MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection

Wu, Shusheng; Liu, Liyue; Zohaib, Ali; Lin, Li; Yuan, Junfa; Wang, Min; Liu, Xueqin

doi:10.1016/j.dci.2014.09.012

Cited by 22 publications

(10 citation statements)

References 40 publications

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“…Therefore, different miRNA expression profiles might be acquired when we use different tissues from the same organism. The miRNA expression profile of several teleost fishes has recently been identified in different tissues, including bighead carp and silver carp [ 23 ], common carp [ 24 ], blunt snout bream [ 25 ] and epithelial cells of carp [ 14 ]. Since SHVV could infect and replicate in several tissues of snakehead fish [ 18 ], we choose SNN-1 cells, which are derived from a whole snakehead fry fish [ 26 ], to study the differential miRNA expression profile of snakehead fish upon SHVV infection.…”

Section: Discussionmentioning

confidence: 99%

“…The RNA samples were subjected to 15% polyacrylamide gel electrophoresis (PAGE) for the enrichment of molecules with a length of 17–30 nt [ 14 ]. After 5′ and 3′ adaptors were added, RT-PCR with adaptor-specific primers was used to generate a small RNA library from SHVV-infected and non-infected SSN-1 cells at 3 and 24 h poi.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, miRNAs are also involved in the modulation of gene expression and replication of viruses and play a pivotal role in host-virus interactions [ 1 , 13 ]. Therefore, the study of miRNA-mediated host-virus interactions is important to understand the mechanisms of virus infection and host counteraction [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection

Liu

Yuan

et al. 2016

IJMS

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MicroRNAs (miRNAs) play important roles in mediating multiple biological processes in eukaryotes and are being increasingly studied to evaluate their roles associated with cellular changes following viral infection. Snakehead fish Vesiculovirus (SHVV) has caused mass mortality in snakehead fish during the past few years. To identify specific miRNAs involved in SHVV infection, we performed microRNA deep sequencing on a snakehead fish cell line (SSN-1) with or without SHVV infection. A total of 205 known miRNAs were identified when they were aligned with the known zebrafish miRNAs, and nine novel miRNAs were identified using MiRDeep2 software. Eighteen and 143 of the 205 known miRNAs were differentially expressed at three and 24 h post-infection (poi), respectively. From the differentially-expressed miRNAs, five were randomly selected to validate their expression profiles using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and their expression profiles were consistent with the microRNA sequencing results. In addition, the target gene prediction of the SHVV genome was performed for the differentially-expressed host miRNAs, and a total of 10 and 58 differentially-expressed miRNAs were predicted to bind to the SHVV genome at three and 24 h poi, respectively. The effects of three selected miRNAs (miR-130-5p, miR-214 and miR-216b) on SHVV multiplication were evaluated using their mimics and inhibitors via qRT-PCR and Western blotting. The results showed that all three miRNAs were able to inhibit the multiplication of SHVV; whereas the mechanisms underlying the SHVV multiplication inhibited by the specific miRNAs need to be further characterized in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection

Liu

Yuan

et al. 2016

IJMS

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“…Accordingly, our most recent data thus suggest that these two miRNAs contribute to the IFN-related innate protection as induced by the TLR3 agonist poly I:C [ 102 ]. Very recently, the miRNA response to another fish rhabdovirus, Spring viremia of carp virus (SVCV), was studied in cell culture, and among many others, miR-462 and miR-731 were found only to be moderately upregulated [ 103 ]. However, in vivo experiments will be needed to determine how these findings relate to our observations.…”

Section: Discussionmentioning

confidence: 99%

Two Virus-Induced MicroRNAs Known Only from Teleost Fishes Are Orthologues of MicroRNAs Involved in Cell Cycle Control in Humans

et al. 2015

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MicroRNAs (miRNAs) are ~22 base pair-long non-coding RNAs which regulate gene expression in the cytoplasm of eukaryotic cells by binding to specific target regions in mRNAs to mediate transcriptional blocking or mRNA cleavage. Through their fundamental roles in cellular pathways, gene regulation mediated by miRNAs has been shown to be involved in almost all biological phenomena, including development, metabolism, cell cycle, tumor formation, and host-pathogen interactions. To address the latter in a primitive vertebrate host, we here used an array platform to analyze the miRNA response in rainbow trout (Oncorhynchus mykiss) following inoculation with the virulent fish rhabdovirus Viral hemorrhagic septicaemia virus. Two clustered miRNAs, miR-462 and miR-731 (herein referred to as miR-462 cluster), described only in teleost fishes, were found to be strongly upregulated, indicating their involvement in fish-virus interactions. We searched for homologues of the two teleost miRNAs in other vertebrate species and investigated whether findings related to ours have been reported for these homologues. Gene synteny analysis along with gene sequence conservation suggested that the teleost fish miR-462 and miR-731 had evolved from the ancestral miR-191 and miR-425 (herein called miR-191 cluster), respectively. Whereas the miR-462 cluster locus is found between two protein-coding genes (intergenic) in teleost fish genomes, the miR-191 cluster locus is found within an intron of a protein-coding gene (intragenic) in the human genome. Interferon (IFN)-inducible and immune-related promoter elements found upstream of the teleost miR-462 cluster locus suggested roles in immune responses to viral pathogens in fish, while in humans, the miR-191 cluster functionally associated with cell cycle regulation. Stimulation of fish cell cultures with the IFN inducer poly I:C accordingly upregulated the expression of miR-462 and miR-731, while no stimulatory effect on miR-191 and miR-425 expression was observed in human cell lines. Despite high sequence conservation, evolution has thus resulted in different regulation and presumably also different functional roles of these orthologous miRNA clusters in different vertebrate lineages.

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“…To validate the existence of predicted novel miRNAs, ten novel miRNAs were selected for RT-PCR analysis as described previously [74]. To validate the Illumina sequencing data, nine miRNAs were randomly selected for qRT-PCR analysis.…”

Section: Methodsmentioning

confidence: 99%

Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila

Cui

Wei

et al. 2016

IJMS

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MicroRNAs (miRNAs) are small RNA molecules that play key roles in regulation of various biological processes. In order to better understand the biological significance of miRNAs in the context of Aeromonas hydrophila infection in Megalobrama amblycephala, small RNA libraries obtained from fish liver at 0 (non-infection), 4, and 24 h post infection (poi) were sequenced using Illumina deep sequencing technology. A total of 11,244,207, 9,212,958, and 7,939,157 clean reads were obtained from these three RNA libraries, respectively. Bioinformatics analysis identified 171 conserved miRNAs and 62 putative novel miRNAs. The existence of ten randomly selected novel miRNAs was validated by RT-PCR. Pairwise comparison suggested that 61 and 44 miRNAs were differentially expressed at 4 and 24 h poi, respectively. Furthermore, the expression profiles of nine randomly selected miRNAs were validated by qRT-PCR. MicroRNA target prediction, gene ontology (GO) annotation, and Kyoto Encylopedia of Genes and Genomes (KEGG) analysis indicated that a variety of biological pathways could be affected by A. hydrophila infection. Additionally, transferrin (TF) and transferrin receptor (TFR) genes were confirmed to be direct targets of miR-375. These results will expand our knowledge of the role of miRNAs in the immune response of M. amblycephala to A. hydrophila infection, and facilitate the development of effective strategies against A. hydrophila infection in M. amblycephala.

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MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection

Cited by 22 publications

References 40 publications

Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection

Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection

Two Virus-Induced MicroRNAs Known Only from Teleost Fishes Are Orthologues of MicroRNAs Involved in Cell Cycle Control in Humans

Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila

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