microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
microRNA target predictions across seven Drosophila species and comparison to mammalian targets.
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DOI：
10.1371/journal.pcbi.0010013
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发表时间：
2005-06
影响因子：
4.3
通讯作者：
Rajewsky N
中科院分区：
文献类型：
--
作者：
Grün D;Wang YL;Langenberger D;Gunsalus KC;Rajewsky N
microRNAs是一种小的非编码基因，通过结合靶基因mrna中的部分互补位点来调节基因的蛋白质产生。在这里，使用我们的算法PicTar，我们利用跨物种比较来预测，在果蝇噪声之上，平均每个microRNA有54个靶向基因。对靶基因功能注释的分析进一步揭示了许多microrna的特异性生物学功能。我们还预测了簇状microRNAs的组合靶标，并发现一些簇状microRNAs可能协调调节靶基因。此外，我们比较了昆虫和脊椎动物之间的microRNA调控。我们发现，果蝇和哺乳动物之间microRNAs基因调控的广泛程度是相似的，但某些microRNAs可能在进化枝特异性的基因调控模式中起作用。其中一种microrna （miR-210）被预测参与果蝇卵发生的调控。我们还列出了苍蝇和哺乳动物之间似乎保守的特定调节关系。我们的研究结果提供了迄今为止果蝇中最广泛的microRNA靶标预测，提示了大多数microRNA的特定功能作用，表明存在由集群microRNA执行的协调基因调控，并揭示了microRNA功能在大进化距离上的进化。所有的预测都可以在我们可搜索的网站http://pictar.bio.nyu.edu上免费获取。MicroRNA基因是近年来发现的一类小的非编码基因。这些基因已被证明通过结合靶标mrna中的部分互补位点来调节靶基因的表达。因此，为了了解microRNA的功能，确定它们的靶标是很重要的。在这里，作者使用他们的生物信息学方法PicTar和几种新测序的苍蝇物种的跨物种比较来预测果蝇中microrna的全基因组靶点。他们发现，已知的果蝇microrna控制着黑腹果蝇至少15%的基因。他们还表明，microrna的基因组簇可能协调调节靶基因。对靶基因功能注释的分析进一步揭示了许多microrna的特异性生物学功能。所有预测都可以在http://pictar.bio.nyu.edu上免费获取。最后，gr<s:1>等人比较了microrna在果蝇和哺乳动物中的功能。他们发现(a)两个进化支之间microRNA基因调控的总体程度是相似的，(b)果蝇中保守microRNA的靶标数量与哺乳动物中的靶标数量相关，(c)一些保守microRNA可能在进化支特异性的基因调控模式中起作用，(d)一些特定的microRNA -靶标调控关系在两个进化支之间可能是保守的。
microRNAs are small noncoding genes that regulate the protein production of genes by binding to partially complementary sites in the mRNAs of targeted genes. Here, using our algorithm PicTar, we exploit cross-species comparisons to predict, on average, 54 targeted genes per microRNA above noise in Drosophila melanogaster. Analysis of the functional annotation of target genes furthermore suggests specific biological functions for many microRNAs. We also predict combinatorial targets for clustered microRNAs and find that some clustered microRNAs are likely to coordinately regulate target genes. Furthermore, we compare microRNA regulation between insects and vertebrates. We find that the widespread extent of gene regulation by microRNAs is comparable between flies and mammals but that certain microRNAs may function in clade-specific modes of gene regulation. One of these microRNAs (miR-210) is predicted to contribute to the regulation of fly oogenesis. We also list specific regulatory relationships that appear to be conserved between flies and mammals. Our findings provide the most extensive microRNA target predictions in Drosophila to date, suggest specific functional roles for most microRNAs, indicate the existence of coordinate gene regulation executed by clustered microRNAs, and shed light on the evolution of microRNA function across large evolutionary distances. All predictions are freely accessible at our searchable Web site http://pictar.bio.nyu.edu. MicroRNA genes are a recently discovered large class of small noncoding genes. These genes have been shown to regulate the expression of target genes by binding to partially complementary sites in the mRNAs of the targets. To understand microRNA function it is thus important to identify their targets. Here, the authors use their bioinformatic method, PicTar, and cross-species comparisons of several newly sequenced fly species to predict, genome wide, targets of microRNAs in Drosophila. They find that known fly microRNAs control at least 15% of all genes in D. melanogaster. They also show that genomic clusters of microRNAs are likely to coordinately regulate target genes. Analysis of the functional annotation of target genes furthermore suggests specific biological functions for many microRNAs. All predictions are freely accessible at http://pictar.bio.nyu.edu. Finally, Grün et al. compare the function of microRNAs across flies and mammals. They find that (a) the overall extent of microRNA gene regulation is comparable between both clades, (b) the number of targets for a conserved microRNA in flies correlates with the number of targets in mammals, (c) some conserved microRNAs may function in clade-specific modes of gene regulation, and (d) some specific microRNA–target regulatory relationships may be conserved between both clades.
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影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S
影响因子：
64.5
作者：
Lewis, BP;Shih, IH;Burge, CB
通讯作者：
Burge, CB
影响因子：
14.9
作者：
Pruitt KD;Tatusova T;Maglott DR
通讯作者：
Maglott DR
影响因子：
12.3
作者：
Mignone F;Gissi C;Liuni S;Pesole G
通讯作者：
Pesole G
影响因子：
9.8
作者：
John B;Enright AJ;Aravin A;Tuschl T;Sander C;Marks DS
通讯作者：
Marks DS