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Ander SE, Carpentier KS, Sanders W, Lucas CJ, Jolly AJ, Johnson CN, Hawman DW, Heise MT, Moorman NJ, Morrison TE. A 44-Nucleotide Region in the Chikungunya Virus 3' UTR Dictates Viral Fitness in Disparate Host Cells. Viruses 2024; 16:861. [PMID: 38932154 PMCID: PMC11209300 DOI: 10.3390/v16060861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
We previously reported that deletion of a 44-nucleotide element in the 3' untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic fibroblasts in a manner independent of the type I interferon response, the same mutation decreases viral fitness in C6/36 mosquito cells. Further, the fitness advantage conferred by the UTR deletion in mammalian cells is maintained in vivo in a mouse model of CHIKV dissemination. Finally, SHAPE-MaP analysis of the CHIKV 3' UTR revealed this 44-nucleotide element forms a distinctive two-stem-loop structure that is ablated in the mutant 3' UTR without altering additional 3' UTR RNA secondary structures.
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Affiliation(s)
- Stephanie E. Ander
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - Kathryn S. Carpentier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - Wes Sanders
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cormac J. Lucas
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - Austin J. Jolly
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - David W. Hawman
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
| | - Mark T. Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel J. Moorman
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas E. Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA (A.J.J.)
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2
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Lodha M, Muchsin I, Jürges C, Juranic Lisnic V, L'Hernault A, Rutkowski AJ, Prusty BK, Grothey A, Milic A, Hennig T, Jonjic S, Friedel CC, Erhard F, Dölken L. Decoding murine cytomegalovirus. PLoS Pathog 2023; 19:e1010992. [PMID: 37172056 DOI: 10.1371/journal.ppat.1010992] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/24/2023] [Accepted: 03/17/2023] [Indexed: 05/14/2023] Open
Abstract
The genomes of both human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) were first sequenced over 20 years ago. Similar to HCMV, the MCMV genome had initially been proposed to harbor ≈170 open reading frames (ORFs). More recently, omics approaches revealed HCMV gene expression to be substantially more complex comprising several hundred viral ORFs. Here, we provide a state-of-the art reannotation of lytic MCMV gene expression based on integrative analysis of a large set of omics data. Our data reveal 365 viral transcription start sites (TiSS) that give rise to 380 and 454 viral transcripts and ORFs, respectively. The latter include >200 small ORFs, some of which represented the most highly expressed viral gene products. By combining TiSS profiling with metabolic RNA labelling and chemical nucleotide conversion sequencing (dSLAM-seq), we provide a detailed picture of the expression kinetics of viral transcription. This not only resulted in the identification of a novel MCMV immediate early transcript encoding the m166.5 ORF, which we termed ie4, but also revealed a group of well-expressed viral transcripts that are induced later than canonical true late genes and contain an initiator element (Inr) but no TATA- or TATT-box in their core promoters. We show that viral upstream ORFs (uORFs) tune gene expression of longer viral ORFs expressed in cis at translational level. Finally, we identify a truncated isoform of the viral NK-cell immune evasin m145 arising from a viral TiSS downstream of the canonical m145 mRNA. Despite being ≈5-fold more abundantly expressed than the canonical m145 protein it was not required for downregulating the NK cell ligand, MULT-I. In summary, our work will pave the way for future mechanistic studies on previously unknown cytomegalovirus gene products in an important virus animal model.
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Affiliation(s)
- Manivel Lodha
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Ihsan Muchsin
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Christopher Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Vanda Juranic Lisnic
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Anne L'Hernault
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Andrzej J Rutkowski
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Bhupesh K Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Arnhild Grothey
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Andrea Milic
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Stipan Jonjic
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität-Würzburg, Würzburg, Germany
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
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3
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Affiliation(s)
- Lucy Ginn
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Manuela La Montagna
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
| | - Qinghua Wu
- College of Life Science Yangtze University Jingzhou Hubei China
- Department of Chemistry Faculty of Science University of Hradec Kralove Hradec Kralove East Bohemia Czech Republic
| | - Lei Shi
- Transcriptional Networks in Lung Cancer Group Cancer Research UK Manchester Institute University of Manchester Manchester UK
- Cancer Research UK Lung Cancer Centre of Excellence At Manchester and University College London England UK
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4
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Finkel Y, Schmiedel D, Tai-Schmiedel J, Nachshon A, Winkler R, Dobesova M, Schwartz M, Mandelboim O, Stern-Ginossar N. Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features. eLife 2020; 9:e50960. [PMID: 31944176 PMCID: PMC6964970 DOI: 10.7554/elife.50960] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Human herpesvirus-6 (HHV-6) A and B are ubiquitous betaherpesviruses, infecting the majority of the human population. They encompass large genomes and our understanding of their protein coding potential is far from complete. Here, we employ ribosome-profiling and systematic transcript-analysis to experimentally define HHV-6 translation products. We identify hundreds of new open reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HHV-6 proteome. By integrating systematic data from the prototypic betaherpesvirus, human cytomegalovirus, we uncover numerous uORFs and iORFs conserved across betaherpesviruses and we show uORFs are enriched in late viral genes. We identified three highly abundant HHV-6 encoded long non-coding RNAs, one of which generates a non-polyadenylated stable intron appearing to be a conserved feature of betaherpesviruses. Overall, our work reveals the complexity of HHV-6 genomes and highlights novel features conserved between betaherpesviruses, providing a rich resource for future functional studies.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Dominik Schmiedel
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
| | | | - Aharon Nachshon
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Roni Winkler
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Martina Dobesova
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Michal Schwartz
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
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Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annu Rev Virol 2019; 6:297-317. [PMID: 31039329 PMCID: PMC6768742 DOI: 10.1146/annurev-virology-092818-015811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Like their host cells, many viruses express noncoding RNAs (ncRNAs). Despite the technical challenge of ascribing function to ncRNAs, diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs.
