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Chen TC, Tallo-Parra M, Cao QM, Kadener S, Böttcher R, Pérez-Vilaró G, Boonchuen P, Somboonwiwat K, Díez J, Sarnow P. Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells. PLoS Pathog 2020; 16:e1008346. [PMID: 32764824 PMCID: PMC7437927 DOI: 10.1371/journal.ppat.1008346] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/19/2020] [Accepted: 06/28/2020] [Indexed: 12/14/2022] Open
Abstract
Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded, noncoding RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Though circPSD3 has been shown to bind factor eIF4A3 that modulates the cellular nonsense-mediated decay (NMD) pathway, circPSD3 regulates RNA amplification in a pro-viral manner at a post-translational step, while eIF4A3 exhibits the anti-viral property of the NMD pathway. Findings from the global analyses of the circular RNA landscape argue that pro-, and likely, anti-viral functions are executed by circRNAs that modulate viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis.
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Affiliation(s)
- Tzu-Chun Chen
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Marc Tallo-Parra
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Qian M. Cao
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Sebastian Kadener
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - René Böttcher
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Pérez-Vilaró
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Pakpoom Boonchuen
- Department of Biochemistry, Chulalongkorn University, Bangkog, Thailand
| | | | - Juana Díez
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University SOM, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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