Institute of Molecular Oncology, Biomedical Sciences Research Center, Vari, Greece.
Bioinformatics. 2012 Mar 15;28(6):771-6. doi: 10.1093/bioinformatics/bts043. Epub 2012 Jan 27.
Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.
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.
实验证据积累表明，蛋白质编码序列（CDS）内的 microRNA（miRNA）结合位点在控制基因表达方面具有功能。
在这里，我们报告了一种基于从现有的哺乳动物高通量免疫沉淀和测序数据中提取的特征对这种 miRNA 靶位点的计算分析。该分析分别针对 CDS 和 3'非翻译区（3'UTR）进行，并为两个区域揭示了不同的特征集和模型。将这两个模型组合成一个新的 miRNA 靶基因计算模型 DIANA-microT-CDS，与其他流行的程序和仅使用 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 的基因在 CDS 中更优先被靶向，这表明在 3'UTR 上的空间有限的情况下，进化选择可能有利于 CDS 上的其他位点。
