UC Santa Cruz

This dissertation investigates the multifaceted roles of transfer RNAs (tRNAs) in gene expression regulation, extending beyond their traditional roles in protein translation. Chapter I explores tRNAs in human brain development, utilizing cerebral cortical organoids and specialized tRNA sequencing to reveal dynamic expression patterns of tRNAs and tRNA-derived small RNAs (tDRs) in the early human cerebral cortex. Notably, it identifies a variety of upregulated tDRs from diverse isodecoders, with sequence-specific conservation among neural-specific groups, suggesting a pivotal role in neural development. Chapter II examines the impact of complete telomere-to-telomere (T2T) assemblies of great ape (and human) genomes on tRNA gene discovery. This has led to the identification of nearly 100 new human cytosolic-tRNA gene loci, particularly in regions of chromosome 1 associated with neural gene regulation and implicated in the neural expansion of humans and primates. The chapter also discusses the dynamic nature of tRNA loci copy number variation across tandem repeats and their roles on adjacent neural genes. Chapter III introduces two novel bioinformatics tools, tRNAgraph, and tRNAmap, designed to address the challenges of analyzing tRNA sequencing data across multiple species and experimental conditions. tRNAgraph offers multi-variate analysis, automated clustering, and classification of tRNAseq data, while tRNAmap aligns the ‘tRNAnome’ of eukaryotic species for cross-species comparison. These tools enable advanced analysis of the increasingly common tRNA sequencing data, contributing significantly to our understanding of tRNAs in neural development and evolution. This dissertation’s exploration into the complex roles of tRNAs and the innovative tools developed for their analysis not only advances our understanding of neural development and evolution but also paves the way for future genomic research to uncover the intricate mechanisms of gene regulation.