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Ni H, Zhang X, Huang J, Wang M, Cheng A, Liu M, Zhu D, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Ou X, Sun D, Tian B, Jing B, Jia R. Duck plague virus-encoded microRNA dev-miR-D28-3p inhibits viral replication via targeting UL27. Vet Microbiol 2024; 297:110202. [PMID: 39094384 DOI: 10.1016/j.vetmic.2024.110202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Herpesviruses-encoded microRNAs (miRNAs) have been discovered to be essential regulators in viral life cycle, participating in viral replication, latent or lytic infection, and immunological escape. However, the roles of miRNAs encoded by duck plague virus (DPV) are still unknown. Dev-miR-D28-3p is a miRNA uniquely encoded by DPV CHv strain. The aim of this study was to explore the effect of dev-miR-D28-3p on DPV replication and explore the potential mechanisms involved. Our findings demonstrated that transfection of dev-miR-D28-3p mimic into duck embryo fibroblasts (DEFs) effectively suppressed viral copies, viral titers and viral protein expressions during DPV infection, while the results above were reversed after transfection with dev-miR-D28-3p inhibitor. Subsequently, we further discovered that dev-miR-D28-3p specifically bound to DPV-encoded UL27 and inhibited its expression, suggesting that UL27 was the target gene of dev-miR-D28-3p. Finally, we investigated the role of UL27 in DPV replication and found the overexpression of UL27 increased viral copies, viral titers, and viral protein expressions; whereas the opposite results appear when knockdown of UL27. Our findings illustrated a novel mechanism that DPV regulated itself replication via dev-miR-D28-3p, paving the way for exploring the role of DPV-encoded miRNAs.
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Affiliation(s)
- Hui Ni
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Xingcui Zhang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Juan Huang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China.
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Shaqiu Zhang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Xumin Ou
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Di Sun
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Bin Tian
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Bo Jing
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education, Wenjiang District, Chengdu City, Sichuan Province 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu City, Sichuan Province 611130, China.
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Gouzouasis V, Tastsoglou S, Giannakakis A, Hatzigeorgiou AG. Virus-Derived Small RNAs and microRNAs in Health and Disease. Annu Rev Biomed Data Sci 2023; 6:275-298. [PMID: 37159873 DOI: 10.1146/annurev-biodatasci-122220-111429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that can regulate all steps of gene expression (induction, transcription, and translation). Several virus families, primarily double-stranded DNA viruses, encode small RNAs (sRNAs), including miRNAs. These virus-derived miRNAs (v-miRNAs) help the virus evade the host's innate and adaptive immune system and maintain an environment of chronic latent infection. In this review, the functions of the sRNA-mediated virus-host interactions are highlighted, delineating their implication in chronic stress, inflammation, immunopathology, and disease. We provide insights into the latest viral RNA-based research-in silico approaches for functional characterization of v-miRNAs and other RNA types. The latest research can assist toward the identification of therapeutic targets to combat viral infections.
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Affiliation(s)
- Vasileios Gouzouasis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Laboratory of Molecular Genetics, Department of Immunology, Hellenic Pasteur Institute, Athens, Greece
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Athens, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
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Paul S, Saikia M, Chakraborty S. Identification of novel microRNAs in Rous sarcoma Virus (RSV) and their target sites in tumor suppressor genes of chicken. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105139. [PMID: 34798320 DOI: 10.1016/j.meegid.2021.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
A small non-coding, evolutionarily conserved regulatory RNA molecule known as microRNA (miRNA) regulates various cellular activities and pathways. MicroRNAs remain evolutionarily conserved in different species of same taxa. They are present in all organisms including viruses. Viral miRNAs are small, less conserved and less stable and have higher negative minimal folding free energy than miRNAs of different organisms. The size of viral precursor miRNA is approximately 60-119 nucleotides in length. The structure of the mature miRNA sequences is predicted by using higher negative MFE (ΔG) value. Rous sarcoma Virus (RSV), named after its inventor Peyton Rous, has been known for causing tumors in the chicken for which it is known as an oncogenic retrovirus. Using specific criteria we have predicted 5 potential miRNAs in RSV which targeted 8 tumor suppressor genes in Gallus gallus. This study aims to predict the potential miRNAs, secondary structures and their targets for better understanding of the regulatory network of Rous sarcoma virus miRNA in forming sarcoma.
