Genome-wide analysis of gene expression and regulation is important for elucidating basic principles of how cells function. In addition to gene expression, this dissertation will also discuss two methods of RNA-mediated RNA regulation: mRNA splicing and microRNAs. Three projects investigating gene expression and regulation using the Illumina platform are discussed here. The first project describes mRNA expression analysis of dozens of genes on the mating locus of the multicellular green alga, Volvox carteri in both the male and female mating types. The analysis describes sex-specific genes for both male and female mating types, and reveals the evolutionary history of the locus. The second project describes very low frequency splice products in a unicellular fungus with a fairly simple splicing landscape, Saccharomyces cerevisiae. These extremely rare splice events shed light on the mechanism of selecting splice sites in eukaryotic organisms. The third project describes an algorithm for predicting novel candidate microRNAs from small RNA sequence data. We describe a Naive Bayes Classifier to differentiate microRNAs from contaminants and provide experimental validation of top candidates.
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