1. Chromosomes and Gene Expression
  2. Developmental Biology
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Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility

  1. Mehdi Goudarzi  Is a corresponding author
  2. Kathryn Berg
  3. Lindsey M Pieper
  4. Alexander F Schier  Is a corresponding author
  1. Harvard University, United States
Research Article
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Cite this article as: eLife 2019;8:e40815 doi: 10.7554/eLife.40815

Abstract

Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs have no overt roles in embryogenesis, viability and fertility.

Article and author information

Author details

  1. Mehdi Goudarzi

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    For correspondence
    mgoudarzi@fas.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6669-5800
  2. Kathryn Berg

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Lindsey M Pieper

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Alexander F Schier

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    For correspondence
    schier@fas.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7645-5325

Funding

NIH Office of the Director (R01HD076708)

  • Alexander F Schier

Leopoldina (Postdoctorial fellowship LPDS2014-01)

  • Mehdi Goudarzi

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

Reviewing Editor

  1. Elisabeth M Busch-Nentwich, University of Cambridge, United Kingdom

Publication history

  1. Received: August 5, 2018
  2. Accepted: January 8, 2019
  3. Accepted Manuscript published: January 8, 2019 (version 1)

Copyright

© 2019, Goudarzi 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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