Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.
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DOI：
10.1093/nar/gkw1031
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发表时间：
2017-02-17
影响因子：
14.9
通讯作者：
Enright AJ
中科院分区：
文献类型：
--
作者：
Vitsios DM;Davis MP;van Dongen S;Enright AJ
MicroRNAs在动植物中都是重要的遗传调节因子。它们具有一系列跨越发育、分化、生长、新陈代谢和疾病的功能。新一代测序技术的出现使得通过测序来检测这些分子及其相对表达成为一项相对简单的任务。有大量已发表的研究使用存储的数据集。然而，目前很少有资源利用这些数据来更好地了解miRNAs的特征、分布和生物发生。在这里，我们关注的是拥有大部分数据的人和老鼠。我们重新分析了461个样本的测序数据，将其归入一个协调的microRNA表达目录。我们用它来进行miRNA功能和生物发生的大规模分析。这些分析包括全局表达比较、miRNA簇的共表达以及miRNA链特异性和潜在限制因素的预测。此外，我们首次报道了对miRNA表观转录修饰的全球分析，并评估了它们在组织、样本和家族中的流行率。最后，我们根据miRBase中聚合的修改配置文件报告了一系列可能被错误注释的miRNAs。这些结果已经整理成一个关于miRNA表达和修饰和RNA编辑事件等特征的综合在线储存库，可在以下网址获得：http://wwwdev.ebi.ac.uk/enright-dev/miratlas.我们相信这些发现将有助于我们进一步了解miRNA在动物中的功能，并使miRNA社区总体受益。
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs. Herein, we focus on Human and Mouse for which the majority of data are available. We reanalyse sequencing data from 461 samples into a coordinated catalog of microRNA expression. We use this to perform large-scale analyses of miRNA function and biogenesis. These analyses include global expression comparison, co-expression of miRNA clusters and the prediction of miRNA strand-specificity and underlying constraints. Additionally, we report for the first time a global analysis of miRNA epi-transcriptomic modifications and assess their prevalence across tissues, samples and families. Finally, we report a list of potentially mis-annotated miRNAs in miRBase based on their aggregated modification profiles. The results have been collated into a comprehensive online repository of miRNA expression and features such as modifications and RNA editing events, which is available at: http://wwwdev.ebi.ac.uk/enright-dev/miratlas. We believe these findings will further contribute to our understanding of miRNA function in animals and benefit the miRNA community in general.