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Liao KC, Xie X, Sundstrom AKB, Lim XN, Tan KK, Zhang Y, Zou J, Bifani AM, Poh HX, Chen JJ, Ng WC, Lim SY, Ooi EE, Sessions OM, Tay Y, Shi PY, Huber RG, Wan Y. Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells. Genome Biol 2023; 24:279. [PMID: 38053173 DOI: 10.1186/s13059-023-03110-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication. RESULTS Here, we use proximity ligation sequencing to identify virus-host RNA interactions for four strains of Zika virus (ZIKV) and one strain of dengue virus (DENV-1) in human cells. We find hundreds of coding and non-coding RNAs that bind to DENV and ZIKV viruses. Host RNAs tend to bind to single-stranded regions along the virus genomes according to hybridization energetics. Compared to SARS-CoV-2 interactors, ZIKV-interacting host RNAs tend to be downregulated upon virus infection. Knockdown of several short non-coding RNAs, including miR19a-3p, and 7SK RNA results in a decrease in viral replication, suggesting that they act as virus-permissive factors. In addition, the 3'UTR of DYNLT1 mRNA acts as a virus-restrictive factor by binding to the conserved dumbbell region on DENV and ZIKV 3'UTR to decrease virus replication. We also identify a conserved set of host RNAs that interacts with DENV, ZIKV, and SARS-CoV-2, suggesting that these RNAs are broadly important for RNA virus infection. CONCLUSIONS This study demonstrates that host RNAs can impact virus replication in permissive and restrictive ways, expanding our understanding of host factors and RNA-based gene regulation during viral pathogenesis.
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Affiliation(s)
- Kuo-Chieh Liao
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna Karin Beatrice Sundstrom
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Xin Ni Lim
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Kiat Kee Tan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Yu Zhang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Amanda Makha Bifani
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hui Xian Poh
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Jia Jia Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wy Ching Ng
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Su Ying Lim
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore
| | - October M Sessions
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
- Department of Pharmacy, National University of Singapore, Singapore, 117559, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Roland G Huber
- Biomolecular Function Discovery, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix #07-01, Singapore, 138671, Singapore.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Boon PLS, Martins AS, Lim XN, Enguita FJ, Santos NC, Bond PJ, Wan Y, Martins IC, Huber RG. Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging. Int J Mol Sci 2023; 24:ijms24098158. [PMID: 37175867 PMCID: PMC10179140 DOI: 10.3390/ijms24098158] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2'-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA-RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.
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Affiliation(s)
- Priscilla L S Boon
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Ana S Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Xin Ni Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 16 Science Drive 4, Singapore 117558, Singapore
| | - Yue Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Ivo C Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Roland G Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore
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