5′ tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene expression

Abstract

Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA-derived small RNAs (tsRNAs) play prominent roles in diverse cellular processes across a wide spectrum of species. Contrasting the situation in other small RNA pathways the mechanisms behind these effects appear more diverse, more complex, and are generally less well understood. In addition, surprisingly little is known about the expression profiles of tsRNAs across different tissues and species. Here, we provide an initial overview of tsRNA expression in different species and tissues, revealing very high levels of 5′′ tRNA halves (5′′ tRHs) particularly in the primate hippocampus. We further modulated the regulation capacity of selected 5′′ tRHs in human cells by transfecting synthetic tsRNA mimics (“overexpression”) or antisense-RNAs (“inhibition”) and identified differentially expressed transcripts based on RNA-seq. We then used a novel k-mer mapping approach to dissect the underlying targeting rules, suggesting that 5′′ tRHs silence genes in a sequence-specific manner, while the most efficient target sites align to the mid-region of the 5′′ tRH and are located within the CDS or 3′′ UTR of the target. This amends previous observations that tsRNAs guide Argonaute proteins to silence their targets via a miRNA-like 5′′ seed match and suggests a yet unknown mechanism of regulation. Finally, our data suggest that some 5′′ tRHs that are also able to sequence-specifically stabilize mRNAs as up-regulated mRNAs are also significantly enriched for 5′′ tRH target sites.