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A transfer-RNA-derived small RNA regulates ribosome biogenesis

Nature volume 552, pages 5762 (07 December 2017) | Download Citation


Transfer-RNA-derived small RNAs (tsRNAs; also called tRNA-derived fragments) are an abundant class of small non-coding RNAs whose biological roles are not well understood. Here we show that inhibition of a specific tsRNA, LeuCAG3′tsRNA, induces apoptosis in rapidly dividing cells in vitro and in a patient-derived orthotopic hepatocellular carcinoma model in mice. This tsRNA binds at least two ribosomal protein mRNAs (RPS28 and RPS15) to enhance their translation. A decrease in translation of RPS28 mRNA blocks pre-18S ribosomal RNA processing, resulting in a reduction in the number of 40S ribosomal subunits. These data establish a post-transcriptional mechanism that can fine-tune gene expression during different physiological states and provide a potential new target for treating cancer.

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We thank J. Sage for HCC tissues from conditional TKO (Rblox/lox; p130lox/lox; p107−/−) adult mice and liver tissues from p107−/− mice. This work was supported by grants to M.A.K. from the National Institutes of Health (R01AI071068 and R01DK114483). M.A.K. received support from the Stanford Cancer Institute, and S.S. from the CJ Huang Foundation and the TS Kwok Liver Cancer Foundation.

Author information

Author notes

    • Gabriele Fuchs
    • , Shengchun Wang
    • , Yue Zhang
    •  & Biswajoy Roy-Chaudhuri

    Present addresses: The RNA Institute and Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA (G.F.); Medtronic Vascular, 3576 Unocal Place, Santa Rosa, California 95403, USA (S.W.); Stanford Center for Genomics and Personalized Medicine, 3165 Porter Drive, Palo Alto, California 94304, USA (Y.Z.); Impossible Foods Inc., 525 Chesapeake Drive, Redwood City, California 94063, USA (B.R.-C.).


  1. Department of Pediatrics, Stanford University, Stanford, California 94305, USA

    • Hak Kyun Kim
    • , Shengchun Wang
    • , Yue Zhang
    • , Hyesuk Park
    • , Biswajoy Roy-Chaudhuri
    • , Jianpeng Xu
    • , Kirk Chu
    • , Feijie Zhang
    •  & Mark A. Kay
  2. Department of Genetics, Stanford University, Stanford, California 94305, USA

    • Hak Kyun Kim
    • , Shengchun Wang
    • , Yue Zhang
    • , Hyesuk Park
    • , Biswajoy Roy-Chaudhuri
    • , Jianpeng Xu
    • , Kirk Chu
    • , Feijie Zhang
    •  & Mark A. Kay
  3. Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA.

    • Gabriele Fuchs
    •  & Peter Sarnow
  4. Asian Liver Center, Department of Surgery, Stanford University School of Medicine, Stanford, California 94305, USA

    • Wei Wei
    • , Mei-Sze Chua
    •  & Samuel So
  5. MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China

    • Pan Li
    •  & Qiangfeng Cliff Zhang


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H.K.K. contributed to experimental design, interpretation, execution, and manuscript writing and editing. G.F. performed experiments in Fig. 3a, b and Extended Data Fig. 1g, h, and assisted with interpretation, discussion and manuscript editing. S.W. performed experiments in Figs 1c, 2b and Extended Data Figs 1i, 2c. W.W. designed experiments with the PDX model and conducted experiments in Fig. 2c and Extended Data Fig. 2h, i, k. Y.Z. performed computational analyses (RNA-seq and predictions of tsRNA binding sites on pre-45S rRNA) in Extended Data Figs 3d and 5a. H.P. performed multiple experiments including Figs 2a, d, 4a, e, and 5b. B.R.-C. conducted the experiment in Extended Data Fig. 8a. P.L. analysed icSHAPE data in Extended Data Fig. 9d. J.X. performed LeuCAG3′tsRNA target site prediction in Extended Data Figs 8b and 9b. F.Z. performed RNA extraction and mouse experiments. K.C. conducted protein extraction. M.-S.C. designed experiments with the PDX model, interpreted animal data and assisted in manuscript editing. S.S. provided discussion regarding the xenograft model. Q.C.Z. analysed, interpreted and discussed icSHAPE data. P.S. interpreted and discussed experimental results and assisted in manuscript editing. M.A.K. contributed to the experimental design, data interpretation, and manuscript writing and editing.

Competing interests

H.K.K., S.W. and M.A.K. are inventors on relevant patents filed by Stanford University.

Corresponding author

Correspondence to Mark A. Kay.

Reviewer Information Nature thanks N. Polacek and L. Zender for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Figure 1

    This file contains gel source data.

  3. 3.

    Supplementary Table 1

    This file contains the DNA sequences of the CUG (original) and CUC/CUU (modified) Renilla genes from the psiCHECK-2 plasmid from Fig. 1c.Red colored nucleotides show the LeuCUG codon and blue colored nucleotides are LeuCUU or LeuCUC codons. There are thirteen LeuCUG, four LeuCUU, and five LeuCUC codons in original Renilla gene. Thirteen LeuCUG codons were replaced by CUU or CUC codons in the modified Renilla gene.

  4. 4.

    Supplementary Table 2

    This file contains samples that were sequenced in Extended Data Fig. 3d. 50bp paired-end reads were generated on an Illumina HiSeq 2000 machine yielding a total of 10 to 40 million paired-end reads. Sequences were mapped to the human hg19 genome.

  5. 5.

    Supplementary Table 3

    This file contains quantification of each ribosomal RNA in Fig. 3d. Each pre-rRNA was normalized by each mature 28S rRNA. Normalized pre-rRNA from Anti-Leu3′ts LNA was again normalized to that of control (con). Normalized pre-rRNA from siRPS6, 10, 13, and 29 were normalized to the siRNA control (sicontrol).

  6. 6.

    Supplementary Table 4

    This file contains the list of antisense Locked nucleic acid (LNA), synthetic RNA, and northern probe oligonucleotides. LNA bases are upper-case letters and DNA bases are lower –case letters.

  7. 7.

    Supplementary Table 5

    This file contains DNA oligonucleotides used for the target sequences of tsRNAs and microRNAs in the luciferase vector in Extended Data Fig. 3a.

  8. 8.

    Supplementary Table 6

    This file contains PCR primers for the generation of the Northern probes.

  9. 9.

    Supplementary Table 7

    This file contains Biotin labelled oligonuclotides used for the ChIRP studies in Extended Data Fig. 8a.

  10. 10.

    Supplementary Table 8

    This file contains modified nucleotide sequences of the ribosomal protein mutants. Upper characters are altered sequences and the numbers next to each sequence indicate the sequence position in the each ribosomal protein gene.

  11. 11.

    Supplementary Table 9

    This file contains primers for site-directed mutageneis.

  12. 12.

    Supplementary Table 10

    This file contains icSHAPE scores for the full-length studied mRNAs. Each number represents the scores for each nucleotide. The icSHAPE data are scaled from 0 (no reactivity; double-strandedness) to 1 (maximum reactivity; single-strandedness).

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