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.
-
Data from: Tertiary siRNAs mediate paramutation in C. elegansNCBI Gene Expression Omnibus: GSE66344.
-
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/.
-
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.
-
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.
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.
Metrics
-
- 5,353
- views
-
- 752
- downloads
-
- 50
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
Further reading
-
- Developmental Biology
Although the impact of gender-affirming hormone therapy (GAHT) on spermatogenesis in trans women has already been studied, data on its precise effects on the testicular environment is poor. Therefore, this study aimed to characterize, through histological and transcriptomic analysis, the spermatogonial stem cell niche of 106 trans women who underwent standardized GAHT, comprising estrogens and cyproterone acetate. A partial dedifferentiation of Sertoli cells was observed, marked by the co-expression of androgen receptor and anti-Müllerian hormone which mirrors the situation in peripubertal boys. The Leydig cells also exhibited a distribution analogous to peripubertal tissue, accompanied by a reduced insulin-like factor 3 expression. Although most peritubular myoid cells expressed alpha-smooth muscle actin 2, the expression pattern was disturbed. Besides this, fibrosis was particularly evident in the tubular wall and the lumen was collapsing in most participants. A spermatogenic arrest was also observed in all participants. The transcriptomic profile of transgender tissue confirmed a loss of mature characteristics - a partial rejuvenation - of the spermatogonial stem cell niche and, in addition, detected inflammation processes occurring in the samples. The present study shows that GAHT changes the spermatogonial stem cell niche by partially rejuvenating the somatic cells and inducing fibrotic processes. These findings are important to further understand how estrogens and testosterone suppression affect the testis environment, and in the case of orchidectomized testes as medical waste material, their potential use in research.
-
- Computational and Systems Biology
- Developmental Biology
The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in Chinese hamster and mouse cell lines. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors, although Jag1-Notch1 signaling was substantially weaker than other ligand-receptor combinations. Cis-interactions were predominantly inhibitory, with the exception of the Dll1- and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.