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Affiliation(s)
- Sunanda Paul
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Momi Saikia
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Su J, Wang G, Li C, Xing D, Yan T, Zhu X, Liu Q, Wu Q, Guo X, Zhao T. Screening for differentially expressed miRNAs in Aedes albopictus (Diptera: Culicidae) exposed to DENV-2 and their effect on replication of DENV-2 in C6/36 cells. Parasit Vectors 2019; 12:44. [PMID: 30658692 PMCID: PMC6339288 DOI: 10.1186/s13071-018-3261-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The mosquito Aedes albopictus is an important vector for dengue virus (DENV) transmission. The midgut is the first barrier to mosquito infection by DENV, and this barrier is a critical factor affecting the vector competence of the mosquito. However, the molecular mechanism of the interaction between midgut and virus is unknown. RESULTS Six small libraries of Ae. albopictus midgut RNAs were constructed, three of which from mosquitoes that were infected with DENV-2 after feeding on infected blood, and another three that remained uninfected with DENV-2 after feeding on same batch of infected blood. A total of 46 differentially expressed miRNAs were identified of which 17 significant differentially expressed miRNAs were selected. Compared to microRNA expression profiles of mosquitoes that were uninfected with DENV-2, 15 microRNAs were upregulated and two were downregulated in mosquitoes that were infected with DENV-2. Among these differentially expressed microRNAs, miR-1767, miR-276-3p, miR-4448 and miR-622 were verified by stem-loop qRT-PCR in samples from seven-day-infected and uninfected midguts and chosen for an in vitro transient transfection assay. miR-1767 and miR-276-3p enhanced dengue virus replication in C6/36 cells, and miR-4448 reduced dengue virus replication. CONCLUSIONS To our knowledge, this study is the first to reveal differences in expression levels between mosquitoes infected and uninfected with DENV-2 after feeding on an infected blood meal. It provides useful information on microRNAs expressed in the midgut of Aedes albopictus after exposure to the virus.
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Affiliation(s)
- Jianxin Su
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.,Center for Disease Control and Prevention of Guangzhou Military Region, Guangzhou, 510507, People's Republic of China
| | - Gang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.,Hangzhou Customs District, Hangzhou, 310012, People's Republic of China
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Ting Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaojuan Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qinmei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qun Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoxia Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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Comparison of the MicroRNA Expression Profiles of Male and Female Avian Primordial Germ Cell Lines. Stem Cells Int 2018; 2018:1780679. [PMID: 30123283 PMCID: PMC6079386 DOI: 10.1155/2018/1780679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/08/2018] [Accepted: 06/03/2018] [Indexed: 11/18/2022] Open
Abstract
Primordial germ cells (PGCs) are the precursors of adult germ cells, and among the embryonic stem-like cells in the bird embryo, only they can transmit the genetic information to the next generation. Despite the wide range of applications, very little is known about the mechanism that governs primordial germ cell self-renewal and differentiation. As a first step, we compared 12 newly established chicken PGC lines derived from two different chicken breeds, performing CCK-8 proliferation assay. All of the lines were derived from individual embryos. A significant difference was found among the lines. As microRNAs have been proved to play a key role in the maintenance of pluripotency and the cell cycle regulation of stem cells, we continued with a complex miRNA analysis. We could discover miRNAs expressing differently in PGC lines with high proliferation rate, compared to PGC lines with low proliferation rate. We found that gga-miR-2127 expresses differently in female and male cell lines. The microarray analysis also revealed high expression level of the gga-miR-302b-3p strand (member of the miR-302/367 cluster) in slowly proliferating PGC lines compared to the gga-miR-302b-5p strand. We confirmed that the inhibition of miR-302b-5p significantly increases the doubling time of the examined PGC lines. In conclusion, we found that gga-miR-181-5p, gga-miR-2127, and members of the gga-miR-302/367 cluster have a dominant role in the regulation of avian primordial germ cell proliferation.
