Identification of transcriptome dynamic patterns and their cognate cis-elements in defense genes in Arabidopsis
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Successful defense responses depend on the timely detection of pathogens and rapid transcriptional changes of defense genes. These transcriptional changes are mainly controlled by transcription factors binding to the regulatory regions of defense genes. To track these transcriptional changes and group these into a few related patterns, I analyzed the genome-wide expression profiles of Arabidopsis thaliana plants responding to Pseudomonas syringae infection at multiple times points. There are two distinct groups of defense genes rapidly upregulated or downregulated, reacting to Pseudomonas infection. I clustered these highly dynamical genes by their expression patterns into nine groups. I analyzed the gene ontology of each cluster and found that up-regulated clusters were mostly represented by traditional defense genes and down-regulated ones included a significant number of photosynthesis-related genes. Assessment of the promoter sequences also found that upregulated and downregulated clusters have distinct groups of cis-elements and their potential binding factors. In sum, my thesis research identified nine clusters with separable expression patterns and suggested a few candidate master regulators in transcriptional reprogramming associated with biotic stress in Arabidopsis.