Letter | Published:

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

Nature volume 541, pages 228232 (12 January 2017) | Download Citation

Abstract

Although long non-coding RNAs (lncRNAs) are non-protein-coding transcripts by definition, recent studies have shown that a fraction of putative small open reading frames within lncRNAs are translated1,2,3. However, the biological significance of these hidden polypeptides is still unclear. Here we identify and functionally characterize a novel polypeptide encoded by the lncRNA LINC00961. This polypeptide is conserved between human and mouse, is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation. This regulation of mTORC1 is specific to activation of mTORC1 by amino acid stimulation, rather than by growth factors. Hence, we termed this polypeptide ‘small regulatory polypeptide of amino acid response’ (SPAR). We show that the SPAR-encoding lncRNA is highly expressed in a subset of tissues and use CRISPR/Cas9 engineering to develop a SPAR-polypeptide-specific knockout mouse while maintaining expression of the host lncRNA. We find that the SPAR-encoding lncRNA is downregulated in skeletal muscle upon acute injury, and using this in vivo model we establish that SPAR downregulation enables efficient activation of mTORC1 and promotes muscle regeneration. Our data provide a mechanism by which mTORC1 activation may be finely regulated in a tissue-specific manner in response to injury, and a paradigm by which lncRNAs encoding small polypeptides can modulate general biological pathways and processes to facilitate tissue-specific requirements, consistent with their restricted and highly regulated expression profile.

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European Nucleotide Archive

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Acknowledgements

We thank members of the P.P.P. laboratory, C. C. Dibble for critical discussions and Cell Signaling Technology for generation of SPAR antibodies. A.M. was supported by a postdoctoral fellowship from JSPS, The Uehara Memorial Foundation and The Naito Foundation. This work was supported in part by NIH grant R01 CA082328 and R35 CA197529 to P.P.P. and JST and PREST to A.M.

Author information

Author notes

    • Alessandra Pasut
    • , Masaki Matsumoto
    •  & Riu Yamashita

    These authors contributed equally to this work.

Affiliations

  1. Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA

    • Akinobu Matsumoto
    • , Alessandra Pasut
    • , Jacqueline Fung
    • , Emanuele Monteleone
    • , John G. Clohessy
    •  & Pier Paolo Pandolfi
  2. Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan

    • Masaki Matsumoto
    •  & Keiichi I. Nakayama
  3. Department of BioBank, Tohoku Medical Megabank Organization (ToMMo), Tohoku University, Sendai 980-8573, Japan

    • Riu Yamashita
  4. Molecular Biotechnology Center and Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy

    • Emanuele Monteleone
  5. The Clayton Foundation Laboratories for Peptide Biology, Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Alan Saghatelian

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Contributions

A.M. conceived the project, designed and performed most experiments, interpreted the results, and co-wrote the manuscript. A.P. performed muscle experiments. M.M. performed mass spectrometry. R.Y. performed informatic analysis. J.F. performed histology and immunoblotting experiments. E.M. analysed whole-genome sequencing data. A.S. and K.I.N. supervised experimental designs. J.G.C. supervised experimental designs and co-wrote the manuscript. P.P.P. conceived the project, supervised experimental designs, interpreted results, and co-wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Pier Paolo Pandolfi.

Reviewer Information Nature thanks K.-L. Guan, M. Rüegg and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Notes 1-6, Supplementary References and Supplementary Figure 1, which contains immunoblot source data.

Excel files

  1. 1.

    Supplementary Table 1

    This file contains the full list of protein interaction partners for the SPAR polypeptide identified by mass spectrometric analyses.

  2. 2.

    Supplementary Table 2

    Whole genome sequencing data summary, this file contains the variant sites (Read depth > 50) observed by whole genome sequencing of three independent Spar KO mice.

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DOI

https://doi.org/10.1038/nature21034

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