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Affiliation(s)
- Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Vanessa Mondol
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Salehe Ghasempur
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Seyed F Torabi
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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6
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ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data. QUANTITATIVE BIOLOGY 2019; 6:267-274. [PMID: 31404415 DOI: 10.1007/s40484-018-0141-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post-splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions. Methods We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape. Results We developed ShapeShifter, a novel approach for identifying and quantifying stable lariat species in RNAseq datasets. We learned a characteristic "lariat" curve from ENCODE RNAseq data and were able to estimate abundances for introns based on read coverage. Using this method we discovered new stable introns in these samples that were not represented using the older, branchpoint-traversing read method. Conclusions ShapeShifter provides a robust approach towards detecting and quantifying stable lariat species.
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7
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Hancock MH, Skalsky RL. Roles of Non-coding RNAs During Herpesvirus Infection. Curr Top Microbiol Immunol 2019; 419:243-280. [PMID: 28674945 DOI: 10.1007/82_2017_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Non-coding RNAs (ncRNAs) play essential roles in multiple aspects of the life cycles of herpesviruses and contribute to lifelong persistence of herpesviruses within their respective hosts. In this chapter, we discuss the types of ncRNAs produced by the different herpesvirus families during infection, some of the cellular ncRNAs manipulated by these viruses, and the overall contributions of ncRNAs to the viral life cycle, influence on the host environment, and pathogenesis.
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Affiliation(s)
- Meaghan H Hancock
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA
| | - Rebecca L Skalsky
- Vaccine and Gene Therapy Institute at Oregon Health and Science University, Beaverton, OR, USA.
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8
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An H, Cai Z, Yang Y, Wang Z, Liu DX, Fang S. Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus. Virology 2019; 528:176-180. [PMID: 30616206 PMCID: PMC7112027 DOI: 10.1016/j.virol.2018.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/19/2018] [Accepted: 12/26/2018] [Indexed: 12/12/2022]
Abstract
Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3'-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5' end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism.
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Affiliation(s)
- Hongliu An
- College of Agriculture, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China
| | - Zhichao Cai
- College of Agriculture, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China
| | - Yuying Yang
- College of Animal Sciences, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China
| | - Zhaoxiong Wang
- College of Animal Sciences, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China
| | - Ding Xiang Liu
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, PR China.
| | - Shouguo Fang
- College of Agriculture, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China; College of Animal Sciences, Yangtze University, 88 Jingmilu, Jingzhou 434025, Hubei, PR China.
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9
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Guan X, Liu J, Jiang H, Wu CX, Chen HC, Liu ZF. Expression of pseudorabies virus-encoded long noncoding RNAs in epithelial cells and neurons. J Neurovirol 2018; 24:597-605. [PMID: 29987580 DOI: 10.1007/s13365-018-0651-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in regulating eukaryotic genome replication and gene expression in diverse biological systems. Here, we identified lncRNAs transcribed from pseudorabies virus (PRV)-infected PK-15 cells. Based on high-throughput sequencing data, we obtained 87,263,926 and 93,947,628 clean reads from mock-infected and PRV-infected PK-15 cells, respectively. Through a normalized analytic protocol, we identified three novel viral lncRNAs. According to an analysis of differential expression between the mock-infected and PRV-infected cells, 4151 host lncRNAs were significantly upregulated and 2327 host lncRNAs were significantly downregulated in the latter group. Viral lncRNAs and several host lncRNAs were verified by northern blotting and real-time PCR. The findings showed that the viral lncRNA LDI might regulate the expression of IE180, a potent transcriptional activator of viral genes. Furthermore, we characterized the expression of viral lncRNAs in a culture of infected primary chicken dorsal root ganglia (DRG). Collectively, the obtained data suggest that PRV generates lncRNAs in both epithelial cells and chick DRG neurons.
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Affiliation(s)
- Xiang Guan
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Jiang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Xian Wu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Ahmed W, Liu ZF. Long Non-Coding RNAs: Novel Players in Regulation of Immune Response Upon Herpesvirus Infection. Front Immunol 2018; 9:761. [PMID: 29706968 PMCID: PMC5906719 DOI: 10.3389/fimmu.2018.00761] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Herpesviruses have developed a variety of sophisticated immune evasion strategies to establish lifelong latent infection, including the use of long non-coding RNAs (lncRNAs). In this review, we summarize the lncRNA action modes, i.e., RNA-protein, RNA-RNA, and RNA-DNA interactions, involved in regulating important aspects of immunity by controlling gene expression at various stages. Upon herpesvirus infection, host lncRNAs, such as nuclear paraspeckle assembly transcript 1, negative regulator of antiviral, and B-cell integration cluster have been functionally characterized as negative or positive antiviral regulators in the immune response. Herpesviruses have also evolved multiple strategies to modulate the host immune response using lncRNAs, such as latency-associated transcript, β 2.7 RNA, 5 kb and 7.2 kb lncRNAs, Epstein-Barr virus-encoded non-coding RNA, BamH I-A rightward transcripts, polyadenylated nuclear, and herpesvirus saimiri U-rich RNAs. We discuss the various mechanisms of immune-related lncRNAs, and their diversified and important functions in the modulation of innate and adaptive immunity upon herpesvirus infection as well as in host-pathogen interactions, which will facilitate our understanding of rational design of novel strategies to combat herpesvirus infection.
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Affiliation(s)
- Waqas Ahmed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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11
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Sackman AM, Pfeifer SP, Kowalik TF, Jensen JD. On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts. Pathogens 2018; 7:pathogens7010016. [PMID: 29382090 PMCID: PMC5874742 DOI: 10.3390/pathogens7010016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/08/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a member of the β -herpesvirus subfamily within Herpesviridae that is nearly ubiquitous in human populations, and infection generally results only in mild symptoms. However, symptoms can be severe in immunonaive individuals, and transplacental congenital infection of HCMV can result in serious neurological sequelae. Recent work has revealed much about the demographic and selective forces shaping the evolution of congenitally transmitted HCMV both on the level of hosts and within host compartments, providing insight into the dynamics of congenital infection, reinfection, and evolution of HCMV with important implications for the development of effective treatments and vaccines.
