A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
复制标题
DOI：
10.1093/bioinformatics/btr276
复制
发表时间：
2011-07-01
期刊：
影响因子：
5.8
通讯作者：
Asai, Kiyoshi
中科院分区：
文献类型：
--
作者：
Kiryu, Hisanori;Terai, Goro;Asai, Kiyoshi
动机：自从发现在动物细胞中转录的各种类型的非编码RNA以来，RNA序列分析的重要性一直在增加。传统的RNA序列分析主要集中在结构化区域，这些区域由作用于相邻碱基对的堆积能量稳定。另一方面，最近关于小干扰RNAs(SiRNAs)和microRNAs(MiRNAs)转录调控机制的研究结果表明，分析不存在碱基对的可接近区域的重要性。结果：我们对siRNAs和miRNAs靶点周围的可达性进行了详细的调查。我们详尽地计算了目标位点周围的可及性与相应mRNAs抑制水平之间的相关性。我们用一个名为RAccess的软件包计算了可及性，该软件包计算了当碱基对之间的最大距离限制在固定大小W时，给定RNA序列所有固定长度片段的可及性。我们发现，计算的可及性对最大跨度W的选择相对不敏感。我们发现，siRNAs的有效性强烈依赖于其结合位点的可及性，这可能反映了RNA诱导的沉默复合体中的目标位点识别机制。我们还表明，miRNAs的有效性与可及性有类似的依赖关系，但一些miRNAs的有效性与其假定结合位点下游广泛区域的可达性呈正相关，这可能意味着靶点下游区域与其他允许miRNAs实现其功能的蛋白质结合。我们还研究了siRNA作为一种潜在的RNAi治疗药物的靶外效应。我们发现siRNA的脱靶效应与miRNA抑制具有相似的相关性，表明它们是由相同的机制引起的。
Motivation: The importance of RNA sequence analysis has been increasing since the discovery of various types of non-coding RNAs transcribed in animal cells. Conventional RNA sequence analyses have mainly focused on structured regions, which are stabilized by the stacking energies acting on adjacent base pairs. On the other hand, recent findings regarding the mechanisms of small interfering RNAs (siRNAs) and transcription regulation by microRNAs (miRNAs) indicate the importance of analyzing accessible regions where no base pairs exist. So far, relatively few studies have investigated the nature of such regions.Results: We have conducted a detailed investigation of accessibilities around the target sites of siRNAs and miRNAs. We have exhaustively calculated the correlations between the accessibilities around the target sites and the repression levels of the corresponding mRNAs. We have computed the accessibilities with an originally developed software package, called 'Raccess', which computes the accessibility of all the segments of a fixed length for a given RNA sequence when the maximal distance between base pairs is limited to a fixed size W. We show that the computed accessibilities are relatively insensitive to the choice of the maximal span W. We have found that the efficacy of siRNAs depends strongly on the accessibility of the very 3'-end of their binding sites, which might reflect a target site recognition mechanism in the RNA-induced silencing complex. We also show that the efficacy of miRNAs has a similar dependence on the accessibilities, but some miRNAs also show positive correlations between the efficacy and the accessibilities in broad regions downstream of their putative binding sites, which might imply that the downstream regions of the target sites are bound by other proteins that allow the miRNAs to implement their functions. We have also investigated the off-target effects of an siRNA as a potential RNAi therapeutic. We show that the off-target effects of the siRNA have similar correlations to the miRNA repression, indicating that they are caused by the same mechanism.