Article

mRNA 3′-UTR shortening is a molecular signature of mTORC1 activation

  • Nature Communications 6, Article number: 7218 (2015)
  • doi:10.1038/ncomms8218
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Abstract

Mammalian target of rapamycin (mTOR) enhances translation from a subset of messenger RNAs containing distinct 5′-untranslated region (UTR) sequence features. Here we identify 3′-UTR shortening of mRNAs as an additional molecular signature of mTOR activation and show that 3′-UTR shortening enhances the translation of specific mRNAs. Using genetic or chemical modulations of mTOR activity in cells or mouse tissues, we show that cellular mTOR activity is crucial for 3′-UTR shortening. Although long 3′-UTR-containing transcripts minimally contribute to translation, 3-′UTR-shortened transcripts efficiently form polysomes in the mTOR-activated cells, leading to increased protein production. Strikingly, selected E2 and E3 components of ubiquitin ligase complexes are enriched by this mechanism, resulting in elevated levels of protein ubiquitination on mTOR activation. Together, these findings identify a previously uncharacterized role for mTOR in the selective regulation of protein synthesis by modulating 3′-UTR length of mRNAs.

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Acknowledgements

We thank Dr Kwiatkowski at Bringham and Women’s Hospital and Harvard Medical School for providing us TSC1+/+ and TSC1−/− MEF cell lines and HCV29 bladder cancer cell lines used in this study. We also thank Mr Todd Markowski and Dr LeeAnn Higgins at the Center for Mass Spectrometry and Proteomics, University of Minnesota, for their work in peptide fractionation and LC–MS/MS analysis. This work was supported in part by the following funding: Institutional Research Grant (118198-IRG-58-001-52-IRG76) from the American Cancer Society for J.Y., and the grant for the Bio & Medical Technology Development Program (2012M3A9B4028738) by the National Research Foundation of Korea (NRF) for K.-S.K and J.Y., NSF III 117153 for R.K. and GM097057, AG039758, ADA 7-12-BS-093 and W81XWH-13-1-0060 for D.-H.K.

Author information

Author notes

    • Jae-Woong Chang
    •  & Wei Zhang

    These authors contributed equally to this work

Affiliations

  1. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, 321 Church Street, SE 6-155 Jackson Hall, Minneapolis, Minnesota 55455, USA

    • Jae-Woong Chang
    • , Hsin-Sung Yeh
    • , Ebbing P. de Jong
    • , Semo Jun
    • , Kwan-Hyun Kim
    • , Do-Hyung Kim
    • , Timothy J. Griffin
    •  & Jeongsik Yong
  2. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA

    • Wei Zhang
    •  & Rui Kuang
  3. Department of Pharmacology, Pusan National University School of Medicine, Yangsan 626-870, Republic of Korea

    • Sun S. Bae
  4. Biomedical Genomics Center, University of Minnesota, Minneapolis, Minnesota 55455, USA

    • Kenneth Beckman
  5. Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

    • Tae Hyun Hwang
  6. Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea

    • Kye-Seong Kim

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Contributions

J.-W.C., H.-S.Y., S.J., K.-H.K. and S.S.B. designed and performed experiments. W.Z., T.-H.H. analysed RNA-seq and protemics data, and produced figures. E.d.J. performed quantitative proteomics studies and analysed proteomics data. K.B. supported data acquisition and designed RNA-seq experiments. K.-S.K. and D.-H.K. designed experiments. T.J.G., R.K. and J.Y. designed experiments and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jeongsik Yong.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1-8, Supplementary Table 1, Supplementary Methods and Supplementary References.

Excel files

  1. 1.

    Supplementary Data 1

    3'UTR shortened transcripts in the mTOR-activated transcriptome.

  2. 2.

    Supplementary Data 2

    The catalogue of proteins identified in 2D LC-MS/MS.

  3. 3.

    Supplementary Data 3

    The catalogue of differentially expressed genes in WT and TSC1-/- MEFs.

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