Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array.
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).
Matsui
Akihiro
A
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.
Ishida
Junko
J
Morosawa
Taeko
T
Mochizuki
Yoshiki
Y
Kaminuma
Eli
E
Endo
Takaho A
TA
Okamoto
Masanori
M
Nambara
Eiji
E
Nakajima
Maiko
M
Kawashima
Makiko
M
Satou
Masakazu
M
Kim
Jong-Myong
JM
Kobayashi
Norio
N
Toyoda
Tetsuro
T
Shinozaki
Kazuo
K
Seki
Motoaki
M
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*
D029681:Arabidopsis Proteins; D014867:Water; D012965:Sodium Chloride; D000040:Abscisic Acid