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Wu X, Jia R, Zhou J, Wang M, Chen S, Liu M, Zhu D, Zhao X, Sun K, Yang Q, Wu Y, Yin Z, Chen X, Wang J, Cheng A. Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs. BMC Vet Res 2018; 14:144. [PMID: 29704894 PMCID: PMC5923184 DOI: 10.1186/s12917-018-1468-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Duck enteritis virus (DEV) belongs to the family Herpesviridae and is an important epornitic agent that causes economic losses in the waterfowl industry. The Chinese virulent (CHv) and attenuate vaccines (VAC) are two different pathogenic DEV strains. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression in viral infection. Nonetheless, there is little information on virulent duck enteritis virus (DEV)-encoded miRNAs. Results Using high-throughput sequencing, we identified 39 mature viral miRNAs from CHv-infected duck embryo fibroblasts cells. Compared with the reported 33 VAC-encoded miRNAs, only 13 miRNA sequences and 22 “seed sequences” of miRNA were identical, and 8 novel viral miRNAs were detected and confirmed by stem-loop RT-qPCR in this study. Using RNAhybrid and PITA software, 38 CHv-encoded miRNAs were predicted to target 41 viral genes and formed a complex regulatory network. Dual luciferase reporter assay (DLRA) confirmed that viral dev-miR-D8-3p can directly target the 3’-UTR of CHv US1 gene (p < 0.05). Gene Ontology analysis on host target genes of viral miRNAs were mainly involved in biological regulation, cellular and metabolic processes. In addition, 598 novel duck-encoded miRNAs were detected in this study. Thirty-eight host miRNAs showed significant differential expression after CHv infection: 13 miRNAs were up-regulated, and 25 miRNAs were down-regulated, which may affect viral replication in the host cell. Conclusions These data suggested that CHv encoded a different set of microRNAs and formed a unique regulatory network compared with VAC. This is the first report of DEF miRNAs expression profile and an analysis of these miRNAs regulatory mechanisms during DEV infection. These data provide a basis for further exploring miRNA regulatory roles in the pathogenesis of DEV infection and contribute to the understanding of the CHv-host interaction at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12917-018-1468-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianglong Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
| | - Jiakun Zhou
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Kunfeng Sun
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xiaoyue Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Jue Wang
- BGI Genomics Co,shenzhen Ltd, Shenzhen, 518083, Guangdong Province, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
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Dhama K, Kumar N, Saminathan M, Tiwari R, Karthik K, Kumar MA, Palanivelu M, Shabbir MZ, Malik YS, Singh RK. Duck virus enteritis (duck plague) - a comprehensive update. Vet Q 2017; 37:57-80. [PMID: 28320263 DOI: 10.1080/01652176.2017.1298885] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duck virus enteritis (DVE), also called duck plague, is one of the major contagious and fatal diseases of ducks, geese and swan. It is caused by duck enteritis virus (DEV)/Anatid herpesvirus-1 of the genus Mardivirus, family Herpesviridae, and subfamily Alpha-herpesvirinae. Of note, DVE has worldwide distribution, wherein migratory waterfowl plays a crucial role in its transmission within and between continents. Furthermore, horizontal and/ or vertical transmission plays a significant role in disease spread through oral-fecal discharges. Either of sexes from varying age groups of ducks is vulnerable to DVE. The disease is characterized by sudden death, vascular damage and subsequent internal hemorrhage, lesions in lymphoid organs, digestive mucosal eruptions, severe diarrhea and degenerative lesions in parenchymatous organs. Huge economic losses are connected with acute nature of the disease, increased morbidity and mortality (5%-100%), condemnations of carcasses, decreased egg production and hatchability. Although clinical manifestations and histopathology can provide preliminary diagnosis, the confirmatory diagnosis involves virus isolation and detection using serological and molecular tests. For prophylaxis, both live-attenuated and killed vaccines are being used in broiler and breeder ducks above 2 weeks of age. Since DEV is capable of becoming latent as well as shed intermittently, recombinant subunit and DNA vaccines either alone or in combination (polyvalent) are being targeted for its benign prevention. This review describes DEV, epidemiology, transmission, the disease (DVE), pathogenesis, and advances in diagnosis, vaccination and antiviral agents/therapies along with appropriate prevention and control strategies.
