Fig. 4. Comparison of the morphogenic patterns and genome expression profiles of Arabidopsis seedlings grown under different light intensity conditions. (A) Phenotype of different intensity white light-grown wild-type seedlings. The seedlings were grown under 1.5 (1.5), 15 (15) or 150 (150) µmol/m²/second continuous white light or in the dark (D) for 6 days, or under 150 µmol/m²/second continuous white light for 5.5 days, then transferred to 2500 µmol/m²/second continuous white light for another 12 hours (2500). Seedlings were photographed at the same magnification. (B) An overview of the hierarchical cluster display of the genome expression profiles for all these different intensity light- and dark-grown wild-type sample pairs is shown in A. The dark-grown det1-6 or cop1-8 and wild-type sample pairs were used for comparison. Lane 1, 1.5 µmol/m²second white light- and dark-grown wild-type seedlings; lane 2, 15 µmol/m²second white light- and dark-grown wild-type seedlings; lane 3, 150 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 4, 2500 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 5, dark-grown det1-6 and wild-type seedlings; lane 6, dark-grown cop1-8 and wild-type seedlings. Only those genes that exhibited twofold or more differential expression in at least one sample pair of the six pairs examined were included for comparison. 2614 genes were included in the cluster analysis (see supplementary data at http://dev.biologists.org/supplemental/ or http://plantgenomics.biology.yale.edu/ for detail). (C) The number of differentially regulated genes by distinct light intensities and different alleles of COP1, in comparison with oppositely regulated genes in each case. Lane 1, 1.5 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 2, 15 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 3, normal 150 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 4, 2500 µmol/m²/second white light- and dark-grown wild-type seedlings; lane 5, dark-grown cop1-6 and wild-type seedlings; lane 6, dark-grown cop1-1 and wild-type seedlings; lane 7, dark-grown cop1-8 and wild-type seedlings. Only those genes that exhibited twofold or more differential expression in each sample pair and showed opposite regulation toward normal light regulation were selected as oppositely regulated genes.

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