Abstract

A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided. All sequencing data are deposited in public archives and made available upon publication.

The following previously published data sets were used

Article and author information

Author details

  1. Luca Minati

    Ribosome engineering, IMMAGINA biotechnology, Trento, Italy
    Competing interests
    Luca Minati, L.M is an employee of IMMAGINA BioTechnology S.r.l..
  2. Claudia Firrito

    Ribosome engineering, IMMAGINA biotechnology, Trento, Italy
    Competing interests
    Claudia Firrito, C.F. is an employee of IMMAGINA BioTechnology S.r.l..
  3. Alessia Del Piano

    Ribosome engeneering, IMMAGINA biotechnology, Trento, Italy
    Competing interests
    Alessia Del Piano, A.D.P is an employee of IMMAGINA BioTechnology S.r.l..
  4. Alberto Peretti

    Ribosome engineering, IMMAGINA biotechnology, Trento, Italy
    Competing interests
    Alberto Peretti, A.P. is an employee of IMMAGINA BioTechnology S.r.l..
  5. Simone Sidoli

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    No competing interests declared.
  6. Daniele Peroni

    Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0862-266X
  7. Romina Belli

    Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5690-2797
  8. Francesco Gandolfi

    Laboratory of Bioinformatics and Computational Genomics, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
  9. Alessandro Romanel

    Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
  10. Paola Bernabo

    Ribosome engineering, IMMAGINA biotechnology, Trento, Italy
    Competing interests
    Paola Bernabo, P.B is an employee of IMMAGINA BioTechnology S.r.l..
  11. Jacopo Zasso

    Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3151-6443
  12. Alessandro Quattrone

    Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
    Competing interests
    Alessandro Quattrone, A.Q is a shareholder of IMMAGINA BioTechnology S.r.l.
  13. Graziano Guella

    Department of Physics, University of Trento, Trento, Italy
    Competing interests
    Graziano Guella, G.G. is shareholders of IMMAGINA BioTechnology S.r.l.
  14. Fabio Lauria

    Institute of Biophysics, CNR Unit at Trento, Trento, Italy
    Competing interests
    No competing interests declared.
  15. Gabriella Viero

    Institute of Biophysics, CNR Unit at Trento, Trento, Italy
    Competing interests
    Gabriella Viero, G.V is a scientific advisor of IMMAGINA BioTechnology S.r.l..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6755-285X
  16. Massimiliano Clamer

    Ribosome engineering, IMMAGINA biotechnology, Trento, Italy
    For correspondence
    mclamer@immaginabiotech.com
    Competing interests
    Massimiliano Clamer, M.C. is the founder of, director of, and a shareholder in IMMAGINA BioTechnology S.r.l., a company engaged in the development of new technologies for gene expression analysis at the ribosomal level..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8185-059X

Funding

Autonumus Province of Trento adn Banca Intesa (LP6/99)

  • Luca Minati
  • Claudia Firrito
  • Alessia Del Piano
  • Alberto Peretti
  • Paola Bernabo
  • Massimiliano Clamer

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Howard Y Chang, Stanford University, United States

Version history

  1. Received: May 25, 2020
  2. Accepted: February 16, 2021
  3. Accepted Manuscript published: February 17, 2021 (version 1)
  4. Version of Record published: March 4, 2021 (version 2)

Copyright

© 2021, Minati et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Luca Minati
  2. Claudia Firrito
  3. Alessia Del Piano
  4. Alberto Peretti
  5. Simone Sidoli
  6. Daniele Peroni
  7. Romina Belli
  8. Francesco Gandolfi
  9. Alessandro Romanel
  10. Paola Bernabo
  11. Jacopo Zasso
  12. Alessandro Quattrone
  13. Graziano Guella
  14. Fabio Lauria
  15. Gabriella Viero
  16. Massimiliano Clamer
(2021)
One-shot analysis of translated mammalian lncRNAs with AHARIBO
eLife 10:e59303.
https://doi.org/10.7554/eLife.59303

Share this article

https://doi.org/10.7554/eLife.59303

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