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Affiliation(s)
- Andrew M Sackman
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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12
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Li W, Sheng J, Xu M, Vu GP, Yang Z, Liu Y, Sun X, Trang P, Lu S, Liu F. Inhibition of Murine Cytomegalovirus Infection in Animals by RNase P-Associated External Guide Sequences. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:322-332. [PMID: 29246310 PMCID: PMC5684469 DOI: 10.1016/j.omtn.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 11/21/2022]
Abstract
External guide sequence (EGS) RNAs are associated with ribonuclease P (RNase P), a tRNA processing enzyme, and represent promising agents for gene-targeting applications as they can direct RNase-P-mediated cleavage of a target mRNA. Using murine cytomegalovirus (MCMV) as a model system, we examined the antiviral effects of an EGS variant, which was engineered using in vitro selection procedures. EGSs were used to target the shared mRNA region of MCMV capsid scaffolding protein (mCSP) and assemblin. In vitro, the EGS variant was 60 times more active in directing RNase P cleavage of the target mRNA than the EGS originating from a natural tRNA. In MCMV-infected cells, the variant reduced mCSP expression by 92% and inhibited viral growth by 8,000-fold. In MCMV-infected mice hydrodynamically transfected with EGS-expressing constructs, the EGS variant was more effective in reducing mCSP expression, decreasing viral production, and enhancing animal survival than the EGS originating from a natural tRNA. These results provide direct evidence that engineered EGS variants with higher targeting activity in vitro are also more effective in reducing gene expression in animals. Furthermore, our findings imply the possibility of engineering potent EGS variants for therapy of viral infections.
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Affiliation(s)
- Wei Li
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jingxue Sheng
- Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mengqiong Xu
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Gia-Phong Vu
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zhu Yang
- Jiangsu Affynigen Biotechnolgies, Inc., Taizhou, Jiangsu 225300, China; Guangzhou Qinheli Biotechnolgies, Inc., Guangzhou, Guangdong 510600, China
| | - Yujun Liu
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China; School of Medicine, St. George's University, Grenada, West Indies; School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, China
| | - Xu Sun
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China; Guangzhou Qinheli Biotechnolgies, Inc., Guangzhou, Guangdong 510600, China
| | - Phong Trang
- Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sangwei Lu
- Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Fenyong Liu
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, China; Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, CA 94720, USA; School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA.
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13
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Liu W, Ding C. Roles of LncRNAs in Viral Infections. Front Cell Infect Microbiol 2017; 7:205. [PMID: 28603696 PMCID: PMC5445353 DOI: 10.3389/fcimb.2017.00205] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
Many proteins and signaling pathways participate in anti-viral host responses. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs greater than 200 nucleotides in length, have been recently described as critical regulators in viral infections. Accumulating research indicates that lncRNAs are important in the development and progression of infectious diseases. LncRNAs are not only involved in anti-viral responses, but in many different virus-host interactions, some of which may be beneficial to the virus. Here we review the current knowledge regarding host and viral lncRNAs and their roles in viral infections. In addition, the potential of using lncRNAs as diagnostic biomarkers is discussed.
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Affiliation(s)
- Weiwei Liu
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
| | - Chan Ding
- Avian infectious Department, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural ScienceShanghai, China
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14
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Osman I, Tay MLI, Pek JW. Stable intronic sequence RNAs (sisRNAs): a new layer of gene regulation. Cell Mol Life Sci 2016; 73:3507-19. [PMID: 27147469 PMCID: PMC11108444 DOI: 10.1007/s00018-016-2256-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023]
Abstract
Upon splicing, introns are rapidly degraded. Hence, RNAs derived from introns are commonly deemed as junk sequences. However, the discoveries of intronic-derived small nucleolar RNAs (snoRNAs), small Cajal body associated RNAs (scaRNAs) and microRNAs (miRNAs) suggested otherwise. These non-coding RNAs are shown to play various roles in gene regulation. In this review, we highlight another class of intron-derived RNAs known as stable intronic sequence RNAs (sisRNAs). sisRNAs have been observed since the 1980 s; however, we are only beginning to understand their biological significance. Recent studies have shown or suggested that sisRNAs regulate their own host's gene expression, function as molecular sinks or sponges, and regulate protein translation. We propose that sisRNAs function as an additional layer of gene regulation in the cells.
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Affiliation(s)
- Ismail Osman
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
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15
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Functional Dissection of an Alternatively Spliced Herpesvirus Gene by Splice Site Mutagenesis. J Virol 2016; 90:4626-4636. [PMID: 26912612 DOI: 10.1128/jvi.02987-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Herpesviruses have large and complex DNA genomes. The largest among the herpesviruses, those of the cytomegaloviruses, include over 170 genes. Although most herpesvirus gene products are expressed from unspliced transcripts, a substantial number of viral transcripts are spliced. Some viral transcripts are subject to alternative splicing, which leads to the expression of several proteins from a single gene. Functional analysis of individual proteins derived from an alternatively spliced gene is difficult, as deletion and nonsense mutagenesis, both common methods used in the generation of viral gene knockout mutants, affect several or all gene products at the same time. Here, we show that individual gene products of an alternatively spliced herpesvirus gene can be inactivated selectively by mutagenesis of the splice donor or acceptor site and by intron deletion or substitution mutagenesis. We used this strategy to dissect the essential M112/113 gene of murine cytomegalovirus (MCMV), which encodes the MCMV Early 1 (E1) proteins. The expression of each of the four E1 protein isoforms was inactivated individually, and the requirement for each isoform in MCMV replication was analyzed in fibroblasts, endothelial cells, and macrophages. We show that the E1 p87 isoform, but not the p33, p36, and p38 isoforms, is essential for viral replication in cell culture. Moreover, the presence of one of the two medium-size isoforms (p36 or p38) and the presence of intron 1, but not its specific sequence, are required for viral replication. This study demonstrates the usefulness of splice site mutagenesis for the functional analysis of alternatively spliced herpesvirus genes. IMPORTANCE Herpesviruses include up to 170 genes in their DNA genomes. The functions of most viral gene products remain poorly defined. The construction of viral gene knockout mutants has thus been an important tool for functional analysis of viral proteins. However, this strategy is of limited use when viral gene transcripts are alternatively spliced, leading to the expression of several proteins from a single gene. In this study, we showed, as a proof of principle, that each protein product of an alternatively spliced gene can be eliminated individually by splice site mutagenesis. Mutant viruses lacking individual protein products displayed different phenotypes, demonstrating that the products of alternatively spliced genes have nonredundant functions.
