Abstract
The present study was conducted to identify the differentially expressed miRNAs (DE miRNAs) in the peripheral blood mononuclear cells of crossbred pigs in response to CSF vaccination on 7 and 21 days of post vaccination as compared to unvaccinated control (0 dpv). Simultaneously, set of miRNA was predicted using mRNA seq data at same time point. The proportion of CD4−CD8+ and CD4+CD8+ increased after vaccination, and the mean percentage inhibition was 86.89% at 21 dpv. It was observed that 22 miRNAs were commonly expressed on both the time points. Out of predicted DE miRNAs, it was found that 40 and 35 DE miRNAs were common, obtained from miRNA seq analysis and predicted using mRNA seq data on 7 dpv versus 0 dpv and 21 dpv versus 0 dpv respectively. Two DE miRNAs, ssc-miR-22-5p and ssc-miR-27b-5p, were selected based on their log2 fold change and functions of their target genes in immune process/pathway of viral infections. The validations of DE miRNAs using qRT-PCR were in concordance with miRNA seq analysis. Two set of target genes, CD40 and SWAP70 (target gene of ssc-miR-22-5p) and TLR4 and Lyn (target gene of ssc-miR-27b-5p), were validated and were in concordance with results of RNA seq analysis at a particular time point (except TLR4). The first report of genome-wide identification of differentially expressed miRNA in response to live attenuated vaccine virus of classical swine fever revealed miR-22-5p and miR-27b-5p were differentially expressed at 7 dpv and 21 dpv.
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Abbreviations
- BIOGRID:
-
Biological General Repository for Interaction Datasets
- cELISA:
-
competitive enzyme-linked immunosorbent assay
- CSF:
-
classical swine fever
- CSFV:
-
classical swine fever virus
- DEGs:
-
differentially expressed genes
- DEHC:
-
differentially expressed highly connected
- DE miRNA:
-
differentially expressed microRNA
- FACS:
-
fluorescent-activated cell sorter
- FDR:
-
false discovery rate
- FPKMs:
-
fragments per kilobase for a million reads
- GO:
-
Gene ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- qRT-PCR:
-
quantitative real-time polymerase chain reaction
- RNA seq:
-
RNA sequencing
- RSEM:
-
RNA seq by expectation–maximization
- TPM:
-
transcript per million
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Acknowledgements
Authors are thankful to the Director, ICAR-IVRI and CABin project of IASRI for providing necessary facility for executing this research project.
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The CABIN project of IASRI and SubDIC (BTISnet), ICAR-IVRI provided financial assistance.
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Sailo, L., Kumar, A., Sah, V. et al. Genome-wide integrated analysis of miRNA and mRNA expression profiles to identify differentially expressed miR-22-5p and miR-27b-5p in response to classical swine fever vaccine virus. Funct Integr Genomics 19, 901–918 (2019). https://doi.org/10.1007/s10142-019-00689-w
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DOI: https://doi.org/10.1007/s10142-019-00689-w