: Nambara
authors.forename: Maiko
authors.initials: M
authors.lastname: Nakajima
authors.forename: Makiko
authors.initials: M
authors.lastname: Kawashima
authors.forename: Masakazu
authors.initials: M
authors.lastname: Satou
authors.forename: Jong-Myong
authors.initials: JM
authors.lastname: Kim
authors.forename: Norio
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology*; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D003080:Cold Temperature; D015536:Down-Regulation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D040081:Protein Array Analysis; D012965:Sodium Chloride / Q000494:pharmacology*; D015854:Up-Regulation; D014867:Water / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D014867:Water; D012965:Sodium Chloride; D000040:Abscisic Acid