A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Abstract

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin+ cells, in a manner independent of the nearby TF FOXA2. One-by-one deletion of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.

Data availability

All mRNA-seq and Ribo-seq datasets generated for this study have been deposited at GEO under the accession number GSE144682.

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

Article and author information

Author details

  1. Bjoern Gaertner

    Department of Pediatrics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sebastiaan van Heesch

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9593-1980
  3. Valentin Schneider-Lunitz

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Jana Felicitas Schulz

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Franziska Witte

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Susanne Blachut

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Steven Nguyen

    Department of Pediatrics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Regina Wong

    Department of Pediatrics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Ileana Matta

    Department of Pediatrics, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Norbert Hübner

    Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Maike Sander

    Department of Pediatrics and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    For correspondence
    masander@ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5308-7785

Funding

National Institutes of Health (DK068471 and DK078803)

  • Maike Sander

Alexander von Humboldt-Stiftung

  • Maike Sander

Larry L. Hillblom Foundation (2015-D-021-FEL)

  • Bjoern Gaertner

European Molecular Biology Organization (ALTF 186-2015)

  • Sebastiaan van Heesch

Horizon 2020 Framework Programme (AdG788970)

  • Norbert Hübner

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

Reviewing Editor

  1. Lori Sussel

Version history

  1. Received: May 7, 2020
  2. Accepted: August 1, 2020
  3. Accepted Manuscript published: August 3, 2020 (version 1)
  4. Version of Record published: August 12, 2020 (version 2)

Copyright

© 2020, Gaertner 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. Bjoern Gaertner
  2. Sebastiaan van Heesch
  3. Valentin Schneider-Lunitz
  4. Jana Felicitas Schulz
  5. Franziska Witte
  6. Susanne Blachut
  7. Steven Nguyen
  8. Regina Wong
  9. Ileana Matta
  10. Norbert Hübner
  11. Maike Sander
(2020)
A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
eLife 9:e58659.
https://doi.org/10.7554/eLife.58659

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https://doi.org/10.7554/eLife.58659

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