| This study combines genetic and genomic approaches to study the interactions of light and carbon signaling and their role in the regulation of gene expression in Arabidopsis. Genome-wide analysis of the effects of light and carbon interactions on gene expression in mature plants and etiolated seedlings was carried out. A novel informatic approach to analyzing gene expression data from a limited number of gene chip experiments called InterAct class is described. By combining InterAct class analysis with a statistical analysis of gene function (MIPS analysis) biological processes were identified that were highly (or minimally) regulated by light and carbon signaling. This analysis was used to develop models to describe the intersection of light and carbon signaling found in vivo and revealed that genes involved in the processes metabolism, energy, protein synthesis, protein fate, and cell rescue, defense, and virulence were highly regulated by these two factors in mature plants. Analysis of etiolated seedlings further confirmed that metabolism, energy, and protein synthesis were biological processes that are highly regulated by light and carbon signaling at the level of gene expression. Further, candidate co-regulated genes were used to identify putative Light-and-Carbon-Responsive (LCR) cis-element motifs in promoters that were proposed to mediate regulation by light and carbon signaling. Two genetic screens were also conducted to isolate light and/or carbon signaling mutants in Arabidopsis. One mutant, cli186, isolated as a putative mutant impaired in the light and carbon regulation of the gene encoding asparagine synthetase (ASN1), is described herein. A genomic analysis of gene expression using microarrays on wildtype and cli186 mutant plants grown under various light and carbon treatments revealed how gene regulation by light and carbon signaling interactions were disrupted in this mutant. Specifically, the genes and processes that were disrupted in light and carbon signaling were identified in the cli186 mutant. This analysis revealed that metabolism and energy genes were over-represented among the subset of mis-regulated genes, including clusters of genes encoding proteins involved in photosynthesis, protein synthesis and fate, and potential regulatory factors. Potential cis-acting elements that may be involved in mediating light and carbon responsiveness were also identified. |
