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. 2005 Nov;17(11):3155-75.
doi: 10.1105/tpc.105.035568. Epub 2005 Oct 7.

The Arabidopsis cold-responsive transcriptome and its regulation by ICE1

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The Arabidopsis cold-responsive transcriptome and its regulation by ICE1

Byeong-ha Lee et al. Plant Cell. 2005 Nov.

Abstract

To understand the gene network controlling tolerance to cold stress, we performed an Arabidopsis thaliana genome transcript expression profile using Affymetrix GeneChips that contain approximately 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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Figures

Figure 1.
Figure 1.
Venn Diagrams of Cold-Regulated Genes. Percentages in parentheses were calculated with the total numbers of cold-regulated genes (939). Figures in rectangles indicate cold treatment hours (h) and total number of cold-regulated genes at each time point.
Figure 2.
Figure 2.
RNA Gel Blot Analysis of Cold-Regulated Genes Selected from Microarray Analysis. Cold-responsive genes were tested by RNA gel blot analysis. For expression pattern comparisons, each corresponding gene transcript level was plotted using intensities from RNA gel blots and microarrays. The x axis shows time points during cold treatment (0°C), and y axis shows signal intensities in arbitrary units. Gene names and treatments for RNA gel blot pictures: (A) At3g11410 (protein phosphatase 2C, 0°C 24 h), (B) At4g38840 (SAUR, 0°C 6 h), and (C) At5g57560 (TCH4, 0°C 3 h). Tubulin was used as a loading control.
Figure 3.
Figure 3.
Quantification of DR5-GUS Activity during Cold Stress. GUS quantification is shown in pmol·4-MU/min/mg on the y axis during cold treatment (h, x axis) of DR5-GUS–expressing Arabidopsis.
Figure 4.
Figure 4.
RNA Gel Blot Analysis of Cold-Regulated Genes in the Wild Type and ice1. (A) At3g24520 (HSF1, 0°C 24 h). (B) At5g57560 (TCH4, 0°C 0 h). Tubulin was used as a loading control.

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