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Montavon TC, Baldaccini M, Lefèvre M, Girardi E, Chane-Woon-Ming B, Messmer M, Hammann P, Chicher J, Pfeffer S. Human DICER helicase domain recruits PKR and modulates its antiviral activity. PLoS Pathog 2021; 17:e1009549. [PMID: 33984068 PMCID: PMC8118307 DOI: 10.1371/journal.ppat.1009549] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.
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Affiliation(s)
- Thomas C Montavon
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Morgane Baldaccini
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Mathieu Lefèvre
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Erika Girardi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Mélanie Messmer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Philippe Hammann
- Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg-Esplanade, Strasbourg, France
| | - Johana Chicher
- Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg-Esplanade, Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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2
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Zhang Y, Li Z, Ye Z, Xu Y, Wang B, Wang C, Dai Y, Lu J, Lu B, Zhang W, Li Y. The activation of antiviral RNA interference not only exists in neural progenitor cells but also in somatic cells in mammals. Emerg Microbes Infect 2021; 9:1580-1589. [PMID: 32576094 PMCID: PMC7473182 DOI: 10.1080/22221751.2020.1787798] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The RNA interference (RNAi) pathway directs an important antiviral immunity mechanism in plants and invertebrates. Recently, we and others have demonstrated that the antiviral RNAi response is also conserved in mammals, at least to five distinct RNA viruses, including Zika virus (ZIKV). ZIKV may preferentially infect neuronal progenitor cells (NPCs) in the developing foetal brain. Ex vivo ZIKV infection induces RNAi-mediated antiviral response in human NPCs, but not in the more differentiated NPCs or somatic cells. However, litter is known about the in vivo property or function of the virus-derived small-interfering RNAs (vsiRNAs) targeting ZIKV. Here we report a surprising observation: different from ex vivo observations, viral small RNAs (vsRNAs) targeting ZIKV were produced in vivo upon infection in both central neuron system (CNS) and muscle tissues. In addition, our findings demonstrate the production of canonical vsiRNAs in murine CNS upon antiviral RNAi activation by Sindbis virus (SINV), suggesting the possibility of antiviral immune strategy applied by mammals in the CNS.
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Affiliation(s)
- Yuqiang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhi Ye
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Binbin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Congcong Wang
- State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunpeng Dai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinfeng Lu
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wanju Zhang
- Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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3
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Ren Y, Li X, Tian Z, Xu Y, Zhang R, Li Y. Zebrafish as an animal model for the antiviral RNA interference pathway. J Gen Virol 2021; 102. [PMID: 33507144 DOI: 10.1099/jgv.0.001552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The zebrafish (Danio rerio) possesses evolutionarily conserved innate and adaptive immunity as a mammal and has recently become a popular vertebrate model to exploit infection and immunity. Antiviral RNA interference (RNAi) has been illuminated in various model organisms, including Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and mice. However, to date, there is no report on the antiviral RNAi pathway of zebrafish. Here, we have evaluated the possible use of zebrafish to study antiviral RNAi with Sindbis virus (SINV), vesicular stomatitis virus (VSV) and Nodamura virus (NoV). We find that SINVs and NoVs induce the production of virus-derived small interfering RNAs (vsiRNAs), the hallmark of antiviral RNAi, with a preference for a length of 22 nucleotides, after infection of larval zebrafish. Meanwhile, the suppressor of RNAi (VSR) protein, NoV B2, may affect the accumulation of the NoV in zebrafish. Furthermore, taking advantage of the fact that zebrafish argonaute-2 (Ago2) protein is naturally deficient in cleavage compared with that of mammals, we provide evidence that the slicing activity of human Ago2 can virtually inhibit the accumulation of RNA virus after being ectopically expressed in larval zebrafish. Thus, zebrafish may be a unique model organism to study the antiviral RNAi pathway.