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Abstract
EBV expresses a number of viral noncoding RNAs (ncRNAs) during latent infection, many of which have known regulatory functions and can post-transcriptionally regulate viral and/or cellular gene expression. With recent advances in RNA sequencing technologies, the list of identified EBV ncRNAs continues to grow. EBV-encoded RNAs (EBERs) , the BamHI-A rightward transcripts (BARTs) , a small nucleolar RNA (snoRNA) , and viral microRNAs (miRNAs) are all expressed during EBV infection in a variety of cell types and tumors. Recently, additional novel EBV ncRNAs have been identified. Viral miRNAs, in particular, have been under extensive investigation since their initial identification over ten years ago. High-throughput studies to capture miRNA targets have revealed a number of miRNA-regulated viral and cellular transcripts that tie into important biological networks. Functions for many EBV ncRNAs are still unknown; however, roles for many EBV miRNAs in latency and in tumorigenesis have begun to emerge. Ongoing mechanistic studies to elucidate the functions of EBV ncRNAs should unravel additional roles for ncRNAs in the viral life cycle. In this chapter, we will discuss our current knowledge of the types of ncRNAs expressed by EBV, their potential roles in viral latency, and their potential involvement in viral pathogenesis.
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17
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Pek JW, Okamura K. Regulatory RNAs discovered in unexpected places. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:671-86. [DOI: 10.1002/wrna.1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/14/2015] [Accepted: 08/21/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jun Wei Pek
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory; 1 Research Link, National University of Singapore; Singapore Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore Singapore
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18
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Renzette N, Kowalik TF, Jensen JD. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Mol Ecol 2015. [PMID: 26211679 DOI: 10.1111/mec.13331] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
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Affiliation(s)
- Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.,Immunology and Microbiology Program, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Jeffrey D Jensen
- Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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19
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Zhang Y, Cao X. Long noncoding RNAs in innate immunity. Cell Mol Immunol 2015; 13:138-47. [PMID: 26277893 PMCID: PMC4786632 DOI: 10.1038/cmi.2015.68] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in immune cell development and immune responses through different mechanisms, such as dosage compensation, imprinting, enhancer function, and transcriptional regulation. Although the functions of most lncRNAs are unclear, some lncRNAs have been found to control transcriptional or post-transcriptional regulation of the innate and adaptive immune responses via new methods of protein–protein interactions or pairing with DNA and RNA. Interestingly, increasing evidence has elucidated the importance of lncRNAs in the interaction between hosts and pathogens. In this review, an overview of the lncRNAs modes of action, as well as the important and diversified roles of lncRNAs in immunity, are provided, and an emerging paradigm of lncRNAs in regulating innate immune responses is highlighted.
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20
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Abstract
Eukaryotic cells produce several classes of long and small noncoding RNA (ncRNA). Many DNA and RNA viruses synthesize their own ncRNAs. Like their host counterparts, viral ncRNAs associate with proteins that are essential for their stability, function, or both. Diverse biological roles--including the regulation of viral replication, viral persistence, host immune evasion, and cellular transformation--have been ascribed to viral ncRNAs. In this review, we focus on the multitude of functions played by ncRNAs produced by animal viruses. We also discuss their biogenesis and mechanisms of action.
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Affiliation(s)
- Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Yang Eric Guo
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Nara Lee
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Walter N Moss
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Tenaya K Vallery
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Mingyi Xie
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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21
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Talhouarne GJS, Gall JG. Lariat intronic RNAs in the cytoplasm of Xenopus tropicalis oocytes. RNA (NEW YORK, N.Y.) 2014; 20:1476-87. [PMID: 25051970 PMCID: PMC4138330 DOI: 10.1261/rna.045781.114] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We previously demonstrated that the oocyte nucleus (germinal vesicle or GV) of Xenopus tropicalis contains a population of stable RNA molecules derived from the introns of most expressed genes. Here we show that similar stable intronic sequence (sis) RNAs occur in the oocyte cytoplasm. About 9000 cytoplasmic sisRNAs have been identified, all of which are resistant to the exonuclease RNase R. About half have been confirmed as lariat molecules and the rest are presumed to be lariats, whereas nuclear sisRNAs are a mixture of lariat and linear molecules. Cytoplasmic sisRNAs are more abundant on a molar basis than nuclear sisRNAs and are derived from short introns, mostly under 1 kb in length. Both nuclear and cytoplasmic sisRNAs are transmitted intact to the egg at GV breakdown and persist until at least the blastula stage of embryogenesis, when zygotic transcription begins. We compared cytoplasmic sisRNAs derived from orthologous genes of X. tropicalis and X. laevis, and found that the specific introns from which sisRNAs are derived are not conserved. The existence of sisRNAs in the cytoplasm of the oocyte, their transmission to the fertilized egg, and their persistence during early embryogenesis suggest that they might play a regulatory role in mRNA translation.
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Affiliation(s)
- Gaëlle J S Talhouarne
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Abstract
Cytomegalovirus is a ubiquitous herpesvirus that persistently replicates in glandular epithelial tissue. Murine cytomegalovirus expresses a 7.2-kb-long noncoding RNA (RNA7.2) that is a determinant of viral persistence in the salivary gland. RNA7.2 is an extremely long-lived intron, yet the basis of its stability is unknown. We present data that localize key sequence determinants of RNA stability to the 3' end of RNA7.2 and suggest that stability is a result of sustained lariat conformation.
