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Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants

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Abstract

Evidence is emerging that tRNA-derived fragments (tRFs) are regulatory molecules. Studies of tRFs in plants have been based on conventional small RNA sequencing, and focused on profiling of tRF-5 and tRF-3 species. A more comprehensive and quantitative analysis of the entire tRF population is highly necessary. Here, we employ tRNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of tRNAs and tRFs in plants. We show that in Arabidopsis, approximately half of tRNA genes are extremely weakly expressed, accounting for only 1% of total tRNA abundance, while ~12% of tRNA genes contribute to ~80% of tRNA abundance. Our tRNA sequencings in various plants reveal that tRNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous tRF population, we show that tRNA halves and previously unnoticed 10–16-nt tiny tRFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny tRFs in Arabidopsis indicate that tiny tRFs are not random tRNA degradation products. Finally, we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of tRNAs and tRFs in the model plants Arabidopsis and rice.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31871321, 31788103, and 31770874), Tianjin Natural Science Foundation of China (16JCZDJC33400), and Tianjin Rice Industrial Technology System of China (ITTRRS2018006). We thank the members in Dr. Shuzhen Men’s lab for help with this work. We also thank Dr. Junbin Wang in Tianjin Agricultural University for providing crop seeds.

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  1. Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China

    Xuan Ma, Xiaocong Kong, Jing Liu, Siju Zhang, Shanshan Liang & Weijiang Luan

  2. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Chunyan Liu & Xiaofeng Cao

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  1. Xuan Ma
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Correspondence to Xuan Ma, Weijiang Luan or Xiaofeng Cao.

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Ma, X., Liu, C., Kong, X. et al. Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants. Sci. China Life Sci. 64, 495–511 (2021). https://doi.org/10.1007/s11427-020-1891-8

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