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Affiliation(s)
- Kuldeep Dhama
- a Division of Pathology , ICAR - Indian Veterinary Research Institute , Izatnagar , India
| | - Naveen Kumar
- b National Center for Veterinary Type Cultures, ICAR-National Research Center on Equines , Hisar , India
| | - Mani Saminathan
- a Division of Pathology , ICAR - Indian Veterinary Research Institute , Izatnagar , India
| | - Ruchi Tiwari
- c Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences , Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Kumaragurubaran Karthik
- d Central University Laboratory , Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - M Asok Kumar
- a Division of Pathology , ICAR - Indian Veterinary Research Institute , Izatnagar , India
| | - M Palanivelu
- a Division of Pathology , ICAR - Indian Veterinary Research Institute , Izatnagar , India
| | - Muhammad Zubair Shabbir
- e Quality Operations Laboratory , University of Veterinary and Animal Sciences , Lahore , Pakistan
| | - Yashpal Singh Malik
- f Division of Biological Standardization , ICAR - Indian Veterinary Research Institute , Bareilly , India
| | - Raj Kumar Singh
- g ICAR - Indian Veterinary Research Institute , Izatnagar , India
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Zhao J, Schnitzler GR, Iyer LK, Aronovitz MJ, Baur WE, Karas RH. MicroRNA-Offset RNA Alters Gene Expression and Cell Proliferation. PLoS One 2016; 11:e0156772. [PMID: 27276022 PMCID: PMC4898817 DOI: 10.1371/journal.pone.0156772] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/19/2016] [Indexed: 11/29/2022] Open
Abstract
MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We demonstrate that endogenous or over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. We report that there is a “seed region” of moR-21 as well as a “seed match region” in the target gene 3’UTR that are indispensable for moR-21-mediated gene down-regulation. We further demonstrate that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. Taken together, these findings provide the first evidence that microRNA offset RNA alters gene expression and is biologically active.
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Affiliation(s)
- Jin Zhao
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Gavin R. Schnitzler
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Lakshmanan K. Iyer
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Mark J. Aronovitz
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Wendy E. Baur
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
| | - Richard H. Karas
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, United States of America
- * E-mail:
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9
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Donohoe OH, Henshilwood K, Way K, Hakimjavadi R, Stone DM, Walls D. Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. PLoS One 2015; 10:e0125434. [PMID: 25928140 PMCID: PMC4416013 DOI: 10.1371/journal.pone.0125434] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/17/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
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Affiliation(s)
- Owen H. Donohoe
- Marine Institute, Rinville, Oranmore, Co. Galway, Ireland
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | | | - Keith Way
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Roya Hakimjavadi
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), The Nothe, Weymouth, Dorset, the United Kingdom
| | - Dermot Walls
- School of Biotechnology and National Centre for Sensor Research, Dublin City University, Dublin, Ireland
- * E-mail:
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Bhaskaran M, Mohan M. MicroRNAs: history, biogenesis, and their evolving role in animal development and disease. Vet Pathol 2014; 51:759-74. [PMID: 24045890 PMCID: PMC4013251 DOI: 10.1177/0300985813502820] [Citation(s) in RCA: 387] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The discovery of microRNAs (miRNAs) in 1993 followed by developments and discoveries in small RNA biology have redefined the biological landscape by significantly altering the longstanding dogmas that defined gene regulation. These small RNAs play a significant role in modulation of an array of physiological and pathological processes ranging from embryonic development to neoplastic progression. Unique miRNA signatures of various inherited, metabolic, infectious, and neoplastic diseases have added a new dimension to the studies that look at their pathogenesis and highlight their potential to be reliable biomarkers. Also, altering miRNA functionality and the development of novel in vivo delivery systems to achieve targeted modulation of specific miRNA function are being actively pursued as novel approaches for therapeutic intervention in many diseases. Here we review the current body of knowledge on the role of miRNAs in development and disease and discuss future implications.
