Specific residues at every third position of siRNA shape its efficient RNAi activity.
Specific residues at every third position of siRNA shape its efficient RNAi activity.
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DOI：
10.1093/nar/gkl1120
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发表时间：
2007
影响因子：
14.9
通讯作者：
Suzuki T
中科院分区：
文献类型：
--
作者：
Katoh T;Suzuki T
小干扰RNA（siRNA）在哺乳动物细胞中诱导序列特异性转录后基因沉默。每种siRNA的不同功效被认为是由RNAi中蛋白质组分的序列偏好引起的。为了获得对siRNA功能的机理性洞察，在这里，我们描述了靶向人类细胞中单个mRNA的所有可能位置的siRNA活性的完整数据集。以最小的误差因子检查了702个覆盖增强型绿色荧光蛋白mRNA的开放阅读框（720个碱基）的siRNA。最重要的发现是siRNA中每隔3个位置的特定残基对其RNAi活性有很大影响，siRNA中3 n + 1（4，7，10，13，16，19）位碱基组成的优化对活性有积极影响，这可以解释siRNA活性在mRNA序列位置上以3个核苷酸（nt）周期波动的现象。由于siRNA活性与其与TRBP（人Dicer的伴侣蛋白）的结合亲和力之间存在明显的相关性，因此3-nt周期性可能与TRBP的亲和力相关。由于通过该观察开发的算法（“siExplorer”）成功地计算了靶向内源性人类基因的siRNA的活性，3-nt周期性提供了揭示siRNA功能的新方面。
Small interfering RNA (siRNA) induces sequence-specific post-transcriptional gene silencing in mammalian cells. Different efficacy of each siRNA is considered to result from sequence preference by protein components in RNAi. To obtain mechanistic insight into siRNA functionality, here we describe a complete data set of siRNA activities targeting all possible position of a single mRNA in human cells. Seven hundred and two siRNAs covering open reading frame of enhanced green fluorescent protein mRNA ( 720 bases) were examined with minimized error factors. The most important finding is that specific residues at every third position of siRNAs greatly influence its RNAi activity; the optimized base composition at positions 3n + 1 (4,7,10,13,16,19) in siRNAs have positive effects on the activity, which can explain the waving siRNA activity with 3 nucleotides (nt) periodicity in the sequential positions of mRNAs. Since there was an obvious correlation between siRNA activity and its binding affinity to TRBP, a partner protein of human Dicer, the 3-nt periodicity might correlate with the affinity to TRBP. As an algorithm (‘siExplorer’) developed by this observation successfully calculated the activities of siRNAs targeting endogenous human genes, the 3-nt periodicity provides a new aspect unveiling siRNA functionality.
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