Transcriptome Analysis in Abiotic Stress Conditions using Arabidopsis Whole Genome Tiling Array

Abstract

Plants respond and adapt to drought, cold and high-salinity stresses in order to survive. We have applied Arabidopsis Affymetrix tiling arrays to study the whole genome transcriptome under drought, cold, high-salinity stress and ABA treatment conditions. The tiling array experiments showed that 7,719 novel transcription units (TUs) exist in the Arabidopsis genome. These include 1,275 and 181 TUs that are induced and downregulated, respectively, by the stress- or ABA treatments. Most of the novel TUs are hypothetical non-coding RNAs and about 90% of them are mapped on the antisense strand of the AGI code genes. Interestingly, high correlation of the expression ratios (treated/untreated) was observed between AGI code genes and the novel TUs on the antisense strand. 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.