The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans
- Federation University, Australia
- University of Massachusetts Medical School, United States
- Monash University, Australia
- University of Toronto, Canada
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, United States
Abstract
Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 is a bona fide RNA binding protein and, along with RNA-seq data point to a small RNA independent role for NHL-2 in regulating transcripts at the level of RNA stability. Collectively, our data implicate NHL-2 as an essential hub of gene regulatory activity in both the germline and soma.
Data availability
All small RNA and mRNA Illumina sequencing data have been submitted to the NCBI's Sequence Read Archive (SRA), and are included under project accession number SRP115391.
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Caenorhabditis elegans Raw sequences reads NHL-2, Aug 12'17NCBI Sequence Read Archive, SRP115391.
Article and author information
Author details
Funding
National Health and Medical Research Council (606575)
- Peter R Boag
Canada Research Chairs (MOP-274660)
- Julie M Claycomb
Canadian Institutes of Health Research (MOP-125894)
- Quaid D Morris
- Timothy R Hughes
Connaught Fund
- Julie M Claycomb
National Institutes of Health (HD078253)
- Zhiping Weng
Canada Research Chairs (CAP- 783 262134)
- Julie M Claycomb
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans
eLife 7:e35478.
https://doi.org/10.7554/eLife.35478
Further reading
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Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
