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Abstract
The majority of eukaryotes use the enzyme telomerase to ensure that their chromosome ends are completely replicated. The core components of telomerase are the catalytic reverse transcriptase (TERT) and telomerase RNA (TR). The first part of this thesis describes a novel approach to predict the core secondary structure of telomerase RNAs, using TRFolder, a program we developed. With TRFolder, we confirmed and improved the previously studied TR structures in Kluyveromyces and Saccharomyces, and made novel structural predictions of core elements of the TRs from Schizosaccharomyces pombe, Candida albicans, and several other yeast species. In the second study, we showed that the presence of two types of telomeric repeats (A-repeat and C-repeat) in Candida tropicalis strain B-4414 was associated with the presence of a highly divergent allele of telomerase RNA gene TER1. To our knowledge, this is the first identification of a natural organism that has dimorphic telomeric repeats as a result of having two different telomerase RNA gene alleles. Our study also showed that the high degree of allelic sequence divergence was not confined to TER1 but included DNA sequences from across the genome. This striking high sequence divergence may suggest that mating or recombination can occur in this asexual diploid yeast. Together, the studies in this dissertation can help us to get a better understanding of the rapid evolution and functional maintenance of the telomerase RNA template and structure.