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Affiliation(s)
- Yanxin Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Xueyu Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, PR China
| | - Zhonghui Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Yan Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Ruilin Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan, PR China
| | - Yang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, PR China
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4
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Antiviral RNAi in Insects and Mammals: Parallels and Differences. Viruses 2019; 11:v11050448. [PMID: 31100912 PMCID: PMC6563508 DOI: 10.3390/v11050448] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/26/2022] Open
Abstract
The RNA interference (RNAi) pathway is a potent antiviral defense mechanism in plants and invertebrates, in response to which viruses evolved suppressors of RNAi. In mammals, the first line of defense is mediated by the type I interferon system (IFN); however, the degree to which RNAi contributes to antiviral defense is still not completely understood. Recent work suggests that antiviral RNAi is active in undifferentiated stem cells and that antiviral RNAi can be uncovered in differentiated cells in which the IFN system is inactive or in infections with viruses lacking putative viral suppressors of RNAi. In this review, we describe the mechanism of RNAi and its antiviral functions in insects and mammals. We draw parallels and highlight differences between (antiviral) RNAi in these classes of animals and discuss open questions for future research.
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Beckers M, Mohorianu I, Stocks M, Applegate C, Dalmay T, Moulton V. Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. RNA (NEW YORK, N.Y.) 2017; 23:823-835. [PMID: 28289155 PMCID: PMC5435855 DOI: 10.1261/rna.059360.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this.
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Affiliation(s)
- Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Matthew Stocks
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Christopher Applegate
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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6
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Sharma A, Balakathiresan NS, Maheshwari RK. Chikungunya Virus Infection Alters Expression of MicroRNAs Involved in Cellular Proliferation, Immune Response and Apoptosis. Intervirology 2016; 58:332-41. [PMID: 26829480 DOI: 10.1159/000441309] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE(S) Chikungunya virus (CHIKV) is a reemerging virus of significant importance that has caused large-scale outbreaks in the countries with a temperate climate. CHIKV causes debilitating arthralgia which can persist for weeks and up to a year. Fibroblast cells are the main target of CHIKV infection. In this study, we analyzed microRNA (miRNA) modulation in the fibroblast cells infected with CHIKV at an early stage of infection. METHODS 760 miRNAs were analyzed for modulation following infection with CHIKV at 6 h after infection. Bioinformatic analysis was done to identify the signaling pathway that may be targeted by the significantly modulated miRNAs. Validation of the miRNAs was done using a singleplex miRNA assay and protein target validation of modulated miRNAs was done by Western blot analysis. RESULTS Computational analysis of the significantly modulated miRNAs indicated their involvement in signaling pathways such as Toll-like receptor, mTOR, JAK-STAT and Pi3-Akt pathways, which have been shown to play important roles during CHIKV infection. Topoisomerase IIβ, a target of two of the modulated miRNAs, was downregulated upon CHIKV infection. CONCLUSION(S) We identified several miRNAs that may play important roles in early events after CHIKV infection and can be potential therapeutic targets against CHIKV infection.
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Affiliation(s)
- Anuj Sharma
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Md., USA
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7
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Kang W, Friedländer MR. Computational Prediction of miRNA Genes from Small RNA Sequencing Data. Front Bioeng Biotechnol 2015; 3:7. [PMID: 25674563 PMCID: PMC4306309 DOI: 10.3389/fbioe.2015.00007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/07/2015] [Indexed: 01/19/2023] Open
Abstract
Next-generation sequencing now for the first time allows researchers to gage the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. microRNAs (miRNAs) are 22 nucleotide small RNAs (sRNAs) that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq), which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here, we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field.
