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A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during Seedling Development^1,[w]

Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China (Y.J., H.Y., T.L., Y.G., H.G., Z.C., L.-J.Q., X.W.D.); Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8014 (Y.J., L.M., Y.G., X.W.D.); Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520-8034 (N.S., H.Z.); Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114 (H. Yu, M.G.); and Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan (M.W.)

A microarray based on PCR amplicons of 1,864 confirmed and predicted Arabidopsis transcription factor genes was produced and used to profile the global expression pattern in seedlings, specifically their light regulation. We detected expression of 1,371 and 1,241 genes in white-light- and dark-grown 6-d-old seedlings, respectively. Together they account for 84% of the transcription factor genes examined. This array was further used to study the kinetics of transcription factor gene expression change of dark-grown seedlings in response to blue light and the role of specific photoreceptors in this blue-light regulation. The expression of about 20% of those transcription factor genes are responsive to blue-light exposure, with 249 and 115 genes up or down-regulated, respectively. A large portion of blue-light-responsive transcription factor genes exhibited very rapid expression changes in response to blue light, earlier than the bulk of blue-light-regulated genes. This result suggests the involvement of transcription cascades in blue-light control of genome expression. Comparative analysis of the expression profiles of wild type and various photoreceptor mutants demonstrated that during early seedling development cryptochromes are the major photoreceptors for blue-light control of transcription factor gene expression, whereas phytochrome A and phototropins play rather limited roles.

¹ This work was supported by the National Science Foundation of China (strategic international corporation project grant no. 30221120261), by the National Institutes of Health (grant no. GM–47850 to X.W.D.), and by the National Program for R&D of Transgenic Plants of China (grant no. J99–A–001). Y.J. is a recipient of Yale University Joseph F. Cullman, Jr. fellowship. L.M. is a long-term postdoctoral fellow of the Human Frontier Science Program.

^[w] The online version of this article contains Web-only data.

² These authors contributed equally to the paper.

^* Corresponding authors; e-mail xingwang.deng{at}yale.edu, fax 203–432–3854; e-mail qulj{at}lsc.pku.edu.cn, fax 86–10–6275–1841.

Received July 1, 2003; returned for revision August 4, 2003; accepted September 12, 2003.

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