| Transcriptional regulation is a fundamental issue in plant biology. With the availability of completed sequenced genomes and tools for large-scale analysis of gene transcription, such as DNA microarrays, the dynamics of transcriptomes and their developmental regulation are being revealed. In this dissertation, I focused my research primarily on genome-wide analysis of the transcriptome in rice and Arabidopsis, with special interest on light-regulation. First, I investigated blue light regulation of Arabidopsis transcription factor gene expression. Studies of various photoreceptor mutants revealed the predomiant role of cryptochromes in blue light control of genome transcription. Second, I compared light-regulated genome expression in rice and Arabidopsis and found a higher correlation of expression in light than in darkness. Organ-specific expression profiles provide evidence for divergent light effects in different organs with specific light-responsive promoter cis-elements involved. Next, I used a tiling microarray to analyze the transcription of rice chromosome 4. This analysis provided expression support for most of the gene models, detected transcriptional activities in nonannotated regions, and identified correlation between transcriptional activity and chromosome organization. Further, I examined transcriptional activities of selected rice transposon-related genes. Expression was detected and actively transcribed clades were identified, supporting potential adapted host function or active expression (and possible transposition). Finally, I participated in the construction and analysis of RICEATLAS, a cellular transcriptional atlas of rice. My research significantly advanced our knowledge of the genome expression and their regulation in the two plant model species with their genome complete sequenced. |