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23
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The noncoding RNA revolution-trashing old rules to forge new ones. Cell 2014; 157:77-94. [PMID: 24679528 DOI: 10.1016/j.cell.2014.03.008] [Citation(s) in RCA: 1647] [Impact Index Per Article: 164.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/07/2014] [Indexed: 12/14/2022]
Abstract
Noncoding RNAs (ncRNAs) accomplish a remarkable variety of biological functions. They regulate gene expression at the levels of transcription, RNA processing, and translation. They protect genomes from foreign nucleic acids. They can guide DNA synthesis or genome rearrangement. For ribozymes and riboswitches, the RNA structure itself provides the biological function, but most ncRNAs operate as RNA-protein complexes, including ribosomes, snRNPs, snoRNPs, telomerase, microRNAs, and long ncRNAs. Many, though not all, ncRNAs exploit the power of base pairing to selectively bind and act on other nucleic acids. Here, we describe the pathway of ncRNA research, where every established "rule" seems destined to be overturned.
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24
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Abstract
ABSTRACT: Human cytomegalovirus (HCMV) has a tremendous coding capacity within its dsDNA genome that has allowed it to coevolve with its host. Transcription of the virus genome is not limited to protein-coding genes; in fact, most of the transcription from the HCMV genome during lytic replication generates viral ncRNAs that are not translated into protein. Four long ncRNAs (RNA5.0, RNA4.9, RNA1.2 and RNA2.7) account for the majority of HCMV transcription during lytic replication. Here, we review the expression and function of these long ncRNAs in the context of virus replication and pathogenesis. Long ncRNAs may contribute to HCMV evasion of the host response and manipulate cellular and viral programs to successfully persist throughout the lifetime of its host.
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Affiliation(s)
- Toni M Schwarz
- University of Colorado School of Medicine, Department of Microbiology, MS8333, 12800 E 19th Ave, Aurora, CO 80045, USA
| | - Caroline A Kulesza
- University of Colorado School of Medicine, Department of Microbiology, MS8333, 12800 E 19th Ave, Aurora, CO 80045, USA
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25
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Schwarz TM, Volpe LAM, Abraham CG, Kulesza CA. Molecular investigation of the 7.2 kb RNA of murine cytomegalovirus. Virol J 2013; 10:348. [PMID: 24295514 PMCID: PMC4220806 DOI: 10.1186/1743-422x-10-348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background HCMV encodes a stable 5 kb RNA of unknown function that is conserved across cytomegalovirus species. In vivo studies of the MCMV orthologue, a 7.2 kb RNA, demonstrated that viruses that do not express the RNA fail to establish efficient persistent replication in the salivary glands of mice. To gain further insight into the function and properties of this conserved locus, we characterized the MCMV intron in finer detail. Methods We performed multiple analyses to evaluate transcript expression kinetics, identify transcript termini and promoter elements. The half-lives of intron locus RNAs were quantified by measuring RNA levels following actinomycin D treatment in a qRT-PCR-based assay. We also constructed a series of recombinant viruses to evaluate protein coding potential in the locus and test the role of putative promoter elements. These recombinant viruses were tested in both in vitro and in vivo assays. Results We show that the 7.2 kb RNA is expressed with late kinetics during productive infection of mouse fibroblasts. The termini of the precursor RNA that is processed to produce the intron were identified and we demonstrate that the m106 open reading frame, which resides on the spliced mRNA derived from precursor processing, can be translated during infection. Mapping the 5′ end of the primary transcript revealed minimal promoter elements located upstream that contribute to transcript expression. Analysis of recombinant viruses with deletions in the putative promoter elements, however, revealed these elements exert only minor effects on intron expression and viral persistence in vivo. Low transcriptional output by the putative promoter element(s) is compensated by the long half-life of the 7.2 kb RNA of approximately 28.8 hours. Detailed analysis of viral spread prior to the establishment of persistence also showed that the intron is not likely required for efficient spread to the salivary gland, but rather enhances persistent replication in this tissue site. Conclusions This data provides a comprehensive transcriptional analysis of the MCMV 7.2 kb intron locus. Our studies indicate that the 7.2 kb RNA is an extremely long-lived RNA, a feature which is likely to be important in its role promoting viral persistence in the salivary gland.
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Affiliation(s)
| | | | | | - Caroline A Kulesza
- Department of Microbiology, University of Colorado School of Medicine, MS8333, 12800 E, 19th Ave, Aurora, Colorado 80045, USA.
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26
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Juranic Lisnic V, Babic Cac M, Lisnic B, Trsan T, Mefferd A, Das Mukhopadhyay C, Cook CH, Jonjic S, Trgovcich J. Dual analysis of the murine cytomegalovirus and host cell transcriptomes reveal new aspects of the virus-host cell interface. PLoS Pathog 2013; 9:e1003611. [PMID: 24086132 PMCID: PMC3784481 DOI: 10.1371/journal.ppat.1003611] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/26/2013] [Indexed: 11/19/2022] Open
Abstract
Major gaps in our knowledge of pathogen genes and how these gene products interact with host gene products to cause disease represent a major obstacle to progress in vaccine and antiviral drug development for the herpesviruses. To begin to bridge these gaps, we conducted a dual analysis of Murine Cytomegalovirus (MCMV) and host cell transcriptomes during lytic infection. We analyzed the MCMV transcriptome during lytic infection using both classical cDNA cloning and sequencing of viral transcripts and next generation sequencing of transcripts (RNA-Seq). We also investigated the host transcriptome using RNA-Seq combined with differential gene expression analysis, biological pathway analysis, and gene ontology analysis. We identify numerous novel spliced and unspliced transcripts of MCMV. Unexpectedly, the most abundantly transcribed viral genes are of unknown function. We found that the most abundant viral transcript, recently identified as a noncoding RNA regulating cellular microRNAs, also codes for a novel protein. To our knowledge, this is the first viral transcript that functions both as a noncoding RNA and an mRNA. We also report that lytic infection elicits a profound cellular response in fibroblasts. Highly upregulated and induced host genes included those involved in inflammation and immunity, but also many unexpected transcription factors and host genes related to development and differentiation. Many top downregulated and repressed genes are associated with functions whose roles in infection are obscure, including host long intergenic noncoding RNAs, antisense RNAs or small nucleolar RNAs. Correspondingly, many differentially expressed genes cluster in biological pathways that may shed new light on cytomegalovirus pathogenesis. Together, these findings provide new insights into the molecular warfare at the virus-host interface and suggest new areas of research to advance the understanding and treatment of cytomegalovirus-associated diseases.
