In silico screening of the chicken genome for over

Authors: Minja Zorc Tanja Kunej

Publish Date: 2016/01/22

Volume: 24, Issue: 2, Pages: 225-230

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Abstract

MicroRNAs miRNAs are a class of noncoding RNAs involved in posttranscriptional regulation of target genes Regulation requires complementarity between target mRNA and the mature miRNA seed region responsible for their recognition and binding It has been estimated that each miRNA targets approximately 200 genes and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans livestock species and model organisms Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals In our previous study we collected polymorphisms within miRNA genes in chicken In the present study we identified miRNArelated genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases miRNA SNiPer Ensembl miRBase NCBI Blast and QTLdb Out of 740 known premiRNA genes 263 355  contain polymorphisms among them 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are ggamiR6662 containing 23 single nucleotide polymorphisms SNPs within the premiRNA region including five consecutive SNPs and ggamiR6688 containing ten polymorphisms including three consecutive polymorphisms Several miRNArelated genomic hotspots have been revealed in chicken genome polymorphic miRNA genes are located within proteincoding and/or noncoding transcription units and quantitative trait loci QTL associated with production traits The present study includes the first description of an exonic miRNA in a chicken genome an overlap between the miRNA gene and the exon of the proteincoding gene ggamiR6578/HADHB and the first report of a missense polymorphism located within a mature miRNA seed region Identified miRNArelated genomic hotspots in chicken can serve researchers as a starting point for further functional studies and association studies with poultry production and health traits and the basis for systematic screening of exonic miRNAs and missense/miRNA seed polymorphisms in other genomes

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