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

Schyth BD, Bela-Ong DB, Jalali SA, Kristensen LB, Einer-Jensen K, Pedersen FS, Lorenzen N - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

miR-462 and miR-731 are highly upregulated in the liver of VHSV-infected rainbow trout.(A) Microarray analysis of miRNA regulation in liver samples from diseased rainbow trout infected with Viral hemorrhagic septicaemia virus (VHSV). The Ncode V2 probe set covering miRBase v.9 was used to detect up-(blue) and down-regulated (red) miRNAs. The miRNA probes are denoted according to the miRBase nomenclature. Organisms: dre = Danio rerio, hsa = Homo sapiens and dme = Drosophila melanogaster. (B) qPCR validation of miR-462 and miR-731 expression in the liver of VHSV-infected rainbow trout. Fold regulation was calculated from the mean values of duplicate measurements using the ΔΔCt method, using the omy-snoRNA U23 for normalization. miRNA expression was analyzed in 6 VHSV-infected fish relative to 6 uninfected fish.
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pone.0132434.g001: miR-462 and miR-731 are highly upregulated in the liver of VHSV-infected rainbow trout.(A) Microarray analysis of miRNA regulation in liver samples from diseased rainbow trout infected with Viral hemorrhagic septicaemia virus (VHSV). The Ncode V2 probe set covering miRBase v.9 was used to detect up-(blue) and down-regulated (red) miRNAs. The miRNA probes are denoted according to the miRBase nomenclature. Organisms: dre = Danio rerio, hsa = Homo sapiens and dme = Drosophila melanogaster. (B) qPCR validation of miR-462 and miR-731 expression in the liver of VHSV-infected rainbow trout. Fold regulation was calculated from the mean values of duplicate measurements using the ΔΔCt method, using the omy-snoRNA U23 for normalization. miRNA expression was analyzed in 6 VHSV-infected fish relative to 6 uninfected fish.

Mentions: Microarray was carried out in order to analyze which miRNAs are regulated in the liver of rainbow trout in response to infection with a fish rhabdovirus. The liver was chosen as a target because it is a central organ in the systemic innate response to infections. Microarray analysis (using 1492 unique miRNA specific probes) of the liver of VHSV-infected fish versus non-infected controls detected 120 miRNAs expressed significantly above the background level determined as mean of all probe signals. Of these, 13 showed more than two-fold up regulation in infected fish compared to controls (Fig 1A). Among these, miR-462 and miR-731 were particularly strongly upregulated (>50-fold). The strong expression levels of the two miRNAs were confirmed by qPCR, showing that miR-462 was upregulated ~20-fold and miR-731 ~15-fold (Fig 1B).


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

Schyth BD, Bela-Ong DB, Jalali SA, Kristensen LB, Einer-Jensen K, Pedersen FS, Lorenzen N - PLoS ONE (2015)

miR-462 and miR-731 are highly upregulated in the liver of VHSV-infected rainbow trout.(A) Microarray analysis of miRNA regulation in liver samples from diseased rainbow trout infected with Viral hemorrhagic septicaemia virus (VHSV). The Ncode V2 probe set covering miRBase v.9 was used to detect up-(blue) and down-regulated (red) miRNAs. The miRNA probes are denoted according to the miRBase nomenclature. Organisms: dre = Danio rerio, hsa = Homo sapiens and dme = Drosophila melanogaster. (B) qPCR validation of miR-462 and miR-731 expression in the liver of VHSV-infected rainbow trout. Fold regulation was calculated from the mean values of duplicate measurements using the ΔΔCt method, using the omy-snoRNA U23 for normalization. miRNA expression was analyzed in 6 VHSV-infected fish relative to 6 uninfected fish.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4514678&req=5

pone.0132434.g001: miR-462 and miR-731 are highly upregulated in the liver of VHSV-infected rainbow trout.(A) Microarray analysis of miRNA regulation in liver samples from diseased rainbow trout infected with Viral hemorrhagic septicaemia virus (VHSV). The Ncode V2 probe set covering miRBase v.9 was used to detect up-(blue) and down-regulated (red) miRNAs. The miRNA probes are denoted according to the miRBase nomenclature. Organisms: dre = Danio rerio, hsa = Homo sapiens and dme = Drosophila melanogaster. (B) qPCR validation of miR-462 and miR-731 expression in the liver of VHSV-infected rainbow trout. Fold regulation was calculated from the mean values of duplicate measurements using the ΔΔCt method, using the omy-snoRNA U23 for normalization. miRNA expression was analyzed in 6 VHSV-infected fish relative to 6 uninfected fish.
Mentions: Microarray was carried out in order to analyze which miRNAs are regulated in the liver of rainbow trout in response to infection with a fish rhabdovirus. The liver was chosen as a target because it is a central organ in the systemic innate response to infections. Microarray analysis (using 1492 unique miRNA specific probes) of the liver of VHSV-infected fish versus non-infected controls detected 120 miRNAs expressed significantly above the background level determined as mean of all probe signals. Of these, 13 showed more than two-fold up regulation in infected fish compared to controls (Fig 1A). Among these, miR-462 and miR-731 were particularly strongly upregulated (>50-fold). The strong expression levels of the two miRNAs were confirmed by qPCR, showing that miR-462 was upregulated ~20-fold and miR-731 ~15-fold (Fig 1B).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus