Functional microRNA targets in protein coding sequences
Functional microRNA targets in protein coding sequences
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DOI：
10.1093/bioinformatics/bts043
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发表时间：
2012-03-15
期刊：
影响因子：
5.8
通讯作者：
Hatzigeorgiou, Artemis G.
中科院分区：
文献类型：
--
作者：
Reczko, Martin;Maragkakis, Manolis;Hatzigeorgiou, Artemis G.
动机：实验证据已经积累表明，蛋白质编码序列（CDSs）内的microRNA（miRNA）的结合位点的功能在控制基因expression.Results：在这里，我们报告了一个计算分析这样的miRNA靶位点，从现有的哺乳动物高通量免疫沉淀和测序数据提取的功能的基础上。对CDS和3（'）-非翻译区（3（'）-UTR）独立进行分析，并揭示了两个区域的不同特征和模型集。将这两种模型结合起来，构建了一个新的miRNA靶基因计算模型DIANA-microT-CDS，与其他常用程序和仅使用3（'）-UTR靶位点的模型相比，该模型具有更高的灵敏度。进一步的分析表明，具有较短3（'）-UTR的基因优先靶向CDS，这表明在3（'）-UTR上存在有限空间的情况下，进化选择可能有利于CDS上的额外位点。
Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3(')-untranslated regions (3(')-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3(')-UTR target sites. Further analysis indicates that genes with shorter 3(')-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3(')-UTR.