Brief Communication | Published:

Improved Ribo-seq enables identification of cryptic translation events

Nature Methods volume 15, pages 363366 (2018) | Download Citation

Abstract

Ribosome profiling has been used to predict thousands of short open reading frames (sORFs) in eukaryotic cells, but it suffers from substantial levels of noise. PRICE (https://github.com/erhard-lab/price) is a computational method that models experimental noise to enable researchers to accurately resolve overlapping sORFs and noncanonical translation initiation. We experimentally validated translation using major histocompatibility complex class I (MHC I) peptidomics and observed that sORF-derived peptides efficiently enter the MHC I presentation pathway and thus constitute a substantial fraction of the antigen repertoire.

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Proteomics Identifications Database

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Acknowledgements

This work was funded by the MRC (Clinical Fellowship grant G1002523 to L.D.), NHSBT (grant WP11-05 to L.D.), the European Research Council (grant ERC-2016-CoG 721016–HERPES to L.D.) and the Wellcome Trust (Senior Clinical Research Fellowship 108070/Z/15/Z to M.P.W.). R.Z. acknowledges partial funding from the DFG (SFB 1123) and from Bavaria (BioSysNet). We thank S. Gorsky for critical reading of the manuscript.

Author information

Affiliations

  1. Institute for Informatics, Ludwig-Maximilians-Universität München, München, Germany.

    • Florian Erhard
    •  & Ralf Zimmer
  2. Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.

    • Florian Erhard
    •  & Lars Dölken
  3. Institute of Virology, Medical Center, University of Freiburg, Freiburg, Germany.

    • Anne Halenius
    •  & Cosima Zimmermann
  4. Faculty of Medicine, University of Freiburg, Freiburg, Germany.

    • Anne Halenius
    •  & Cosima Zimmermann
  5. Innovative Medicines & Early Development, AstraZeneca UK Ltd, Cambridge, UK.

    • Anne L'Hernault
  6. Interfaculty Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.

    • Daniel J Kowalewski
    •  & Stefan Stevanovic
  7. Immatics Biotechnologies GmbH, Tübingen, Germany.

    • Daniel J Kowalewski
  8. Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

    • Michael P Weekes

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Contributions

F.E. designed and implemented the computational approach. R.Z. supervised the development of the computational methods. A.H., C.Z., D.J.K. and S.S. provided the MHC I peptidome analysis. M.P.W. provided whole-proteome mass spectrometry data. A.L. provided Ribo-seq data used for the validation of this approach. F.E. and L.D. designed the experiments and wrote the paper.

Competing interests

D.J.K. is an employee of Immatics Biotechnologies GmbH.

Corresponding authors

Correspondence to Florian Erhard or Ralf Zimmer or Lars Dölken.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13, Supplementary Notes 1–3 and Supplementary Tables 1–2

  2. 2.

    Life Sciences Reporting Summary

Excel files

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    Supplementary Table 3

    Identified ORFs

Zip files

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    Supplementary Software

    Source code of PRICE version 1.0.1

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DOI

https://doi.org/10.1038/nmeth.4631