Genetic Variability of MicroRNA Genes in 15 Animal Species

Abstract

MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Previous studies have proven that genetic variability of miRNA genes (miR-SNP) has an impact on phenotypic variation and disease susceptibility in human, mice and some livestock species. MicroRNA gene polymorphisms could therefore represent biomarkers for phenotypic traits also in other animal species. We upgraded our previously developed tool miRNA SNiPer to the version 4.0 which enables the search of miRNA genetic variability in 15 animal genomes: http://www.integratomics-time.com/miRNA-SNiPer. Genome-wide in silico screening (GWISS) of 15 genomes revealed that based on the current database releases, miRNA genes are most polymorphic in cattle, followed by human, fruitfly, mouse, chicken, pig, horse, and sheep. The difference in the number of miRNA gene polymorphisms between species is most probably not due to a biological reason and lack of genetic variability in some species, but to different stage of sequencing projects and differences in development of genomic resource databases in different species. Genome screening revealed several interesting genomic hotspots. For instance, several multiple nucleotide polymorphisms (MNPs) are present within mature seed region in cattle. Among miR-SNPs 46 are present on commercial whole-genome SNP chips: 16 in cattle, 26 in chicken, two in sheep and two in pig. The update of the miRNA SNiPer tool and the generated catalogs will serve researchers as a starting point in designing projects dealing with the effects of genetic variability of miRNA genes.

Keywords: cattle; genetic polymorphisms; livestock; miRNA SNiPer; microRNA.

Figure 1

Output of the miRNA SNiPer tool displaying genetic variability of the bta-miR-764 gene. Polymorphisms are marked with the orange color. Details include information regarding the: 1. SNP location within the miRNA gene (seed region in light blue, mature region in dark blue and pre-miRNA region in black), 2. genomic location, 3. allele substitution, and 4. commercial whole-genome SNP chip name.

Figure 2

Number of polymorphic pre-miRNA, mature miRNA and seed regions in 15 animal species included in the miRNA SNiPer tool 4.0.

Figure 3

Comparison of the results between the versions 3.0 and 4.0 of the miRNA SNiPer tool regarding the number of polymorphic pre-miRNA, mature miRNA and seed regions in cattle.

Figure 4

Overlap of three genes in cattle: miRNA gene bta-mir-1839, snoRNA gene SCARNA15, and protein-coding gene MROH1. Two consecutive SNPs are present within mature miRNA seed region. Dark blue - mature miRNA, light blue - seed region.