Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia

Abstract

Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and RPS2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.

Data availability

Lentivector plasmid sequences are available on Dryad. https://doi.org/10.5061/dryad.2330r1band doi:10.5061/dryad.m0cfxpp75.The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD024067.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Anne-Claire Godet

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Emilie Roussel

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Florian P David

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9842-1548
  4. Fransky Hantelys

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Florent Morfoisse

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Joffrey Alves

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Françoise Pujol

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Isabelle Ader

    Inserm, UMR 1301, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  9. Edouard Bertrand

    Institut de Génétique Moléculaire de Montpellier, Mont[ellier, France
    Competing interests
    The authors declare that no competing interests exist.
  10. Odile Burlet-Schiltz

    Institut de Pharmacologie et Biologie Structurale, CNRS, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  11. Carine Froment

    Institut de Pharmacologie et Biologie Structurale, CNRS, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3688-5560
  12. Anthony K Henras

    5Molecular, Cellular and Developmental Biology Unit, CNRS, Université Paul Sabatier, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  13. Patrice Vitali

    5Molecular, Cellular and Developmental Biology Unit, CNRS, Université Paul Sabatier, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  14. Eric Lacazette

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  15. Florence Tatin

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  16. Barbara Garmy-Susini

    Inserm UMR 1297, Toulouse, France
    Competing interests
    The authors declare that no competing interests exist.
  17. Anne-Catherine Prats

    Inserm UMR 1297, Toulouse, France
    For correspondence
    anne-catherine.prats@inserm.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5282-3776

Funding

Agence Nationale de la Recherche (ANR-18-CE11-0020-RIBOCARD)

  • Anne-Catherine Prats

Agence Nationale de la Recherche (ProFI ANR-10-INBS-08)

  • Odile Burlet-Schiltz
  • Carine Froment

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

Reviewing Editor

  1. Nahum Sonenberg, McGill University, Canada

Version history

  1. Preprint posted: February 10, 2021 (view preprint)
  2. Received: April 6, 2021
  3. Accepted: December 18, 2022
  4. Accepted Manuscript published: December 22, 2022 (version 1)
  5. Version of Record published: December 29, 2022 (version 2)

Copyright

© 2022, Godet 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. Anne-Claire Godet
  2. Emilie Roussel
  3. Florian P David
  4. Fransky Hantelys
  5. Florent Morfoisse
  6. Joffrey Alves
  7. Françoise Pujol
  8. Isabelle Ader
  9. Edouard Bertrand
  10. Odile Burlet-Schiltz
  11. Carine Froment
  12. Anthony K Henras
  13. Patrice Vitali
  14. Eric Lacazette
  15. Florence Tatin
  16. Barbara Garmy-Susini
  17. Anne-Catherine Prats
(2022)
Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia
eLife 11:e69162.
https://doi.org/10.7554/eLife.69162

Share this article

https://doi.org/10.7554/eLife.69162

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