MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) involved in regulation of gene expression. Intragenic miRNAs, especially those exhibiting a high degree of evolutionary conservation, have been shown ...to be coordinately regulated and/or expressed with their host genes, either with synergistic or antagonistic correlation patterns. However, the degree of cross-species conservation of miRNA/host gene co-location is not known and co-expression information is incomplete and fragmented among several studies. Using the genomic resources (miRBase and Ensembl) we performed a genome-wide in silico screening (GWISS) for miRNA/host gene pairs in three well-annotated vertebrate species: human, mouse, and chicken. Approximately half of currently annotated miRNA genes resided within host genes: 53.0% (849/1,600) in human, 48.8% (418/855) in mouse, and 42.0% (210/499) in chicken, which we present in a central publicly available Catalog of intragenic miRNAs (http://www.integratomics-time.com/miR-host/catalog). The miRNA genes resided within either protein-coding or ncRNA genes, which include long intergenic ncRNAs (lincRNAs) and small nucleolar RNAs (snoRNAs). Twenty-seven miRNA genes were found to be located within the same host genes in all three species and the data integration from literature and databases showed that most (26/27) have been found to be co-expressed. Particularly interesting are miRNA genes located within genes encoding for miRNA silencing machinery (DGCR8, DICER1, and SND1 in human and Cnot3, Gdcr8, Eif4e, Tnrc6b, and Xpo5 in mouse). We furthermore discuss a potential for phenotype misattribution of miRNA host gene polymorphism or gene modification studies due to possible collateral effects on miRNAs hosted within them. In conclusion, the catalog of intragenic miRNAs and identified 27 miRNA/host gene pairs with cross-species conserved co-location, co-expression, and potential co-regulation, provide excellent candidates for further functional annotation of intragenic miRNAs in health and disease.
The objective of this preliminary study was to identify SNP markers within the FTO gene for evaluation of pedigree data accuracy and determination of haplotypes in paternal half-sib families of ...Slovenian Simmental cattle. Out of 23 polymorphic SNPs identified ten most informative SNPs for genotyping 31 sires and 56 half-sib progeny were used. The ATLAS program was used for paternity testing. Haplotype analysis revealed three haplotype blocks. The effect of SNPs “ex2 T>C” and “int2 indel*>T” was significant on three correlated carcass traits: live weight at slaughter (P= 0.03), carcass weight (P= 0.038), and lean weight (P= 0.048). The FTO gene can thus be regarded as a candidate for the marker assisted selection programs in our and possibly other populations of cattle. Future studies in cattle might also reveal novel roles of the FTO gene in carcass traits on livestock species as well as fatness control in other mammals.
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