Genetic Variability of MicroRNA Genes in 15 Animal Species.
Genetic Variability of MicroRNA Genes in 15 Animal Species.
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DOI：
10.7150/jgen.11246
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发表时间：
2015
影响因子：
--
通讯作者：
Kunej T
中科院分区：
文献类型：
--
作者：
Zorc M;Obsteter J;Dovc P;Kunej T
MicroRNA (miRNA) 是一类在靶基因转录后调控中发挥重要作用的非编码 RNA。先前的研究已经证明，miRNA 基因的遗传变异（miR-SNP）对人类、小鼠和一些牲畜物种的表型变异和疾病易感性有影响。因此，MicroRNA 基因多态性也可以代表其他动物物种表型特征的生物标志物。我们将之前开发的工具 miRNA SNiPer 升级到了 4.0 版，可以搜索 15 种动物基因组中的 miRNA 遗传变异性：http://www.integratomics-time.com/miRNA-SNiPer。对 15 个基因组的全基因组计算机筛选 (GWISS) 显示，根据目前发布的数据库，牛的 miRNA 基因多态性最高，其次是人类、果蝇、小鼠、鸡、猪、马和羊。物种间miRNA基因多态性数量的差异很可能不是由于生物学原因和某些物种缺乏遗传变异性，而是由于测序项目的不同阶段以及不同物种基因组资源数据库开发的差异。基因组筛选揭示了几个有趣的基因组热点。例如，牛的成熟种子区域内存在多种多核苷酸多态性（MNP）。商业全基因组 SNP 芯片上存在 miR-SNP 中的 46 个：牛中 16 个、鸡中 26 个、羊中 2 个、猪中 2 个。 miRNA SNiPer 工具的更新和生成的目录将为研究人员提供设计处理 miRNA 基因遗传变异影响的项目的起点。
MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Previous studies have proven that genetic variability of miRNA genes (miR-SNP) has an impact on phenotypic variation and disease susceptibility in human, mice and some livestock species. MicroRNA gene polymorphisms could therefore represent biomarkers for phenotypic traits also in other animal species. We upgraded our previously developed tool miRNA SNiPer to the version 4.0 which enables the search of miRNA genetic variability in 15 animal genomes: http://www.integratomics-time.com/miRNA-SNiPer. Genome-wide in silico screening (GWISS) of 15 genomes revealed that based on the current database releases, miRNA genes are most polymorphic in cattle, followed by human, fruitfly, mouse, chicken, pig, horse, and sheep. The difference in the number of miRNA gene polymorphisms between species is most probably not due to a biological reason and lack of genetic variability in some species, but to different stage of sequencing projects and differences in development of genomic resource databases in different species. Genome screening revealed several interesting genomic hotspots. For instance, several multiple nucleotide polymorphisms (MNPs) are present within mature seed region in cattle. Among miR-SNPs 46 are present on commercial whole-genome SNP chips: 16 in cattle, 26 in chicken, two in sheep and two in pig. The update of the miRNA SNiPer tool and the generated catalogs will serve researchers as a starting point in designing projects dealing with the effects of genetic variability of miRNA genes.