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Phosphoproteomic Strategy for Profiling Osmotic Stress Signaling in Arabidopsis
Published on: June 25, 2020
Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling
Akihiro Matsui1, Junko Ishida, Taeko Morosawa
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.
Plant & Cell Physiology
|July 16, 2008
Summary
Plants adapt to stress using novel RNA molecules. This study identified thousands of new transcriptional units (TUs) in Arabidopsis, many involved in stress responses and overlapping sense-antisense transcripts (fSATs).
Area of Science:
- Plant Molecular Biology
- Genomics
- Transcriptomics
Background:
- Plants possess complex mechanisms to survive environmental stresses like drought, cold, and high salinity.
- Understanding the full spectrum of gene expression, including non-coding RNAs, is crucial for deciphering stress adaptation.
Purpose of the Study:
- To comprehensively analyze the Arabidopsis thaliana whole-genome transcriptome under various stress conditions (drought, cold, high salinity) and abscisic acid (ABA) treatment.
- To identify and characterize novel transcriptional units (TUs) in previously unannotated genomic regions.
Main Methods:
- Application of Arabidopsis Affymetrix tiling arrays for high-resolution transcriptome profiling.
- Bioinformatic analysis of tiling array data to identify non-AGI TUs and their expression patterns.
- Investigation of the relationship between sense and antisense transcripts, particularly fully overlapping sense-antisense transcripts (fSATs).
Main Results:
- Discovery of 7,719 non-AGI TUs in Arabidopsis intergenic regions.
- Identification of 1,275 stress- or ABA-inducible and 181 downregulated non-AGI TUs.
- Observation that approximately 80% of non-AGI TUs are part of fSATs, with a significant correlation between sense and antisense transcript expression.
- Demonstration that sense TU expression is required for the stress- or ABA-inducible expression of antisense TUs within fSATs.
Conclusions:
- The Arabidopsis genome contains a substantial number of unannotated transcriptional units, many of which are non-protein-coding RNAs.
- These novel TUs, particularly fSATs, play a significant role in the plant's response to abiotic stress and ABA signaling.
- The study elucidates a regulatory mechanism where sense TU expression is essential for the induction of stress-responsive antisense TUs.
