The impact of target site accessibility on the design of effective siRNAs
The impact of target site accessibility on the design of effective siRNAs
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DOI：
10.1038/nbt1404
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发表时间：
2008-05-01
影响因子：
46.9
通讯作者：
Hofacker, Ivo L.
中科院分区：
文献类型：
--
作者：
Tafer, Hakim;Ameres, Stefan L.;Hofacker, Ivo L.
小干扰RNA（siRNA）组装成RISC，RNA诱导的沉默复合物，切割互补的mRNA。尽管它们的功效波动，siRNA被广泛用于评估基因功能。虽然这种限制可以部分归因于RISC的组装和激活的变化，但RNA干扰（RNAi）途径中的下游事件，如靶位点可及性，迄今尚未得到广泛研究。在这项研究中，我们提出了一个全面的分析目标RNA结构的影响RNAi通过计算与siRNA相互作用的靶位点的可及性。基于我们的观察，我们开发了一种新的siRNA设计工具，RNAxs，通过结合已知的siRNA功能标准与靶位点的可及性。我们在包含38个基因的573个siRNA的两个数据集上校准了我们的方法，并在一组独立的360个siRNA上测试了它，这些siRNA靶向另外四个基因。总的来说，RNAxs被证明是一种稳健的siRNA选择工具，可显著提高高效siRNA的预测。
Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.