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

Abstract
Data availability
Article and author information
Metrics

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

1. Seroussi U
2. Lugowski A
3. Wadi L
4. Lao RX
5. Willis AR
6. Zhao W
7. Sundby AE
8. Charlesworth AG
9. Reinke AW
10. Claycomb JM
(2022) Data from: A Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and FunctionsA Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and Functions
NCBI Gene Expression Omnibus, GSE208702.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208702

The following previously published data sets were used

1. Conine CC
2. Batista PJ
3. Gu W
4. Claycomb JM
5. Chaves DA
6. Shirayama M
7. Mello CC
(2010) Data from: Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans
NCBI Gene Expression Omnibus: GSE18731.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18731
1. Vasale JJ
2. Gu W
3. Thivierge C
4. Batista PJ
5. Claycomb JM
6. Youngman EM
7. Duchaine TF
8. Mello CC
9. Conte Jr. D
(2010) Date from: Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway
NCBI Gene Expression Omnibus: GSE18714.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
1. Claycomb JM
2. Batista PJ
3. Pang KM
4. Gu W
5. Vasale JJ
6. van Wolfswinkel JC
7. Chaves DA
8. Shirayama M
9. Mitani S
10. Ketting RF
11. Conte Jr. D
12. Mello CC
(2009) Data from: The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation
NCBI Gene Expression Omnibus: GSE18165.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18165
1. Gu W
2. Shirayama M
3. Conte Jr. D
4. Vasale JJ
5. Batista PJ
6. Claycomb JM
7. Moresco JJ
8. Youngman EM
9. Keys J
10. Stoltz MJ
11. Chen CG
12. Chaves DA
13. Duan Sh
14. Kasschau KD
15. Fahlgren N
16. Yates 3rd JR
17. Mitani S
18. Carrington JC
19. Mello CC
(2009) Data from: Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline
NCBI Gene Expression Omnibus: GSE18215.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18215
(2015) Data from: Tertiary siRNAs mediate paramutation in C. elegans
NCBI Gene Expression Omnibus: GSE66344.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66344
1. Phillips
2. CM
3. Montgomery TA
4. Breen PC
5. Ruvkun G
(2012) Data from: MUT-16 promotes formation of perinuclear Mutator foci required for RNA silencing in the C. elegans germline
N/A Table S3 in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403012/.

http://genesdev.cshlp.org/content/26/13/1433/suppl/DC1
1. Ortiz MA
2. Noble D
3. Sorokin EP
4. Kimble J
(2014) Data from: A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans
N/A Table S1 in https://academic.oup.com/g3journal/article/4/9/1765/6025966#supplementary-data.

https://academic.oup.com/g3journal/article/4/9/1765/6025966
1. Tzur YB
2. Winbter E
3. Gao J
4. Hashimshony T
5. Yanai I
6. Colaiacovo MP
(2018) Data from: Spatiotemporal Gene Expression Analysis of the Caenorhabditis elegans Germline Uncovers a Syncytial Expression Switch
Table S3 in https://figshare.com/articles/dataset/Supplemental_Material_for_Tzur_et_al_2018/6726293?file=12264290.

https://pubmed.ncbi.nlm.nih.gov/30093412/

Article and author information

Author details

Uri Seroussi

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Andrew Lugowski

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Lina Wadi

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Robert X Lao

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Alexandra R Willis

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Winnie Zhao

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Adam E Sundby

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Amanda G Charlesworth

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.
Aaron W Reinke

Department of Molecular Genetics, University of Toronto, Toronto, Canada

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7612-5342
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.

"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.

Copyright

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.