Illuminating the gene regulation underlying meiotic differentiation

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ABSTRACT Meiosis is the conserved differentiation program that is responsible for gamete formation. As a cell progress through meiotic differentiation, it undergoes unidirectional changes in cellular structure and function that are largely driven by gene expression changes. Because the molecular basis for most meiotic transitions remains mysterious, my lab aims to illuminate the gene regulatory circuitry that programs meiotic differentiation. We use budding yeast to study this process because well studied meiotic factors are highly conserved and because this organism uniquely offers access to the large number of highly synchronous cells that is key to genomic approaches that we routinely employ. Our studies have enabled identification of proteins involved in key meiotic processes, and new regulatory events during meiosis. These studies have also uncovered major surprises in the genes that meiotic cells express and how they regulate these genes. Among these surprises, we found an unconventional mode of gene regulation, involving regulated toggling between a translatable mRNA isoform and one that is 5’ extended and poorly translated, to be commonly used to drive meiotic protein levels over time. We have found this mode of regulation to be important in meiosis but also in other conditions, and a major focus of our research is to better understand how it works. Although we know that upstream open reading frames (uORFs) are responsible for repressed ORF translation on some extended mRNA isoforms, we do not know why this is not true of all cases. We will address this question using reporter experiments, and analysis of mRNA structures and sequences of repressed versus non-repressed transcripts. We also do not understand how mRNA degradation impacts this regulation and meiotic gene expression more broadly, which we will study using new metabolic labeling approaches. Beyond unconventional regulation of known genes, we also discovered that meiotic cells translate many genes were not previously identified. These include hundreds of genes that are translated starting with non-AUG codons, and thousands that are shorter than the 100 codon cutoff that was used to annotate genomes. We have validated the expression of these non-canonical proteins and are now studying the molecular mechanisms underlying their synthesis and their specific cellular roles. We are investigating why non-AUG translation initiation is common in meiosis, primarily using study of candidate regulatory factors that we have identified. We are performing pooled screens to identify roles for the many short meiotic proteins, and directed study of cases in which the short proteins include domains of characterized proteins. Together the projects proposed here will explain how and why meiotic cells employ non-canonical gene regulatory features, which we believe is critical to unraveling the molecular control of meiotic progression.