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Affiliation(s)
- Vanda Juranic Lisnic
- Department of Histology and Embryology and the Center for Proteomics, University of Rijeka School of Medicine, Rijeka, Croatia
| | - Marina Babic Cac
- Department of Histology and Embryology and the Center for Proteomics, University of Rijeka School of Medicine, Rijeka, Croatia
| | - Berislav Lisnic
- Laboratory of Biology and Microbial Genetics, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Tihana Trsan
- Department of Histology and Embryology and the Center for Proteomics, University of Rijeka School of Medicine, Rijeka, Croatia
| | - Adam Mefferd
- The Department of Surgery, The Ohio State University, Columbus, Ohio, United States of America
| | | | - Charles H. Cook
- The Department of Surgery, The Ohio State University, Columbus, Ohio, United States of America
| | - Stipan Jonjic
- Department of Histology and Embryology and the Center for Proteomics, University of Rijeka School of Medicine, Rijeka, Croatia
| | - Joanne Trgovcich
- The Department of Surgery, The Ohio State University, Columbus, Ohio, United States of America
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27
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DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One 2013; 8:e73956. [PMID: 24023918 PMCID: PMC3762708 DOI: 10.1371/journal.pone.0073956] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/24/2013] [Indexed: 11/23/2022] Open
Abstract
Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.
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Affiliation(s)
- Christopher DeBoever
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Erin G. Reid
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Erin N. Smith
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Xiaoyun Wang
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Wilmar Dumaop
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Olivier Harismendy
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
- Clinical and Translational Research Institute, University of California San Diego, La Jolla, California, United States of America
| | - Dennis Carson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Douglas Richman
- VA San Diego Healthcare System and Center for AIDS Research, University of California San Diego, La Jolla, California, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Kelly A. Frazer
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
- Clinical and Translational Research Institute, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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28
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Rubtsova K, Rubtsov AV, van Dyk LF, Kappler JW, Marrack P. T-box transcription factor T-bet, a key player in a unique type of B-cell activation essential for effective viral clearance. Proc Natl Acad Sci U S A 2013; 110:E3216-24. [PMID: 23922396 PMCID: PMC3752276 DOI: 10.1073/pnas.1312348110] [Citation(s) in RCA: 211] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
IgG2a is known to be the most efficient antibody isotype for viral clearance. Here, we demonstrate a unique pathway of B-cell activation, leading to IgG2a production, and involving synergistic stimulation via B-cell antigen receptors, toll-like receptor 7 (TLR7), and IFNγ receptors on B cells. This synergistic stimulation leads to induction of T-box transcription factor T-bet expression in B cells, which, in turn, drives expression of CD11b and CD11c on B cells. T-bet/CD11b/CD11c positive B cells appear during antiviral responses and produce high titers of antiviral IgG2a antibodies that are critical for efficient viral clearance. The results thus demonstrate a previously unknown role for T-bet expression in B cells during viral infections. Moreover, the appearance of T-bet(+) B cells during antiviral responses and during autoimmunity suggests a possible link between these two processes.
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Affiliation(s)
- Kira Rubtsova
- Howard HughesMedical Institute, Denver, CO 80206
- Department of Immunology, National Jewish Health and University of Colorado Health Sciences Center, Denver, CO 80206
| | - Anatoly V. Rubtsov
- Howard HughesMedical Institute, Denver, CO 80206
- Department of Immunology, National Jewish Health and University of Colorado Health Sciences Center, Denver, CO 80206
| | - Linda F. van Dyk
- Department of Immunology, National Jewish Health and University of Colorado Health Sciences Center, Denver, CO 80206
- Departments of Microbiology
| | - John W. Kappler
- Howard HughesMedical Institute, Denver, CO 80206
- Department of Immunology, National Jewish Health and University of Colorado Health Sciences Center, Denver, CO 80206
- Pharmacology, and
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
| | - Philippa Marrack
- Howard HughesMedical Institute, Denver, CO 80206
- Department of Immunology, National Jewish Health and University of Colorado Health Sciences Center, Denver, CO 80206
- Medicine, University of Colorado School of Medicine, Aurora, CO 80045; and
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045
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29
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Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013; 14:543. [PMID: 23937650 PMCID: PMC3751371 DOI: 10.1186/1471-2164-14-543] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/07/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV. RESULTS Novel EBV RNAs and RNA structures were identified by computational modeling and RNA-Seq analyses of EBV. Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the closely related Macacine herpesvirus 4 using the RNAz program discovered 265 regions with high probability of forming conserved RNA structures. Secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. The analysis of RNA-Seq data uncovered the first observation of a stable intronic sequence RNA (sisRNA) in EBV. The abundance of this sisRNA rivals that of the well-known and highly expressed EBV-encoded non-coding RNAs (EBERs). CONCLUSION This work identifies regions of the EBV genome likely to generate functional RNAs and RNA structures, provides structural models for these regions, and discusses potential functions suggested by the modeled structures. Enhanced understanding of the EBV transcriptome will guide future experimental analyses of the discovered RNAs and RNA structures.
