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Ma Q, Li L, Tang Y, Fu Q, Liu S, Hu S, Qiao J, Chen C, Ni W. Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection. Res Vet Sci 2017; 115:508-516. [PMID: 28968572 DOI: 10.1016/j.rvsc.2017.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/13/2017] [Accepted: 09/22/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND Bovine viral diarrhea virus (BVDV) infection is a dynamic and complex process that leads to significant economic losses in the dairy and cattle industries. However, our understanding of the protective and pathological mechanism underlying host infection is limited. METHODS To determine whether BVDV regulates specific activities of the host cell, the expression of long non-coding RNA (lncRNA) during BVDV NADL infection was studied by deep sequencing. RESULTS A total of 1236 lncRNA transcripts and 3261 mRNA transcripts were differentially regulated at 2h, 6h, and 18h post-infection. The lncRNAs shared same characteristics with other mammals in terms of exon length, number, expression level, and conservation. The Gene Ontology (GO) enrichment and KEGG pathway analyses showed that lncRNAs regulate immune reaction during BVDV infection. Thirteen differentially expressed genes in 18 hpi were selected and independently validated by reverse-transcription qPCR. CONCLUSIONS The present study is the first to provide insights into the biological connection of lncRNAs and BVDV, which can be further explored for the development of antiviral prevention strategies and in understanding persistent infection between viral and host components.
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Affiliation(s)
- Qiman Ma
- College of Medicine, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Liangyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Yan Tang
- Animal Science and Technology Branch, Xinjiang Agricultural Vocational Technical College, Changji, Xinjiang 831100, China
| | - Qiang Fu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Sheng Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shengwei Hu
- College of Life Technology, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Chuangfu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Wei Ni
- College of Life Technology, Shihezi University, Shihezi, Xinjiang 832003, China.
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Balloy V, Koshy R, Perra L, Corvol H, Chignard M, Guillot L, Scaria V. Bronchial Epithelial Cells from Cystic Fibrosis Patients Express a Specific Long Non-coding RNA Signature upon Pseudomonas aeruginosa Infection. Front Cell Infect Microbiol 2017; 7:218. [PMID: 28611953 PMCID: PMC5447040 DOI: 10.3389/fcimb.2017.00218] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/11/2017] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas aeruginosa (Pa) is the leading cause of chronic lung infection in Cystic Fibrosis (CF) patients. It is well recognized that CF epithelial cells fail to develop an appropriate response to infection, allowing bacterial colonization and a chronic inflammatory response. Since long non-coding RNAs (lncRNAs), are known to play a key role in regulating mammalian innate immune response, we hypothesized that CF cells exposed to Pa could express a specific lncRNA signature responsible of the maladaptative CF response. We analyzed transcriptomic datasets to compare the expression profiles of lncRNAs in primary CF and non-CF epithelial cells infected with Pa at 0, 2, 4, and 6 h of infection. Our analysis identified temporal expression signatures of 25, 73, 15, and 26 lncRNA transcripts differentially expressed at 0, 2, 4, and 6 h post-infection respectively, between CF and non-CF cells. In addition, we identified profiles specific to CF and non-CF cells. The differential expression of two candidate lncRNAs were independently validated using real-time PCR. We identified a specific CF signature of lncRNA expression in a context of Pa infection that could potentially play a role in the maladaptive immune response of CF patients.
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Affiliation(s)
- Viviane Balloy
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA)Paris, France
| | - Remya Koshy
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative BiologyDelhi, India
| | - Lea Perra
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA)Paris, France
| | - Harriet Corvol
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA)Paris, France.,Pneumologie Pédiatrique, AP-HP, Hôpital TrousseauParis, France
| | - Michel Chignard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA)Paris, France
| | - Loïc Guillot
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Centre de Recherche Saint-Antoine (CRSA)Paris, France
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative BiologyDelhi, India.,CSIR Institute of Genomics and Integrative Biology, Academy of Scientific and Innovative ResearchDelhi, India
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Ouyang J, Zhu X, Chen Y, Wei H, Chen Q, Chi X, Qi B, Zhang L, Zhao Y, Gao GF, Wang G, Chen JL. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe 2014; 16:616-26. [PMID: 25525793 PMCID: PMC7104942 DOI: 10.1016/j.chom.2014.10.001] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/04/2014] [Accepted: 09/15/2014] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) modulate various biological processes, but their role in host antiviral responses is largely unknown. Here we identify a lncRNA as a key regulator of antiviral innate immunity. Following from the observation that a lncRNA that we call negative regulator of antiviral response (NRAV) was dramatically downregulated during infection with several viruses, we ectopically expressed NRAV in human cells or transgenic mice and found that it significantly promotes influenza A virus (IAV) replication and virulence. Conversely, silencing NRAV suppressed IAV replication and virus production, suggesting that reduction of NRAV is part of the host antiviral innate immune response to virus infection. NRAV negatively regulates the initial transcription of multiple critical interferon-stimulated genes (ISGs), including IFITM3 and MxA, by affecting histone modification of these genes. Our results provide evidence for a lncRNA in modulating the antiviral interferon response.
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Affiliation(s)
- Jing Ouyang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaomei Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Anhui University, Hefei 230601, China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Wei
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinghuang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaojuan Chi
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baomin Qi
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Beijing 100021, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoshun Wang
- Gene Therapy Program, Departments of Microbiology and Immunology, Medicine and Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ji-Long Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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