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Affiliation(s)
- Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , Stockholm , Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , Stockholm , Sweden
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8
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Schirtzinger EE, Andrade CC, Devitt N, Ramaraj T, Jacobi JL, Schilkey F, Hanley KA. Repertoire of virus-derived small RNAs produced by mosquito and mammalian cells in response to dengue virus infection. Virology 2014; 476:54-60. [PMID: 25528416 DOI: 10.1016/j.virol.2014.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/04/2014] [Accepted: 11/17/2014] [Indexed: 11/26/2022]
Abstract
RNA interference (RNAi) is the major defense of many arthropods against arthropod-borne RNA viruses (arboviruses), but the role of RNAi in vertebrate immunity to arboviruses is not clear. RNA viruses can trigger RNAi in vertebrate cells, but the vertebrate interferon response may obscure this interaction. We quantified virus-derived small RNAs (vRNAs) generated by mosquito (U4.4) cells and interferon-deficient (Vero) and interferon-competent (HuH-7) mammalian cells infected with a single isolate of mosquito-borne dengue virus. Mosquito cells produced significantly more vRNAs than mammalian cells, and mosquito cell vRNAs were derived from both the positive- and negative-sense dengue genomes whereas mammalian cell vRNAs were derived primarily from positive-sense genome. Mosquito cell vRNAs were predominantly 21 nucleotides in length whereas mammalian cell vRNAs were between 12 and 36 nucleotides with a modest peak at 24 nucleotides. Hot-spots, regions of the virus genome that generated a disproportionate number of vRNAs, overlapped among the cell lines.
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Affiliation(s)
| | - Christy C Andrade
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - Nicholas Devitt
- National Center for Genome Resources (NCGR), Santa Fe, NM, USA.
| | | | | | - Faye Schilkey
- National Center for Genome Resources (NCGR), Santa Fe, NM, USA.
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
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9
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The Mammalian response to virus infection is independent of small RNA silencing. Cell Rep 2014; 8:114-25. [PMID: 24953656 DOI: 10.1016/j.celrep.2014.05.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/24/2014] [Accepted: 05/14/2014] [Indexed: 01/18/2023] Open
Abstract
A successful cellular response to virus infection is essential for evolutionary survival. In plants, arthropods, and nematodes, cellular antiviral defenses rely on RNAi. Interestingly, the mammalian response to virus is predominantly orchestrated through interferon (IFN)-mediated induction of antiviral proteins. Despite the potency of the IFN system, it remains unclear whether mammals also have the capacity to employ antiviral RNAi. Here, we investigated this by disabling IFN function, small RNA function, or both activities in the context of virus infection. We find that loss of small RNAs in the context of an in vivo RNA virus infection lowers titers due to reduced transcriptional repression of the host antiviral response. In contrast, enabling a virus with the capacity to inhibit the IFN system results in increased titers. Taken together, these results indicate that small RNA silencing is not a physiological contributor to the IFN-mediated cellular response to virus infection.
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10
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Shapiro JS, Schmid S, Aguado LC, Sabin LR, Yasunaga A, Shim JV, Sachs D, Cherry S, tenOever BR. Drosha as an interferon-independent antiviral factor. Proc Natl Acad Sci U S A 2014; 111:7108-13. [PMID: 24778219 PMCID: PMC4024876 DOI: 10.1073/pnas.1319635111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Utilization of antiviral small interfering RNAs is thought to be largely restricted to plants, nematodes, and arthropods. In an effort to determine whether a physiological interplay exists between the host small RNA machinery and the cellular response to virus infection in mammals, we evaluated antiviral activity in the presence and absence of Dicer or Drosha, the RNase III nucleases responsible for generating small RNAs. Although loss of Dicer did not compromise the cellular response to virus infection, Drosha deletion resulted in a significant increase in virus levels. Here, we demonstrate that diverse RNA viruses trigger exportin 1 (XPO1/CRM1)-dependent Drosha translocation into the cytoplasm in a manner independent of de novo protein synthesis or the canonical type I IFN system. Additionally, increased virus infection in the absence of Drosha was not due to a loss of viral small RNAs but, instead, correlated with cleavage of viral genomic RNA and modulation of the host transcriptome. Taken together, we propose that Drosha represents a unique and conserved arm of the cellular defenses used to combat virus infection.
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Affiliation(s)
- Jillian S Shapiro
- Department of Microbiology,Icahn Graduate School of Biomedical Sciences, and
| | | | - Lauren C Aguado
- Department of Microbiology,Icahn Graduate School of Biomedical Sciences, and
| | - Leah R Sabin
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ari Yasunaga
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029; and
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Benjamin R tenOever
- Department of Microbiology,Icahn Graduate School of Biomedical Sciences, and
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