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Zhuang G, Zhao X, Jin J, Zhu X, Wang R, Zhai Y, Lu W, Liao Y, Teng M, Yao Y, Nair V, Yao W, Sun A, Luo J, Zhang G. Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo. J Med Virol 2023; 95:e28324. [PMID: 36401345 DOI: 10.1002/jmv.28324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
Dynamic alteration of the epitranscriptome exerts regulatory effects on the lifecycle of oncogenic viruses in vitro. However, little is known about these effects in vivo because of the general lack of suitable animal infection models of these viruses. Using a model of rapid-onset Marek's disease lymphoma in chickens, we investigated changes in viral and host messenger RNA (mRNA) N6-methyladenosine (m6 A) modification during Marek's disease virus (MDV) infection in vivo. We found that the expression of major epitranscriptomic proteins varies among viral infection phases, reprogramming both the viral and the host epitranscriptomes. Specifically, the methyltransferase-like 3 (METTL3)/14 complex was suppressed during the lytic and reactivation phases of the MDV lifecycle, whereas its expression was increased during the latent phase and in MDV-induced tumors. METTL3/14 overexpression inhibits, whereas METTL3/14 knockdown enhances, MDV gene expression and replication. These findings reveal the dynamic features of the mRNA m6 A modification program during viral replication in vivo, especially in relation to key pathways involved in tumorigenesis.
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Affiliation(s)
- Guoqing Zhuang
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuyang Zhao
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaxin Jin
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiaojing Zhu
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Rui Wang
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yunyun Zhai
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenlong Lu
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yifei Liao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yongxiu Yao
- Viral Oncogenesis Group & UK-China Centre of Excellence for Research on Avian Diseases, The Pirbright Institute, Surrey, UK
| | - Venugopal Nair
- Viral Oncogenesis Group & UK-China Centre of Excellence for Research on Avian Diseases, The Pirbright Institute, Surrey, UK
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Aijun Sun
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Gaiping Zhang
- Department of Preventive Medicine, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs of China & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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Naipauer J, García Solá ME, Salyakina D, Rosario S, Williams S, Coso O, Abba MC, Mesri EA, Lacunza E. A Non-Coding RNA Network Involved in KSHV Tumorigenesis. Front Oncol 2021; 11:687629. [PMID: 34222014 PMCID: PMC8242244 DOI: 10.3389/fonc.2021.687629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
Regulatory pathways involving non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNA), have gained great relevance due to their role in the control of gene expression modulation. Using RNA sequencing of KSHV Bac36 transfected mouse endothelial cells (mECK36) and tumors, we have analyzed the host and viral transcriptome to uncover the role lncRNA-miRNA-mRNA driven networks in KSHV tumorigenesis. The integration of the differentially expressed ncRNAs, with an exhaustive computational analysis of their experimentally supported targets, led us to dissect complex networks integrated by the cancer-related lncRNAs Malat1, Neat1, H19, Meg3, and their associated miRNA-target pairs. These networks would modulate pathways related to KSHV pathogenesis, such as viral carcinogenesis, p53 signaling, RNA surveillance, and cell cycle control. Finally, the ncRNA-mRNA analysis allowed us to develop signatures that can be used to an appropriate identification of druggable gene or networks defining relevant AIDS-KS therapeutic targets.
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Affiliation(s)
- Julián Naipauer
- Tumor Biology Program, Sylvester Comprehensive Cancer Center and Miami Center for AIDS Research, Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Martín E. García Solá
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
- Departamento de Fisiología y Biología Molecular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daria Salyakina
- Tumor Biology Program, Sylvester Comprehensive Cancer Center and Miami Center for AIDS Research, Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Santas Rosario
- Tumor Biology Program, Sylvester Comprehensive Cancer Center and Miami Center for AIDS Research, Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sion Williams
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
- Neurology Basic Science Division, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Omar Coso
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
- Departamento de Fisiología y Biología Molecular, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martín C. Abba
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Enrique A. Mesri
- Tumor Biology Program, Sylvester Comprehensive Cancer Center and Miami Center for AIDS Research, Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ezequiel Lacunza
- UM-CFAR/Sylvester CCC Argentina Consortium for Research and Training in Virally Induced AIDS-Malignancies, University of Miami Miller School of Medicine, Miami, FL, United States
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