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Affiliation(s)
- M Bhaskaran
- Infectious Disease Aerobiology, Division of Microbiology, Tulane National Primate Research Center, Covington, LA, USA
| | - M Mohan
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
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11
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Spatz SJ, Volkening JD, Ross TA. Molecular characterization of the complete genome of falconid herpesvirus strain S-18. Virus Res 2014; 188:109-21. [PMID: 24685675 DOI: 10.1016/j.virusres.2014.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 10/25/2022]
Abstract
Falconid herpesvirus type 1 (FaHV-1) is the causative agent of falcon inclusion body disease, an acute, highly contagious disease of raptors. The complete nucleotide sequence of the genome of FaHV-1 has been determined using Illumina MiSeq sequencing. The genome is 204,054 nucleotides in length and has a class E organization. The genome encodes approximately 130 putative protein-coding genes, of which 70 are orthologs of conserved alphaherpesvirus and Mardivirus proteins. Three FaHV-1 genes (UL3.5, UL44.5 and CIRC) were identified that encode protein homologues unique to Mardivirus and Varicellovirus. The genome also encodes homologues to the Mardivirus genes LORF2, LORF3, LORF4, LORF5, SORF3 and SORF4. An opal mutation resulting in premature termination was identified in the FaHV-1 UL43 gene. Phylogenetically, FaHV-1 resides in a monophyletic group with the other Mardiviruses but, along with anatid herpesvirus 1, represents a more distant divergence from the rest of the Mardivirus genus.
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Affiliation(s)
- Stephen J Spatz
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA.
| | | | - Teresa A Ross
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
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Role of virus-encoded microRNAs in Avian viral diseases. Viruses 2014; 6:1379-94. [PMID: 24662606 PMCID: PMC3970156 DOI: 10.3390/v6031379] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/23/2014] [Accepted: 02/28/2014] [Indexed: 12/17/2022] Open
Abstract
With total dependence on the host cell, several viruses have adopted strategies to modulate the host cellular environment, including the modulation of microRNA (miRNA) pathway through virus-encoded miRNAs. Several avian viruses, mostly herpesviruses, have been shown to encode a number of novel miRNAs. These include the highly oncogenic Marek’s disease virus-1 (26 miRNAs), avirulent Marek’s disease virus-2 (36 miRNAs), herpesvirus of turkeys (28 miRNAs), infectious laryngotracheitis virus (10 miRNAs), duck enteritis virus (33 miRNAs) and avian leukosis virus (2 miRNAs). Despite the closer antigenic and phylogenetic relationship among some of the herpesviruses, miRNAs encoded by different viruses showed no sequence conservation, although locations of some of the miRNAs were conserved within the repeat regions of the genomes. However, some of the virus-encoded miRNAs showed significant sequence homology with host miRNAs demonstrating their ability to serve as functional orthologs. For example, mdv1-miR-M4-5p, a functional ortholog of gga-miR-155, is critical for the oncogenicity of Marek’s disease virus. Additionally, we also describe the potential association of the recently described avian leukosis virus subgroup J encoded E (XSR) miRNA in the induction of myeloid tumors in certain genetically-distinct chicken lines. In this review, we describe the advances in our understanding on the role of virus-encoded miRNAs in avian diseases.
