Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.

Peng YU; Siting ZHOU; Yan GAO; Yu LIANG; Wenbing GUO; Dan Ohtan WANG; Shuaiwen DING; Shuibin LIN; Jinkai WANG; Yixian CUN

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Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.

Author: Peng YU ¹ ; Siting ZHOU ² ; Yan GAO ² ; Yu LIANG ³ ; Wenbing GUO ² ; Dan Ohtan WANG ⁴ ; Shuaiwen DING ⁵ ; Shuibin LIN ⁶ ; Jinkai WANG ⁷ ; Yixian CUN ⁸
Author Information

1. Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Radiation Oncology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510080, China.
2. Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China.
3. Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
4. RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
5. Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
6. Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China. Electronic address: linshb6@mail.sysu.edu.cn.
7. Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China; RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510080, China. Electronic address: wangjk@mail.sysu.edu.cn.
8. Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Stem Cell Biology and Tissue Engineering, MOE Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Guangzhou 510080, China. Electronic address: cunyx3@mail.sysu.edu.cn.
Publication Type:Journal Article
Keywords: Amino acid composition; Codon usage bias; Tissue-specific; Translational efficiency; tRNA expression
MeSH: Animals; Mice; Anticodon/genetics*; Transcriptome; Protein Biosynthesis; RNA, Transfer/chemistry*; Amino Acids/metabolism*; Mammals/metabolism*
From: Genomics, Proteomics & Bioinformatics 2023;21(4):834-849
CountryChina
Language:English
Abstract: Although the function of tRNAs in the translational process is well established, it remains controversial whether tRNA abundance is tightly associated with translational efficiency (TE) in mammals. Moreover, 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 demethylase-tRNA sequencing (DM-tRNA-seq) and TE of mRNAs using ribosome-tagging sequencing (RiboTag-seq) in the brain, heart, and testis of mice. Remarkable variation in the expression of tRNA isodecoders was observed among 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 at amino acid level. 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 TE of mRNAs, we find that the tRNA adaptation index (tAI) and TE are significantly correlated in the same tissues but not between tissues; and tRNA expression and the amino acid composition 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. This study provides a resource for tRNA and translation studies, as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.