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The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus (RISC bound RNA)

ABSTRACT: Porcine alveolar macrophages were challenged in vitro with a low virulent strain of the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) to identify and characterize the population of host genes subjected to miRNA post-transcriptional regulation durign early viral infection. We employed a high-throughput biochemical assay, i.e. the immunoprecipitation of RISCs followed by microarray analysis of the RISC-bound miRNA targets (RIP-Chip). qPCR analyses were carried out to validate the resolution of the microarray and to determine levels of expression of a panel of eight miRNAs (ssc-miR-142-3p, ssc-miR-142-5p, ssc-let-7f, miR-146a-5p, miR-155-5p, ssc-miR-181a, ssc-miR-21 and ssc-miR-335).

ORGANISM(S): Sus scrofa

PROVIDER: GSE98339 | GEO | 2018/04/14

REPOSITORIES: GEO

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Project description:Solexa/Illumina deep sequencing was used to obtain miRNA transcriptome profiles for control (basal diet, 14.49% crude protein, 13.73 MJ/kg digestible energy, 0.86% available lysine) and traditional Chinese medicine formula (basal diet+2.5 g/kg traditional Chinese medicine formula) groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed using DAVID functional annotation to identify the biological process function of the miRNAs identified as being involved in muscle fiber regulation. We detected 269 mature miRNAs and 14 pre-miRNAs in the porcine muscle samples, of which 211 were previously unreported. Pathway analyses suggested that several independent signaling pathways were involved in the biological process, cellular component, and molecular function categories, with metabolic pathways showing the most enrichment and including some pathways involved in the regulation of muscle fiber phenotype such as mitogen-activated protein kinase (MAPK), mammalian target of rapamycin, and citrate cycle signaling pathways. Thirty-seven miRNAs exhibited normalized expression of over 10,000 reads per million, accounting for 85.91% of the overall counts of the total porcine mature miRNAs. Among these, 9 were muscle-related miRNAs involved in muscle development, including skeletal satellite cell (ssc)-miR-133a-3p, ssc-miR-486, ssc-miR-26a, ssc-miR-21, ssc-miR-1, ssc-miR-10b, ssc-miR-181a, ssc-miR-128, and ssc-miR-23a. In particular, miR-1 and miR-133 are muscle-specific miRNAs, termed myomiRs, which play an important role in muscle differentiation and development. Furthermore, porcine skeletal satellite cell transfection experiments indicated that overexpression or inhibition of ssc-miR-27a repressed or increased, respectively, MYH7 gene and protein expression through the PGC-1-MEF2C pathway, suggesting that miR-27a participated in the regulation of muscle fiber in skeletal muscle. In conclusion, these miRNAome profiles provide novel insight into the mechanism underlying muscle fiber regulation.

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The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus (RISC bound RNA)

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