Spontaneous single nucleotide polymorphism in porcine microRNA-378 seed region leads to functional alteration

Abstract

Sequence variation in a microRNA (miRNA) seed region can influence its biogenesis and effects on target mRNAs; however, in mammals, few seed region mutations leading to functional alterations have been reported to date. Here, we report the identification of a single nucleotide polymorphism (SNP) with functional consequence located in the seed region of porcine miR-378. In vitro analysis of this rs331295049 A17G SNP showed significantly up-regulated expression of the mature miR-378 (miR-378/G). In silico target prediction indicated that the SNP would modulate secondary structure and result in functional loss affecting >85% of the known target genes of the wild-type miR-378 (miR-378/A), and functional gain affecting >700 new target genes, and dual-luciferase reporter assay verified this result. This report of a SNP in the seed region of miR-378 leads to functional alteration and indicates the potential for substantive functional consequences to the molecular physiology of a mammalian organism.

Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome

“…This profound influence of SNPs on target gene switching concurs with other studies, for example, on the human 34 and mouse 35 genomes. Furthermore, an SNP-caused target gene switching of one microRNA, namely ssc-miR-378, was also computationally and experimentally established in the pig 28 .…”

Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non‐model Organisms

“…Studies of miRNAs often do not stop at lists of predicted targets. Many perform functional annotation on the predicted targets, followed by Gene Ontology (GO) enrichment analysis for finding biological pathways regulated by certain miRNAs . When significant enrichment for biological processes is detected, the level of confidence in the “newly discovered” miRNA‐regulated pathway is increased.…”

Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle

“…The impact of a miR-SNP (SNP within a miRNA sequence) on miRNA function depends on the SNP position. For instance, miR-SNPs located in the first 14 nucleotides of the mature sequence, and mainly those located in the seed region (mostly situated at positions 2-7 from the miRNA 5'-end) may lead to novel target sites that potentially affect canonical wild-type miRNA-mRNA interactions [14][15][16]. These changes may lead to an extensive rewiring of the miRNA-mediated regulatory network and, in some instances, substantially modify a phenotype [17].…”