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Characterization of bovine miRNAs by sequencing and bioinformatics analysis

机译:通过测序和生物信息学分析鉴定牛miRNA

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Background MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs or promoters. A large number of miRNAs and their expression patterns have been reported in human, mouse and rat. However, miRNAs and their expression patterns in live stock species such as beef cattle are not well studied. Results We constructed and sequenced small-RNA libraries to yield a total of 13,541 small-RNA sequences from 11 bovine tissues including brain, subcutaneous fat, muscle, liver, kidney, spleen and thymus. In total, 228 miRNAs including 29 novel miRNA candidates were identified. Of the 199 miRNAs, 101 have been previously reported as bovine miRNAs and the other 98 are bovine orthologs of known miRNAs that have been identified in at least one other mammalian species. Of the 29 novel miRNA candidates, 17 appeared at this point in time to be bovine specific, while the remaining 12 had evidence of evolutionary conservation in other mammalian species. Five miRNAs (miR-23a, -23b, -99a, -125b and -126-5p) were very abundant across the 11 tissues, accounting for 44.3% of all small RNA sequences. The expression analysis of selected miRNAs using qRT-PCR also showed that miR-26a and -99a were highly expressed in all tissues, while miR-122 and miR-133a were predominantly expressed in liver and muscle, respectively. Conclusion The miRNA expression patterns among 11 tissues from beef cattle revealed that most miRNAs were ubiquitously expressed in all tissues, while only a few miRNAs were tissue specific. Only 60% miRNAs in this study were found to display strand bias, suggesting that there are some key factors for mature miRNA selection other than internal stability. Most bovine miRNAs are highly conserved in other three mammalian species, indicating that these miRNAs may have a role in different species that are potential molecular markers for evolution.
机译:背景技术MicroRNA(miRNA)是〜22个核苷酸的小RNA分子家族,通过与mRNA或启动子中的互补序列完全或部分结合来调节基因表达。已经在人,小鼠和大鼠中报道了许多miRNA及其表达模式。然而,miRNA及其在牲畜如肉牛中的表达模式尚未得到很好的研究。结果我们构建并测序了小RNA文库,从11个牛组织(包括脑,皮下脂肪,肌肉,肝脏,肾脏,脾脏和胸腺)中提取了13,541个小RNA序列。总共鉴定了228个miRNA,包括29个新的miRNA候选物。在199个miRNA中,以前有101个被报道为牛miRNA,另外98个是已知miRNA的牛直系同源物,已在至少一种其他哺乳动物物种中鉴定出。在这29种新颖的miRNA候选物中,有17种在这一时间点似乎是牛特异性的,而其余12种在其他哺乳动物物种中具有进化保守性的证据。五个miRNA(miR-23a,-23b,-99a,-125b和-126-5p)在11个组织中非常丰富,占所有小RNA序列的44.3%。使用qRT-PCR对选定的miRNA进行的表达分析还显示,miR-26a和-99a在所有组织中均高表达,而miR-122和miR-133a分别主要在肝和肌肉中表达。结论肉牛11个组织中的miRNA表达模式表明,大多数miRNA在所有组织中普遍存在,而只有少数miRNA具有组织特异性。在这项研究中,只有60%的miRNA显示出链偏向,这表明除了内部稳定性外,还有一些影响成熟miRNA选择的关键因素。大多数牛miRNA在其他三个哺乳动物物种中高度保守,表明这些miRNA可能在不同物种中发挥作用,而这些物种是进化的潜在分子标记。

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