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

Plant J. 2009 Jun;58(6):1068-82. doi: 10.1111/j.1365-313X.2009.03835.x. Epub 2009 Feb 13.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscisic Acid / pharmacology
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Cold Temperature
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Plant
  • Genome, Plant*
  • Hot Temperature
  • Oligonucleotide Array Sequence Analysis / methods
  • RNA, Plant / genetics
  • Sodium Chloride / pharmacology
  • Stress, Physiological


  • Arabidopsis Proteins
  • RNA, Plant
  • Sodium Chloride
  • Abscisic Acid