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Xu J, Sabatino B, Yan J, Ermakova G, Doering KRS, Taubert S. The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks. G3 (Bethesda) 2024; 14:jkae017. [PMID: 38267027 PMCID: PMC10989892 DOI: 10.1093/g3journal/jkae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
All animals must maintain genome and proteome integrity, especially when experiencing endogenous or exogenous stress. To cope, organisms have evolved sophisticated and conserved response systems: unfolded protein responses (UPRs) ensure proteostasis, while DNA damage responses (DDRs) maintain genome integrity. Emerging evidence suggests that UPRs and DDRs crosstalk, but this remains poorly understood. Here, we demonstrate that depletion of the DNA primases pri-1 or pri-2, which synthesize RNA primers at replication forks and whose inactivation causes DNA damage, activates the UPR of the endoplasmic reticulum (UPR-ER) in Caenorhabditis elegans, with especially strong activation in the germline. We observed activation of both the inositol-requiring-enzyme 1 (ire-1) and the protein kinase RNA-like endoplasmic reticulum kinase (pek-1) branches of the (UPR-ER). Interestingly, activation of the (UPR-ER) output gene heat shock protein 4 (hsp-4) was partially independent of its canonical activators, ire-1 and X-box binding protein (xbp-1), and instead required the third branch of the (UPR-ER), activating transcription factor 6 (atf-6), suggesting functional redundancy. We further found that primase depletion specifically induces the (UPR-ER), but not the distinct cytosolic or mitochondrial UPRs, suggesting that primase inactivation causes compartment-specific rather than global stress. Functionally, loss of ire-1 or pek-1 sensitizes animals to replication stress caused by hydroxyurea. Finally, transcriptome analysis of pri-1 embryos revealed several deregulated processes that could cause (UPR-ER) activation, including protein glycosylation, calcium signaling, and fatty acid desaturation. Together, our data show that the (UPR-ER), but not other UPRs, responds to replication fork stress and that the (UPR-ER) is required to alleviate this stress.
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Affiliation(s)
- Jiaming Xu
- Graduate Program in Cell & Developmental Biology, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Brendil Sabatino
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Junran Yan
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Edwin S.H. Leong Centre for Healthy Aging, The University of British Columbia, 117-2194 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Glafira Ermakova
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Edwin S.H. Leong Centre for Healthy Aging, The University of British Columbia, 117-2194 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Kelsie R S Doering
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Edwin S.H. Leong Centre for Healthy Aging, The University of British Columbia, 117-2194 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Stefan Taubert
- Graduate Program in Cell & Developmental Biology, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- British Columbia Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
- Edwin S.H. Leong Centre for Healthy Aging, The University of British Columbia, 117-2194 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, The University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada
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Brown JS, Zhang D, Gaylord O, Chen W, Lee HC. Sensitized piRNA reporter identifies multiple RNA processing factors involved in piRNA-mediated gene silencing. Genetics 2023; 224:iyad095. [PMID: 37210214 PMCID: PMC10691750 DOI: 10.1093/genetics/iyad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/10/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
Metazoans guard their germlines against transposons and other foreign transcripts with PIWI-interacting RNAs (piRNAs). Due to the robust heritability of the silencing initiated by piRNAs in Caenorhabditis elegans (C. elegans), previous screens using C. elegans were strongly biased to uncover members of this pathway in the maintenance process but not in the initiation process. To identify novel piRNA pathway members, we have utilized a sensitized reporter strain which detects defects in initiation, amplification, or regulation of piRNA silencing. Using our reporter, we have identified Integrator complex subunits, nuclear pore components, protein import components, and pre-mRNA splicing factors as essential for piRNA-mediated gene silencing. We found the small nuclear processing cellular machine termed the Integrator complex is required for both type I and type II piRNA production. Notably, we identified a role for nuclear pore and nucleolar components NPP-1/Nup54, NPP-6/Nup160, NPP-7/Nup153, and FIB-1 in promoting the perinuclear localization of anti-silencing CSR-1 Argonaute, as well as a role for Importin factor IMA-3 in nuclear localization of silencing Argonaute HRDE-1. Together, we have shown that piRNA silencing in C. elegans is dependent on evolutionarily ancient RNA processing machinery that has been co-opted to function in the piRNA-mediated genome surveillance pathway.
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Affiliation(s)
- Jordan S Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Donglei Zhang
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Olivia Gaylord
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wenjun Chen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong Province 510000, China
| | - Heng-Chi Lee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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