Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
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DOI：
10.1093/nar/gkt072
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发表时间：
2013-04-01
影响因子：
14.9
通讯作者：
Chen W
中科院分区：
文献类型：
--
作者：
Li N;You X;Chen T;Mackowiak SD;Friedländer MR;Weigt M;Du H;Gogol-Döring A;Chang Z;Dieterich C;Hu Y;Chen W
microRNA（miRNAs）是一类重要的小分子调控RNA，它们来源于不同的发夹前体（pre-miRNAs）。与成熟的miRNA相比，成熟的miRNA已经在不同生物体的许多全基因组研究中被表征，对前体miRNA的全局谱分析的研究是有限的。在这里，使用大规模平行测序，我们已经进行了小鼠成熟和前体miRNA的全球表征。总共获得了87369704和252003个测序读数，分别来自887个成熟和281个前体miRNA。我们的分析揭示了miRNA/pre-miRNA加工和修饰的新方面，包括八个Ago2切割的pre-miRNA，八个新的miRNA编辑实例和专门的5 ′尾mirtron。此外，基于成熟和前体miRNA的序列，我们开发了一个miRNA发现管道miRGrep，它不依赖于基因组参考序列的可用性。除了239个已知的小鼠pre-miRNAs外，miRGrep还预测了41个新的pre-miRNAs。与已知的相似，来自这些新基因座中的大多数的成熟miRNA在Dicer敲除后显示出减少的丰度以及与Argonaute2的结合。对秀丽隐杆线虫和小杆线虫11的数据集进行的评价表明，miRGrep可广泛用于后生动物miRNA的发现，特别是在没有基因组参考序列的后生动物中。
MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5′ tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
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影响因子：
56.9
作者：
Lagos-Quintana, M;Rauhut, R;Tuschl, T
通讯作者：
Tuschl, T
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Kozomara A;Griffiths-Jones S
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Griffiths-Jones S
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通讯作者：
Lai, Eric C.
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作者：
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通讯作者：
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