Analysis tool for tRNA Transcriptomes and Translatomes Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues

Introduction

Although the function of tRNA in translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. For example, how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed. Here, we measured both tRNA expression using DM-tRNA-seq and TEs of mRNAs using RiboTag-seq in brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among the different tissues. When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons, we observed an expected reduction in the variation of anticodon expression across all samples, an unexpected smaller variation of anticodon usage bias, and an unexpected larger variation of tRNA isotype expression. Regardless of whether or not they share the same anticodons, the isodecoders encoding the same amino acids are co-expressed across different tissues. Based on the expression of tRNAs and the TEs of mRNAs, we find that the tRNA adaptation index (tAI) values and TEs are significantly correlated in the same tissues but not among tissues; tRNA expression and the amino acid compositions of translating peptides are positively correlated in the same tissues but not between tissues. We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms, such as aminoacylation, modification, and tRNA-derived small RNAs (tsRNAs). This study provides a resource for tRNA and translation studies, the results also provide novel insights into the dynamics of tRNAs and their role in translational regulation.

Publications

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Credits

  1. Siting Zhou zhoust6@mail2.sysu.edu.cn
    Investigator

    Department of Medical Informatics, Sun Yat-sen University, China

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Summary
AccessionBT007304
Tool TypeApplication
CategorytRNA-derived RNA annotation, tRNA data
PlatformsLinux/Unix
TechnologiesBASH, R
User InterfaceTerminal Command Line
Input DataFASTQ
Latest Releasev1.0.0 (April 29, 2022)
Download Count5408
Country/RegionChina
Submitted BySiting Zhou