Defining non-canonical modes of gene regulation in budding yeast meiosis

Gene regulation in budding yeast meiosis is incredibly complex, involving a number of non-canonical strategies. Defining the different modes of regulation is key to fully understanding how the cell functions, especially under changing conditions. Here, we examined two non-canonical gene regulation strategies employed by yeast during meiosis: alternative translation initiation and regulated turnover of ribosomal proteins.In chapter two, we investigated the role of alternative translation initiation site choice in yeast. Genomic analyses in budding yeast have helped define the foundational principles of eukaryotic gene expression. However, in the absence of empirical methods for defining coding regions, these analyses have historically excluded specific classes of possible coding regions, such as those initiating at non-AUG start codons. We applied an experimental approach to globally annotate translation initiation sites in yeast and identified 149 genes with alternative N-terminally extended protein isoforms initiating from near-cognate codons upstream of annotated AUG start codons. These isoforms are produced in concert with canonical isoforms and translated with high specificity, resulting from initiation at only a small subset of possible start codons. The non-AUG initiation driving their production is enriched during meiosis and induced by low eIF5A, which is seen in this context. These findings reveal widespread production of non-canonical protein isoforms and unexpected complexity to the rules by which even a simple eukaryotic genome is decoded.In chapter three, we evaluated the role of protein degradation during yeast meiosis, and found that ribosomes are degraded and resynthesized in spores, revealing an interesting mode of regulation of an important molecular machine. Protein degradation is known to be a key component of expression regulation for individual genes, but its global impact on gene expression has been difficult to determine. We analyzed a parallel gene expression dataset of yeast meiotic differentiation, identifying instances of coordinated protein-level decreases to identify new cases of regulated meiotic protein degradation, including degradation of ribosomes. Comparison of protein and translation measurements over time revealed that ribosomes are degraded and resynthesized in spores, making the biological purpose of ribosome resetting an interesting area of follow-up