Stark Alexander, Kheradpour Pouya, Parts Leopold, Brennecke Julius, Hodges Emily, Hannon Gregory J, Kellis Manolis
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.
Genome Res. 2007 Dec;17(12):1865-79. doi: 10.1101/gr.6593807. Epub 2007 Nov 7.
MicroRNAs (miRNAs) are short regulatory RNAs that inhibit target genes by complementary binding in 3' untranslated regions (3' UTRs). They are one of the most abundant classes of regulators, targeting a large fraction of all genes, making their comprehensive study a requirement for understanding regulation and development. Here we use 12 Drosophila genomes to define structural and evolutionary signatures of miRNA hairpins, which we use for their de novo discovery. We predict >41 novel miRNA genes, which encompass many unique families, and 28 of which are validated experimentally. We also define signals for the precise start position of mature miRNAs, which suggest corrections of previously known miRNAs, often leading to drastic changes in their predicted target spectrum. We show that miRNA discovery power scales with the number and divergence of species compared, suggesting that such approaches can be successful in human as dozens of mammalian genomes become available. Interestingly, for some miRNAs sense and anti-sense hairpins score highly and mature miRNAs from both strands can indeed be found in vivo. Similarly, miRNAs with weak 5' end predictions show increased in vivo processing of multiple alternate 5' ends and have fewer predicted targets. Lastly, we show that several miRNA star sequences score highly and are likely functional. For mir-10 in particular, both arms show abundant processing, and both show highly conserved target sites in Hox genes, suggesting a possible cooperation of the two arms, and their role as a master Hox regulator.
微小RNA（miRNA）是一类短的调节性RNA，通过与3'非翻译区（3'UTR）的互补结合来抑制靶基因。它们是最丰富的调节因子类别之一，靶向大部分基因，因此对其进行全面研究是理解基因调控和发育所必需的。在这里，我们利用12个果蝇基因组来定义miRNA发夹结构和进化特征，并以此进行从头发现。我们预测了超过41个新的miRNA基因，其中包含许多独特的家族，并且通过实验验证了其中28个。我们还定义了成熟miRNA精确起始位置的信号，这表明需要对先前已知的miRNA进行修正，这往往会导致其预测靶标谱的剧烈变化。我们表明，miRNA的发现能力随着所比较物种的数量和差异而增加，这表明随着数十个哺乳动物基因组的可得，这种方法在人类研究中也可能成功。有趣的是，对于一些miRNA，正义链和反义链发夹得分都很高，并且在体内确实可以发现来自两条链的成熟miRNA。同样，5'端预测较弱的miRNA在体内会增加多个交替5'端的加工，并且预测的靶标较少。最后，我们表明几个miRNA*序列得分很高并且可能具有功能。特别是对于mir-10，两条臂都显示出丰富的加工，并且在Hox基因中都显示出高度保守的靶位点，这表明两条臂可能存在协同作用，并且它们作为Hox主调节因子发挥作用。
