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UBC Theses and Dissertations

The conserved role of RNA splicing factors in genome maintenance Tam, Annie S.


RNA splicing mutants have been broadly implicated in genome stability, but mechanistic links are often unclear. Two predominant models have emerged: one involving changes in gene expression that perturb other genome maintenance factors and another in which genotoxic DNA:RNA hybrids, called R-loops, impair DNA replication. Recent efforts in whole genome sequencing have identified splicing factor mutations in several cancers, suggesting that splicing disruption may be a common mechanism involved in oncogenesis. To understand how splicing factor mutations contribute to genetic instability (GIN) in budding yeast, I selected strains with mutations in core snRNP complexes involved in establishing the splicing reaction and characterized GIN phenotypes to find that mitotic defects, and in some cases R-loop accumulation, are causes of GIN. I observed evidence of R-loop induced DNA damage in some cases, while all splicing mutants tested caused GIN through aberrant splicing of the TUB1 transcript, the protein product of which, α-tubulin, is critical in forming the mitotic spindle. GIN is exacerbated by loss of the spindle-assembly checkpoint protein Mad1, and moreover, removal of the intron from the α-tubulin gene TUB1 restores genome integrity. To gain functional insights to how HSH155 could influence GIN in the context of cancer progression, I studied five cancer-associated SF3B1 point mutations in the yeast ortholog HSH155. While the splicing activity in Hsh155 and SF3B1 were conserved, I did not observe measurable phenotypes in the yeast mutant strains. Thus, I used isogenic NALM6 human leukemia cell lines to investigate how a specific SF3B1 hotspot mutation, H662Q contributes to GIN. My data indicate that GIN occurs in two ways: 1) by induction of R-loop-mediated replication stress either directly or indirectly through suboptimal expression of an R-loop modulating factor, and 2) aberrant splicing of the multifunctional protein DYNLL1, which may potentially perturb double strand break repair pathway choice. The results of my study show how differing penetrance and selective effects on the transcriptome in yeast and human splicing factors contribute to GIN through R-loop accumulation and altered gene expression, adding to a growing body of evidence that splicing factors play a key role in genome maintenance across species.

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