CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness

  1. Adam D Norris
  2. Xicotencatl Gracida
  3. John Calarco  Is a corresponding author
  1. Harvard University, United States
  2. University of Toronto, Canada

Abstract

Genetic interaction screens have aided our understanding of complex genetic traits, diseases, and biological pathways. However, approaches for synthetic genetic analysis with null-alleles in metazoans have not been feasible. Here, we present a CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation. Applying this technique in Caenorhabditis elegans, we comprehensively screened interactions within a set of 14 conserved RNA binding protein genes, generating all possible single and double mutants. Many double mutants displayed fitness defects, revealing synthetic interactions. For one interaction between the MBNL1/2 ortholog mbl-1 and the ELAVL ortholog exc-7, double mutants displayed a severely shortened lifespan. Both genes are required for regulating hundreds of transcripts and isoforms, and both may play a critical role in lifespan extension through insulin signaling. Thus, CRISPR-SGI reveals a rich genetic interaction landscape between RNA binding proteins in maintaining organismal health, and will serve as a paradigm applicable to other biological questions.

Article and author information

Author details

  1. Adam D Norris

    FAS Center for Systems Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Xicotencatl Gracida

    FAS Center for Systems Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. John Calarco

    Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
    For correspondence
    john.calarco@utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2197-7801

Funding

NIH Office of the Director (NIH Early Independence Award DP5OD009153)

  • John Calarco

Harvard University (Bauer Fellows Program)

  • John Calarco

University of Toronto

  • John Calarco

Charles King postdoctoral fellowship

  • Adam D Norris

NSERC (Discovery Grant RGPIN-2017-06573)

  • John Calarco

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

Reviewing Editor

  1. Douglas L Black, University of California, Los Angeles, United States

Version history

  1. Received: April 26, 2017
  2. Accepted: July 17, 2017
  3. Accepted Manuscript published: July 18, 2017 (version 1)
  4. Accepted Manuscript updated: July 20, 2017 (version 2)
  5. Version of Record published: August 4, 2017 (version 3)
  6. Version of Record updated: March 13, 2018 (version 4)

Copyright

© 2017, Norris 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. Adam D Norris
  2. Xicotencatl Gracida
  3. John Calarco
(2017)
CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness
eLife 6:e28129.
https://doi.org/10.7554/eLife.28129

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https://doi.org/10.7554/eLife.28129

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