Illuminating the gene regulatory strategies underlying yeast meiosis and beyond

Abstract. Meiosis is the conserved differentiation program that creates gametes. It fails frequently, with devastating consequences for human fertility and health. As a cell progress through meiotic differentiation, it undergoes irreversible 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 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 uncovered major surprises in the genes that meiotic cells express and how they regulate these genes, revealing big gaps in our fundamental understanding of how gene expression works in meiosis, and beyond. These findings have led us to believe that meiosis is a valuable model for identifying and interrogating such broad open questions in gene regulation. Among the surprises we found is the common use of an unconventional mode of gene regulation, involving regulated toggling between a translatable mRNA isoform and one that is 5' extended and poorly translated. A major focus of our future research is to better understand why some of these 5' extended “long undecoded transcript isoforms” (LUTIs) are subject to nonsense mediated decay (NMD), while other are protected from degradation. We will use approaches including machine learning analyses of targeted and protected classes of LUTIs, integrating data including their in vivo structures, to identify NMD transcript cues. This project will not only help us understand the true prevalence of LUTIs in yeast, it aims to leverage this large newly identified class of natural NMD targets to elucidate central principles in NMD targeting in all cellular contexts. We will also use the knowledge gained from our studies of LUTI-based regulation in yeast to determine whether it is a similarly widespread core mode of gene expression regulation in mammalian cells. We also discovered that meiotic cells translate many coding regions were not previously identified. These include hundreds of proteins 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 are studying the specific cellular roles of short proteins by performing pooled screens and focusing on directed study of cases in which the short proteins include domains of characterized proteins. Our goal is to reveal the types of functions mediated by this large and poorly studied class of cellular factors that are now known to be commonly in eukaryotes. Finally, MIRA funding enabled development of an entirely new project in my lab, one that studies the way that protein complex members find each other within the complex environment of a cell. This project has the potential to reveal fundamental principles in cellular regulation, enabled by our background in meiosis, the simplicity and power of the yeast system, and our expertise in global gene expression dataset generation and analysis.