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

Authors

  • Georg Zeller,

    1. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
    2. Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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    • These authors contributed equally to this work.

  • Stefan R. Henz,

    1. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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    • These authors contributed equally to this work.

  • Christian K. Widmer,

    1. Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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  • Timo Sachsenberg,

    1. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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  • Gunnar Rätsch,

    1. Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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  • Detlef Weigel,

    Corresponding author
    1. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
      *(fax +49 7071 601 1412; e-mail weigel@weigelworld.org, sascha.laubinger@tuebingen.mpg.de).
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  • Sascha Laubinger

    Corresponding author
    1. Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
      *(fax +49 7071 601 1412; e-mail weigel@weigelworld.org, sascha.laubinger@tuebingen.mpg.de).
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*(fax +49 7071 601 1412; e-mail weigel@weigelworld.org, sascha.laubinger@tuebingen.mpg.de).

Summary

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.

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