Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays

• Published in: The Plant journal : for cell and molecular biology Vol. 58; no. 6; pp. 1068 - 1082
• Main Authors: Zeller, Georg, Henz, Stefan R, Widmer, Christian K, Sachsenberg, Timo, Rätsch, Gunnar, Weigel, Detlef, Laubinger, Sascha
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01-06-2009; Blackwell Publishing Ltd; Blackwell
• Subjects: ABA; abiotic stress; Abscisic Acid - pharmacology; Acids; Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; At-TAX; Biological and medical sciences; Botany; Classical genetics, quantitative genetics, hybrids; Cold Temperature; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Regulation, Plant; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Genomics; Hot Temperature; Oligonucleotide Array Sequence Analysis - methods; Pteridophyta, spermatophyta; Research methodology; RNA, Plant - genetics; Sodium Chloride - pharmacology; Stress; Stress, Physiological; tiling array; Vegetals; ABA; tiling array; Arabidopsis; DNA chip; Transcriptome; Stress; abiotic stress; Arabidopsis thaliana; At-TAX; Cruciferae; Dicotyledones; Angiospermae; Plant growth substance; Spermatophyta; Genome; Overlapping oligonucleotides
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313x.2009.03835.x

The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.