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The Expression and Nuclear Retention Element of Polyadenylated Nuclear RNA Is Not Required for Productive Lytic Replication of Kaposi's Sarcoma-Associated Herpesvirus. J Virol 2021; 95:e0009621. [PMID: 33853955 DOI: 10.1128/jvi.00096-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic human gammaherpesvirus and the causative agent of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD). During reactivation, viral genes are expressed in a temporal manner. These lytic genes encode transactivators, core replication proteins, or structural proteins. During reactivation, other viral factors that are required for lytic replication are expressed. The most abundant viral transcript is the long noncoding RNA (lncRNA) known as polyadenylated nuclear (PAN) RNA. lncRNAs have diverse functions, including the regulation of gene expression and the immune response. PAN possesses two main cis-acting elements, the Mta response element (MRE) and the expression and nuclear retention element (ENE). While PAN has been demonstrated to be required for efficient viral replication, the function of these elements within PAN remains unclear. Our goal was to determine if the ENE of PAN is required in the context of infection. A KSHV bacmid containing a deletion of the 79-nucleotide (nt) ENE in PAN was generated to assess the effects of the ENE during viral replication. Our studies demonstrated that the ENE is not required for viral DNA synthesis, lytic gene expression, or the production of infectious virus. Although the ENE is not required for viral replication, we found that the ENE functions to retain PAN in the nucleus, and the absence of the ENE results in an increased accumulation of PAN in the cytoplasm. Furthermore, open reading frame 59 (ORF59), LANA, ORF57, H1.4, and H2A still retain the ability to bind to PAN in the absence of the ENE. Together, our data highlight how the ENE affects the nuclear retention of PAN but ultimately does not play an essential role during lytic replication. Our data suggest that PAN may have other functional domains apart from the ENE. IMPORTANCE KSHV is an oncogenic herpesvirus that establishes latency and exhibits episodes of reactivation. KSHV disease pathologies are most often associated with the lytic replication of the virus. PAN RNA is the most abundant viral transcript during the reactivation of KSHV and is required for viral replication. Deletion and knockdown of PAN resulted in defects in viral replication and reduced virion production in the absence of PAN RNA. To better understand how the cis elements within PAN may contribute to its function, we investigated if the ENE of PAN was necessary for viral replication. Although the ENE had previously been extensively studied with both biochemical and in vitro approaches, this is the first study to demonstrate the role of the ENE in the context of infection and that the ENE of PAN is not required for the lytic replication of KSHV.
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Brackett K, Mungale A, Lopez-Isidro M, Proctor DA, Najarro G, Arias C. CRISPR Interference Efficiently Silences Latent and Lytic Viral Genes in Kaposi's Sarcoma-Associated Herpesvirus-Infected Cells. Viruses 2021; 13:783. [PMID: 33924938 PMCID: PMC8146339 DOI: 10.3390/v13050783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022] Open
Abstract
Uncovering viral gene functions requires the modulation of gene expression through overexpression or loss-of-function. CRISPR interference (CRISPRi), a modification of the CRISPR-Cas9 gene editing technology, allows specific and efficient transcriptional silencing without genetic ablation. CRISPRi has been used to silence eukaryotic and prokaryotic genes at the single-gene and genome-wide levels. Here, we report the use of CRISPRi to silence latent and lytic viral genes, with an efficiency of ~80-90%, in epithelial and B-cells carrying multiple copies of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome. Our results validate CRISPRi for the analysis of KSHV viral elements, providing a functional genomics tool for studying virus-host interactions.
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Affiliation(s)
- Kevin Brackett
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Ameera Mungale
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Mary Lopez-Isidro
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Duncan A. Proctor
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Guillermo Najarro
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
| | - Carolina Arias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; (K.B.); (A.M.); (M.L.-I.); (D.A.P.); (G.N.)
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
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5
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Sun A, Zhu X, Liu Y, Wang R, Yang S, Teng M, Zheng L, Luo J, Zhang G, Zhuang G. Transcriptome-wide N6-methyladenosine modification profiling of long non-coding RNAs during replication of Marek's disease virus in vitro. BMC Genomics 2021; 22:296. [PMID: 33888086 PMCID: PMC8063467 DOI: 10.1186/s12864-021-07619-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Background The newly discovered reversible N6-methyladenosine (m6A) modification plays an important regulatory role in gene expression. Long non-coding RNAs (lncRNAs) participate in Marek’s disease virus (MDV) replication but how m6A modifications in lncRNAs are affected during MDV infection is currently unknown. Herein, we profiled the transcriptome-wide m6A modification in lncRNAs in MDV-infected chicken embryo fibroblast (CEF) cells. Results Methylated RNA immunoprecipitation sequencing results revealed that the lncRNA m6A modification is highly conserved with MDV infection increasing the expression of lncRNA m6A modified sites compared to uninfected cell controls. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that lncRNA m6A modifications were highly associated with signaling pathways associated with MDV infection. Conclusions In this study, the alterations seen in transcriptome-wide m6A occurring in lncRNAs following MDV-infection suggest this process plays important regulatory roles during MDV replication. We report for the first time profiling of the alterations in transcriptome-wide m6A modification in lncRNAs of MDV-infected CEF cells.
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Affiliation(s)
- Aijun Sun
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiaojing Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Ying Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Rui Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Shuaikang Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Luping Zheng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.,College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.,Key Laboratory of Animal Immunology, Ministry of Agriculture and Rural Affairs & Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Guoqing Zhuang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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