A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions

Abstract

Argonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode C. elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work we systematically analyzed every C. elegans AGO, using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.

Data availability

All high-throughput sequencing data are available through GEO, accession number GSE208702. Custom R scripts are available via GitHub: https://github.com/ClaycombLab/Seroussi_2022. C. elegans strains generated in this study are available through the Caenorhabditis Genetics Center.

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

Article and author information

Author details

  1. Uri Seroussi

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Andrew Lugowski

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Lina Wadi

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Robert X Lao

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Alexandra R Willis

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Winnie Zhao

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. Adam E Sundby

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Amanda G Charlesworth

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  9. Aaron W Reinke

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7612-5342
  10. Julie M Claycomb

    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    For correspondence
    julie.claycomb@utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3132-5206

Funding

Canadian Institutes of Health Research (Project Grant,PJT-156083,Bridge Grant,PJG-175378,Project Grant,PJT-178076)

  • Julie M Claycomb

Canadian Institutes of Health Research (Project Grant,PJT-400784)

  • Aaron W Reinke

Natural Sciences and Engineering Research Council of Canada (Discovery Grant,RGPIN-2020-06235)

  • Julie M Claycomb

Alfred P. Sloan Foundation (Research Fellowship,FG2019-12040)

  • Aaron W Reinke

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

Reviewing Editor

  1. David E James, University of Sydney, Australia

Publication history

  1. Received: September 30, 2022
  2. Accepted: February 14, 2023
  3. Accepted Manuscript published: February 15, 2023 (version 1)

Copyright

© 2023, Seroussi 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. Uri Seroussi
  2. Andrew Lugowski
  3. Lina Wadi
  4. Robert X Lao
  5. Alexandra R Willis
  6. Winnie Zhao
  7. Adam E Sundby
  8. Amanda G Charlesworth
  9. Aaron W Reinke
  10. Julie M Claycomb
(2023)
A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions
eLife 12:e83853.
https://doi.org/10.7554/eLife.83853

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