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Affiliation(s)
- Walter N Moss
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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Hesselberth JR. Lives that introns lead after splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:677-91. [DOI: 10.1002/wrna.1187] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics; University of Colorado Anschutz Medical School; Aurora CO USA
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Gatherer D, Seirafian S, Cunningham C, Holton M, Dargan DJ, Baluchova K, Hector RD, Galbraith J, Herzyk P, Wilkinson GWG, Davison AJ. High-resolution human cytomegalovirus transcriptome. Proc Natl Acad Sci U S A 2011; 108:19755-60. [PMID: 22109557 PMCID: PMC3241806 DOI: 10.1073/pnas.1115861108] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing was used to bring high resolution to the human cytomegalovirus (HCMV) transcriptome at the stage when infectious virion production is under way, and major findings were confirmed by extensive experimentation using conventional techniques. The majority (65.1%) of polyadenylated viral RNA transcription is committed to producing four noncoding transcripts (RNA2.7, RNA1.2, RNA4.9, and RNA5.0) that do not substantially overlap designated protein-coding regions. Additional noncoding RNAs that are transcribed antisense to protein-coding regions map throughout the genome and account for 8.7% of transcription from these regions. RNA splicing is more common than recognized previously, which was evidenced by the identification of 229 potential donor and 132 acceptor sites, and it affects 58 protein-coding genes. The great majority (94) of 96 splice junctions most abundantly represented in the deep-sequencing data was confirmed by RT-PCR or RACE or supported by involvement in alternative splicing. Alternative splicing is frequent and particularly evident in four genes (RL8A, UL74A, UL124, and UL150A) that are transcribed by splicing from any one of many upstream exons. The analysis also resulted in the annotation of four previously unrecognized protein-coding regions (RL8A, RL9A, UL150A, and US33A), and expression of the UL150A protein was shown in the context of HCMV infection. The overall conclusion, that HCMV transcription is complex and multifaceted, has implications for the potential sophistication of virus functionality during infection. The study also illustrates the key contribution that deep sequencing can make to the genomics of nuclear DNA viruses.
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Affiliation(s)
- Derek Gatherer
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Sepehr Seirafian
- School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom; and
| | - Charles Cunningham
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Mary Holton
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Derrick J. Dargan
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Katarina Baluchova
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Ralph D. Hector
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
| | - Julie Galbraith
- Sir Henry Wellcome Functional Genomics Facility, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Pawel Herzyk
- Sir Henry Wellcome Functional Genomics Facility, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Andrew J. Davison
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G11 5JR, United Kingdom
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Tuddenham L, Pfeffer S. Roles and regulation of microRNAs in cytomegalovirus infection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:613-22. [DOI: 10.1016/j.bbagrm.2011.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/12/2011] [Accepted: 04/14/2011] [Indexed: 12/21/2022]
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Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression at a post-transcriptional level in virtually all eukaryotic organisms and some viruses, particularly herpesviruses. miRNAs are non-immunogenic, stealthy tools for viruses to regulate their as well as host gene expression. The human cytomegalovirus (HCMV) is the major cause of morbidity in immunocompromised patients and allogenic bone-marrow or organ-transplant recipients and the leading cause of congenital birth defects. HCMV miRNAs may provide valuable targets for new urgently needed antiviral drugs. This review focuses on recent findings for viral miRNAs expressed by cytomegaloviruses (CMV) including data from human, chimpanzee, and murine CMV. These are discussed in the context of findings for other viruses to highlight potentially conserved roles exerted by viral miRNAs.
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Effective inhibition in animals of viral pathogenesis by a ribozyme derived from RNase P catalytic RNA. Proc Natl Acad Sci U S A 2008; 105:10919-24. [PMID: 18663226 DOI: 10.1073/pnas.0804922105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A functional RNase P ribozyme (M1GS RNA) was constructed to target the overlapping mRNA region of two murine cytomegalovirus (MCMV) capsid proteins essential for viral replication: the assembly protein (mAP) and M80. The customized ribozyme efficiently cleaved the target mRNA sequence in vitro. Moreover, 80% reduction in the expression of mAP and M80 and a 2,000-fold reduction in viral growth were observed in cells expressing the ribozyme. In contrast, there was no significant reduction in viral gene expression and growth in cells that either did not express the ribozyme or produced a "disabled" ribozyme carrying mutations that abolished its catalytic activity. When the ribozyme-expressing constructs were delivered into MCMV-infected SCID mice via a modified "hydrodynamic transfection" procedure, expression of ribozymes was observed in the livers and spleens. Compared with the control animals that did not receive any M1GS constructs or received the disabled ribozyme construct, animals receiving the functional ribozyme construct exhibited a significant reduction of viral gene expression and infection. Viral titers in the spleens, livers, lungs, and salivary glands of the functional ribozyme-treated SCID mice at 21 days after infection were 200- to 2,000-fold lower than those in the control animals. Moreover, survival of the infected animals significantly improved upon receiving the functional ribozyme construct. Our study examines the use of M1GS ribozymes for inhibition of gene expression in animals and demonstrates the utility of RNase P ribozymes for gene targeting applications in vivo.
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Laboratory strains of murine cytomegalovirus are genetically similar to but phenotypically distinct from wild strains of virus. J Virol 2008; 82:6689-96. [PMID: 18417589 DOI: 10.1128/jvi.00160-08] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Murine cytomegalovirus (MCMV) is widely used to model human cytomegalovirus (HCMV) infection. However, it is known that serially passaged laboratory strains of HCMV differ significantly from recently isolated clinical strains of HCMV. It is therefore axiomatic that clinical models of HCMV using serially passaged strains of MCMV may not be able to fully represent the complexities of the system they are attempting to model and may not fully represent the complex biology of MCMV. To determine whether genotypic and phenotypic differences also exist between laboratory strains of MCMV and wild derived strains of MCMV, we sequenced the genomes of three low-passage strains of MCMV, plus the laboratory strain, K181. We coupled this genetic characterization to their phenotypic characteristics. In contrast to what is seen with HCMV (and rhesus CMV), there were no major genomic rearrangements in the MCMV genomes. In addition, the genome size was remarkably conserved between MCMV strains with no major insertions or deletions. There was, however, significant sequence variation between strains of MCMV, particularly at the genomic termini. These more subtle genetic differences led to considerable differences in in vivo replication with some strains of MCMV, such as WP15B, replicating preferentially in otherwise-MCMV-resistant C57BL/6 mice. CBA mice were no more resistant to MCMV than C57BL/6 mice and for some MCMV strains appeared to control infection less well than C57BL/6 mice. It is apparent that the previously described host resistance patterns of inbred mice and MCMV are not consistently applicable for all MCMV strains.
