Mechanisms of Genome Stability Across Eukaryotes

Abstract

Instability of the overall structure and sequence of the genome can greatly impact the health and survival of organisms; therefore, the mechanisms that preserve the fidelity of genomes are highly conserved biological processes. This thesis presents investigations into the genome instability pathways in two evolutionarily distant eukaryotic organisms, Saccharomyces cerevisiae and Oxytricha trifallax. First, we produced a high-quality, annotated genome sequence of a widely-used laboratory strain, W303, for utilization in comparative analyses, and mutation accumulation or other genome-wide studies. We tested of the utility of this improved genome sequence by mapping mutations accumulated in mismatch repair defective strains onto the new reference and observed a significant decrease in false positives using standard mutation calling algorithms. Second, we examined two pathways that ensure the fidelity of genomes, mismatch repair and telomere maintenance. These repair mechanisms independently safeguard the fidelity of the genome; however, we explored how these pathways interact in Saccharomyces cerevisiae to ensure the maintenance of telomeres. Based on the data presented in this thesis, we propose that in the presence of critically short telomeres, mismatch repair functions to trigger a cell-cycle checkpoint important for the repair process. Third, we identified a gene family expansion of telomere end-binding proteins (TEBPs) specific to ciliates within the lineage of Oxytricha trifallax. TEBPs bind and cap the single-stranded G-rich tail of the telomeres, subsequently recruiting telomerase for repeat addition. We investigated the potential for both divergence and conservation of these canonical functions throughout the paralogs. In summary, similar to the early work in telomere biology, this thesis research examined mechanisms of genome stability across evolutionarily diverse eukaryotes to analyze conserved methods of maintaining chromosomal stability and sequence conservation.