"Trypanosoma brucei is a single celled eukaryote that utilizes a complex RNA editing system to render many of its mitochondrial genes translatable. Editing of these genes requires multiple small RNAs called guide RNAs to direct the insertion and deletion of uridines. These gRNAs act sequentially, each generating the anchor binding site for the next gRNA. This sequential dependence should render the process quite fragile, and mutations in the gRNAs should not be tolerated. In the examination of the gRNA transcriptome of T. brucei, many gRNAs were identified that are capable of generating alternative mRNA sequences, and potentially disrupting the editing process. In this work, the effects of alternative editing are characterized. This analysis revealed the role of gRNAs in developmental regulation of gene expression, showing a correlation between the abundance of the initiating gRNAs across two different points in the life cycle of T. brucei and their expression. This study also revealed the existence of mitochondrial dual-coding genes, which provide protection for genetic material that is not under selection at all points of the life cycle of T. brucei. The examination of these dual-coding genes showed that RNA editing patterns can shift between cell lines and under different energetic conditions. Examining the gRNAs involved in these editing pathways revealed that there is a high amount of mismatching base pairs that are tolerated for editing to function, and that gRNA abundance is not a reliable predictor for editing preference. Finally, a reexamination of the gRNA transcriptome revealed that many gRNAs are still unidentified and most likely are generating new alternatively edited sequences."--Pages ii-iii.
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