Diverse expression and modification of tRNAs and tRNA-derived RNAs in 19 mouse tissues

Abstract

Transfer RNAs (tRNAs) and their derived small RNAs (tDRs) vary in abundance and processing across mammalian tissues. However, these differences and the regulatory mechanisms controlling them are poorly understood. Dysregulation of tRNAs has increasingly been implicated as a critical factor in disease progression; thus, a deeper understanding of the homeostatic variance across somatic tissues is vital. In this study, we applied Ordered Two-Template Relay sequencing (OTTR-seq) to examine small RNAs in 19 tissues from adult mice, quantifying mature tRNAs and tDRs at single-transcript resolution and inferring select base-modification signatures from characteristic reverse-transcriptase-mediated misincorporation. We observed tissue-biased expression of many unique transcripts and identified tDRs with greater tissue specificity than their parent tRNAs. Differences between tRNAs with the same anticodon but containing variations elsewhere in the sequence (isodecoders) suggest diverse regulatory processes across tissues that alter modification, translation functionality, stability, and tDR synthesis. These data provide an isodecoder-resolved reference for tissue-biased tRNA and tDR regulation in mice and form a framework for exploring disease-associated remodeling of the tRNA pool.