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First published online October 7, 2005; 10.1105/tpc.105.035568

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The Plant Cell 17:3155-3175 (2005)
© 2005 American Society of Plant Biologists

The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1{boxw}

Byeong-ha Leea,1, David A. Hendersonb,2 and Jian-Kang Zhua,c,d,3

a Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721
b Department of Animal Science, University of Arizona, Tucson, Arizona 85721
c Institute for Integrative Genome Biology, University of California, Riverside, California 92521
d Department of Botany and Plant Sciences, University of California, Riverside, California 92521

3 To whom correspondence should be addressed. E-mail jian-kang.zhu{at}ucr.edu; fax 951-827-7115.

To understand the gene network controlling tolerance to cold stress, we performed an Arabidopsis thaliana genome transcript expression profile using Affymetrix GeneChips that contain ~24,000 genes. We statistically determined 939 cold-regulated genes with 655 upregulated and 284 downregulated. A large number of early cold-responsive genes encode transcription factors that likely control late-responsive genes, suggesting a multitude of transcriptional cascades. In addition, many genes involved in chromatin level and posttranscriptional regulation were also cold regulated, suggesting their involvement in cold-responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid, and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of the wild type and inducer of CBF expression 1 (ice1), a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1 and will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance.




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