Neural tRNA Expression Patterns in Brain Organoids

Transfer RNAs (tRNAs) are traditionally known for their role in protein translation, yet recent discoveries highlight their broader functions in gene regulation, particularly through tRNA-derived small RNAs (tDRs). Studies have shown the singular importance of one unique ArgUCU tRNA isodecoder in mouse neural development, yet potential function(s) of tDRs derived from this and all other tRNAs remain largely unexplored in early human brain development. In this study, we employed cerebral cortical organoid models and AlkB-facilitated RNA methylation sequencing (ARM-seq) to profile tDRs across distinct stages of early human cerebral cortex development. Our analysis reveals dynamic expression patterns of diverse tDR groups derived from a wide range of isodecoders, with several distinct groups showing neural-specific expression. Computational analyses of these tDRs shows biased sequence motifs in over-represented tRNAs that are enriched with particular RNA modifications, giving initial clues to traits that change within the pool of tDRs during neural development. This expanded catalog of tDRs provides a framework for future studies on tRNA function in brain development and offers a deeper understanding of the complexity of tDR dynamics in neural differentiation. Included are ARM-seq libraries derived from isolated total small RNA from GM-12878-c305 human induced pluripotent stem cells and brain organoids. These experiments were performed in duplicate or triplicate (biological) and subjected to NGS.