Catalog of MicroRNA seed polymorphisms in vertebrates

Minja Zorc (Author), Daša Jevšinek Skok (Author), Irena Godnič (Author), George A. Calin (Author), Simon Horvat (Author), Zhihua Jiang (Author), Peter Dovč (Author), Tanja Kunej (Author)

Abstract

MicroRNAs (miRNAs) are a class of non-coding RNA that plays an important role in posttransriptional regulation of mRNA. Evidence has shown that miRNA gene variability might interfere with its function resulting in phenotypic variation and disease susceptibility. A major role in miRNA target recognition is ascribed to complementarity with the miRNA sees region that can be affected by polymorphisms. In the present study, we devloped an online tool for the detection of miRNA polymorphisms (miRNA SNiPer) in vertebrates (http://www.integratomics-time.com/miRNA-SNiPer) and generated a catalog of miRNA seed region polymorphisms (miR-seed-SNPs) consisting of 149 SNPs in six species. Although a majority of detected polymorhisms were due to point mutations, two consecutive nucleotide substitutions (double nucleotide polymorphisms, DNPs) were also identified in nine miRNAs. We determined that miR-SNPs are frequently located within the quantitative trait loci (QTL), chromosome fragile sites, and cancer susceptibility loci, indicating their potential role in the genetic control of various complex traits. To test this further, we performed an association abnalysis between the mmu-miR-717 seed SNP rs30372501, which is polymorphic in a large number of standard inbreed strains, and all phenotypic traits in these strains deposited in the Mouse Phenome Database. Analysis showed a significant association between the mmu-miR-717 seed SNP and a diverse array of traits including behavior, blood-clinical chemistry, body weight size and growth, and immune system suggesting that seed SNps can indeed have major pleiotropic effects. The bioinformatics analyses, data and tools developed in the present study can serve researchers as a starting point in testing more targeted hypotheses and designing experiments using optimal species or strains for further mechanistic studies.

Keywords

molekularna genetika;mikro RNK;polimorfizem;bioinformatika;vretenčarji;

Data

Language:	English
Year of publishing:	2012
Typology:	1.01 - Original Scientific Article
Organization:	UL BF - Biotechnical Faculty
UDC:	575
COBISS:	3003528
ISSN:	1932-6203
Views:	1101
Downloads:	573
Average score:	0 (0 votes)
Metadata:

Other data

Secondary language:	Unknown
Type (COBISS):	Not categorized
Pages:	str. 1-8, e30737
Volume:	ǂVol. ǂ7
Issue:	ǂno. ǂ1
Chronology:	2012
DOI:	10.1371/journal.pone.0030737
ID:	1445732