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Reddehase MJ, Simon CO, Seckert CK, Lemmermann N, Grzimek NKA. Murine model of cytomegalovirus latency and reactivation. Curr Top Microbiol Immunol 2008; 325:315-31. [PMID: 18637514 DOI: 10.1007/978-3-540-77349-8_18] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Efficient resolution of acute cytopathogenic cytomegalovirus infection through innate and adaptive host immune mechanisms is followed by lifelong maintenance of the viral genome in host tissues in a state of replicative latency, which is interrupted by episodes of virus reactivation for transmission. The establishment of latency is the result of aeons of co-evolution of cytomegaloviruses and their respective host species. Genetic adaptation of a particular cytomegalovirus to its specific host is reflected by private gene families not found in other members of the cytomegalovirus group, whereas basic functions of the viral replicative cycle are encoded by public gene families shared between different cytomegaloviruses or even with herpesviruses in general. Private genes include genes coding for immunoevasins, a group of glycoproteins specifically dedicated to dampen recognition by the host's innate and adaptive immune surveillance to protect the virus against elimination. Recent data in the mouse model of cytomegalovirus latency have indicated that viral replicative latency established in the immunocompetent host is a dynamic state characterized by episodes of viral gene desilencing and immune sensing of reactivated presentation of antigenic peptides at immunological checkpoints by CD8 T cells. This sensing maintains viral replicative latency by triggering antiviral effector functions that terminate the viral gene expression program before infectious viral progeny are assembled. According to the immune sensing hypothesis of latency control, immunological checkpoints are unique for each infected individual in reflection of host MHC (HLA) polymorphism and the proteome(s) of the viral variant(s) harbored in latency.
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Affiliation(s)
- M J Reddehase
- Institute for Virology, Johannes Gutenberg-University, Obere Zahlbacher Strasse 67, Hochhaus am Augustusplatz, 55131, Mainz, Germany.
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Abstract
Human cytomegalovirus (HCMV) contains a large and complex E-type genome. There are both clinical isolates of the virus that have been passaged minimally in fibroblasts and so-called laboratory strains that have been extensively passaged and adapted to growth in fibroblasts. The genomes of laboratory strains have undergone rearrangements. To date, the genomes of five clinical isolates have been sequenced. We have re-evaluated the coding content of clinical isolates by identifying the set of open reading frames (ORFs) that are conserved in all five sequenced clinical isolates. We have further determined which of these ORFs are present in the chimpanzee cytomegalovirus (CCMV) genome. A total of 173 ORFs are present in all HCMV genomes and the CCMV genome, and we conclude that these ORFs are very likely to be functional. An additional 59 ORFs are present in the genomes of all five HCMV isolates, but not in CCMV. We have discounted 26 of this latter set of ORFs, because they reside in regions of the genome unlikely to encode functional ORFs. The remaining 33 ORFs are potentially functional ORFs that are specific to HCMV.
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Affiliation(s)
- E Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
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Buck AH, Santoyo-Lopez J, Robertson KA, Kumar DS, Reczko M, Ghazal P. Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J Virol 2007; 81:13761-70. [PMID: 17928340 PMCID: PMC2168849 DOI: 10.1128/jvi.01290-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 10/01/2007] [Indexed: 01/07/2023] Open
Abstract
The prevalence and importance of microRNAs (miRNAs) in viral infection are increasingly relevant. Eleven miRNAs were previously identified in human cytomegalovirus (HCMV); however, miRNA content in murine CMV (MCMV), which serves as an important in vivo model for CMV infection, has not previously been examined. We have cloned and characterized 17 novel miRNAs that originate from at least 12 precursor miRNAs in MCMV and are not homologous to HCMV miRNAs. In parallel, we applied a computational analysis, using a support vector machine approach, to identify potential precursor miRNAs in MCMV. Four of the top 10 predicted precursor sequences were cloned in this study, and the combination of computational and cloning analysis demonstrates that MCMV has the capacity to encode miRNAs clustered throughout the genome. On the basis of drug sensitivity experiments for resolving the kinetic class of expression, we show that the MCMV miRNAs are both early and late gene products. Notably, the MCMV miRNAs occur on complementary strands of the genome in specific regions, a feature which has not previously been observed for viral miRNAs. One cluster of miRNAs occurs in close proximity to the 5' splice site of the previously identified 7.2-kb stable intron, implying a variety of potential regulatory mechanisms for MCMV miRNAs.
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Affiliation(s)
- Amy H Buck
- Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom.
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Tailor P, Tamura T, Kong HJ, Kubota T, Kubota M, Borghi P, Gabriele L, Ozato K. The feedback phase of type I interferon induction in dendritic cells requires interferon regulatory factor 8. Immunity 2007; 27:228-39. [PMID: 17702615 PMCID: PMC2768351 DOI: 10.1016/j.immuni.2007.06.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 04/03/2007] [Accepted: 06/11/2007] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DCs) produce type I interferons (IFNs) in greater amounts than other cells, but the mechanisms remain elusive. Here we studied the role of a transcription factor, IRF8, in DC induction of type I IFNs. Upon newcastle disease virus (NDV) infection, bone marrow-derived plasmacytoid and conventional DCs induced IFN transcripts, exhibiting two-phase kinetics. The second, amplifying phase represented an IFN feedback response that accounted for much of IFN protein production. Induction of second phase transcription required IRF8. Mouse cytomegalovirus (MCMV) and Toll-like receptor-mediated IFN induction in DCs also required IRF8. Chromatin immunoprecipitation analysis showed that IRF7, IRF8, and RNA polymerase II were recruited to the IFN promoters upon stimulation. Moreover, sustained RNA polymerase II recruitment to the promoters critically depended on IRF8. Together, these data indicate that IRF8 magnifies the second phase of IFN transcription in DCs by prolonging binding of basic transcription machinery to the IFN promoters, thereby playing a role in innate immunity.
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Affiliation(s)
- Prafullakumar Tailor
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
| | - Tomohiko Tamura
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
| | - Hee Jeong Kong
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
| | - Toru Kubota
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
| | - Mayumi Kubota
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
| | - Paola Borghi
- Laboratory of Virology, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gabriele
- Laboratory of Virology, Istituto Superiore di Sanità, Rome, Italy
| | - Keiko Ozato
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, &National Institutes of Health, Bethesda MD 20892
- Corresponding author: Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Room 2A01, Building 6, 6 Center Drive, Bethesda MD 20892-2753, TEL: (301) 496-9184 Fax (301) 402-2974,
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