Biocomputational genome-wide analysis of micro RNA genetic variability in some vertebrates

Abstract

MicroRNAs (miRNAs) are small endogenously expressed single-stranded RNAs that regulate gene expression post transcriptionally and shape diverse cellular pathways. miRNAs regulate a wide range of biological processes through the recognition of complementary sequences between miRNAs and their target genes. The present investigation aimed at determining in-silico the genetic variability of miRNA genes in some livestock and non-livestock species. Effects of single nucleotide polymorphisms (SNPs) in genes? 3'UTR on target gain/loss of human miRNAs were also explored. A total of twenty four mature miRNA sequences and genomic coordinates in three livestock [chicken (5), pig (1) and cattle (9)] and two non-livestock (human (6) and mouse (3)] species were retrieved from the miRBase 15 release. Computational scanning of polymorphisms in the miRNAs revealed 33 and 20 polymorphic sites in livestock and non-livestock species, respectively. Of this, 7 (chicken), 11 (cattle) and 2 (mouse) were located within the seed region. The de novo computational prediction revealed that SNPs rs1042725 (C/U) and rs1044129 (A/G) in genes? 3'UTR of human miRNAs positively influenced the target site thereby resulting in target gain. However, the effects of SNPs rs56109847 (A/G), rs28927680, rs12720208 (G/A) and rs5186 (A/C) were negative. The evolutionary tree showed that the relationship between miRNA consensus sequences of livestock (pig, chicken and cattle) was closer compared to non-livestock species (mouse and human), which could be implicated in morphological complexity among vertebrates. Although the function of miRNA is only beginning to be understood, future in-silico research evaluating the functional effect of miRNA in gene translation and subsequent biological pathways especially in livestock is of paramount importance; and this should be complemented with hypothesis-driven experimental studies to evaluate the phenotypic effect of identified miRNA genetic polymorphisms in animals.

In silico analysis of Beta-Lactoglobulin gene in some selected mammalian species

“…Only pig and buffalo had ω >1 signifying positive selection; while other species with ω<1 are under purifying selection. Yakubu et al (2013b), in their study on MHC reported that, positive selection favours new variants thereby increasing allelic polymorphism (Bergstronm and Gyllensten, 1995) which in turn favours the ability of antigen-presenting cells to bind a wide array of self and nonself-peptides, thus conferring higher resistance to infectious diseases (Hedrick and Kim, 2000). Mutation in pig and buffalo increases fitness (Kosakovsky Pond, 2011) and this is expected to reflect on performance.…”