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Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. PLoS One 2013; 8:e78316. [PMID: 24250753 PMCID: PMC3824063 DOI: 10.1371/journal.pone.0078316] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/11/2013] [Indexed: 01/01/2023] Open
Abstract
Apoptosis of lymphocytes governs the response of the immune system to environmental stress and toxic insult. Signaling through the ubiquitously expressed glucocorticoid receptor, stress-induced glucocorticoid hormones induce apoptosis via mechanisms requiring altered gene expression. Several reports have detailed the changes in gene expression mediating glucocorticoid-induced apoptosis of lymphocytes. However, few studies have examined the role of non-coding miRNAs in this essential physiological process. Previously, using hybridization-based gene expression analysis and deep sequencing of small RNAs, we described the prevalent post-transcriptional repression of annotated miRNAs during glucocorticoid-induced apoptosis of lymphocytes. Here, we describe the development of a customized bioinformatics pipeline that facilitates the deep sequencing-mediated discovery of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. This analysis identifies the potential presence of over 200 novel glucocorticoid-responsive miRNAs. We have validated the expression of two novel glucocorticoid-responsive miRNAs using small RNA-specific qPCR. Furthermore, through the use of Ingenuity Pathways Analysis (IPA) we determined that the putative targets of these novel validated miRNAs are predicted to regulate cell death processes. These findings identify two and predict the presence of additional novel glucocorticoid-responsive miRNAs in the rat transcriptome, suggesting a potential role for both annotated and novel miRNAs in glucocorticoid-induced apoptosis of lymphocytes.
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14
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An avian retrovirus uses canonical expression and processing mechanisms to generate viral microRNA. J Virol 2013; 88:2-9. [PMID: 24155381 PMCID: PMC3911700 DOI: 10.1128/jvi.02921-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To date, the vast majority of known virus-encoded microRNAs (miRNAs) are derived from polymerase II transcripts encoded by DNA viruses. A recent demonstration that the bovine leukemia virus, a retrovirus, uses RNA polymerase III to directly transcribe the pre-miRNA hairpins to generate viral miRNAs further supports the common notion that the canonical pathway of miRNA biogenesis does not exist commonly among RNA viruses. Here, we show that an exogenous virus-specific region, termed the E element or XSR, of avian leukosis virus subgroup J (ALV-J), a member of avian retrovirus, encodes a novel miRNA, designated E (XSR) miRNA, using the canonical miRNA biogenesis pathway. Detection of novel microRNA species derived from the E (XSR) element, a 148-nucleotide noncoding RNA with hairpin structure, showed that the E (XSR) element has the potential to function as a microRNA primary transcript, demonstrating a hitherto unknown function with possible roles in myeloid leukosis associated with ALV-J.
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Yao Y, Charlesworth J, Nair V, Watson M. MicroRNA expression profiles in avian haemopoietic cells. Front Genet 2013; 4:153. [PMID: 23967013 PMCID: PMC3743212 DOI: 10.3389/fgene.2013.00153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 07/22/2013] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) are small, abundant, non-coding RNAs that modulate gene expression by interfering with translation or stability of mRNA transcripts in a sequence-specific manner. A total of 734 precursor and 996 mature miRNAs have so far been identified in the chicken genome. A number of these miRNAs are expressed in a cell type-specific manner, and understanding their function requires detailed examination of their expression in different cell types. We carried out deep sequencing of small RNA populations isolated from stimulated or transformed avian haemopoietic cell lines to determine the changes in the expression profiles of these important regulatory molecules during these biological events. There were significant changes in the expression of a number of miRNAs, including miR-155, in chicken B cells stimulated with CD40 ligand. Similarly, avian leukosis virus (ALV)-transformed DT40 cells also showed changes in miRNA expression in relation to the naïve cells. Embryonic stem cell line BP25 demonstrated a distinct cluster of upregulated miRNAs, many of which were shown previously to be involved in embryonic stem cell development. Finally, chicken macrophage cell line HD11 showed changes in miRNA profiles, some of which are thought to be related to the transformation by v-myc transduced by the virus. This work represents the first publication of a catalog of microRNA expression in a range of important avian cells and provides insights into the potential roles of miRNAs in the hematopoietic lineages of cells in a model non-mammalian species.
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Affiliation(s)
- Yongxiu Yao
- Avian Viral Diseases Programme, Compton Laboratory, The Pirbright Institute Berkshire, UK
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