A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions
- University of Toronto, Canada
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.
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Data from: Tertiary siRNAs mediate paramutation in C. elegansNCBI Gene Expression Omnibus: GSE66344.
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Data from: MUT-16 promotes formation of perinuclear Mutator foci required for RNA silencing in the C. elegans germlineN/A Table S3 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403012/.
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Data from: A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegansN/A Table S1 in https://academic.oup.com/g3journal/article/4/9/1765/6025966#supplementary-data.
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Data from: Spatiotemporal Gene Expression Analysis of the Caenorhabditis elegans Germline Uncovers a Syncytial Expression SwitchTable S3 in https://figshare.com/articles/dataset/Supplemental_Material_for_Tzur_et_al_2018/6726293?file=12264290.
Article and author information
Author details
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
- David E James, University of Sydney, Australia
Version history
- Preprint posted: August 8, 2022 (view preprint)
- Received: September 30, 2022
- Accepted: February 14, 2023
- Accepted Manuscript published: February 15, 2023 (version 1)
- Version of Record published: April 13, 2023 (version 2)
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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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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