Catalog of microRNA seed polymorphisms in vertebrates

Minja Zorc; Dasa Jevsinek Skok; Irena Godnic; George Adrian Calin; Simon Horvat; Zhihua Jiang; Peter Dovc; Tanja Kunej

doi:10.1371/journal.pone.0030737

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Catalog of microRNA seed polymorphisms in vertebrates

Journal article

Open access

Catalog of microRNA seed polymorphisms in vertebrates

Minja Zorc, Dasa Jevsinek Skok, Irena Godnic, George Adrian Calin, Simon Horvat, Zhihua Jiang, Peter Dovc and Tanja Kunej

PloS one, Vol.7(1), pp.e30737-e30737

2012

DOI: https://doi.org/10.1371/journal.pone.0030737

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https://hdl.handle.net/2376/101083

PMCID: PMC3267754

PMID: 22303453

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Abstract

Computational Biology - methods

Disease - genetics

Genetic Association Studies

Vertebrates - genetics

Humans

Molecular Sequence Annotation

Genome - genetics

Molecular Sequence Data

Statistics as Topic

Adiposity - genetics

Body Weight - genetics

Phenotype

Animals

Base Sequence

Polymorphism, Single Nucleotide - genetics

Mice

MicroRNAs - genetics

Quantitative Trait Loci - genetics

MicroRNAs (miRNAs) are a class of non-coding RNA that plays an important role in posttranscriptional 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 seed region that can be affected by polymorphisms. In the present study, we developed 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 polymorphisms 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 analysis between the mmu-miR-717 seed SNP rs30372501, which is polymorphic in a large number of standard inbred 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.

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Title: Catalog of microRNA seed polymorphisms in vertebrates
Creators: Minja Zorc - Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
Dasa Jevsinek Skok
Irena Godnic
George Adrian Calin
Simon Horvat
Zhihua Jiang
Peter Dovc
Tanja Kunej
Publication Details: PloS one, Vol.7(1), pp.e30737-e30737
Academic Unit: Animal Sciences, Department of
Publisher: United States
Grant note: 1R01CA135444 / NCI NIH HHS R01 CA135444 / NCI NIH HHS
Identifiers: 99900546689201842
Language: English
Resource Type: Journal article