Birmingham Amanda, Anderson Emily M, Reynolds Angela, Ilsley-Tyree Diane, Leake Devin, Fedorov Yuriy, Baskerville Scott, Maksimova Elena, Robinson Kathryn, Karpilow Jon, Marshall William S, Khvorova Anastasia
Dharmacon Research, 2650 Crescent Drive, #100, Lafayette, Colorado 80026, USA.
Nat Methods. 2006 Mar;3(3):199-204. doi: 10.1038/nmeth854.
Off-target gene silencing can present a notable challenge in the interpretation of data from large-scale RNA interference (RNAi) screens. We performed a detailed analysis of off-targeted genes identified by expression profiling of human cells transfected with small interfering RNA (siRNA). Contrary to common assumption, analysis of the subsequent off-target gene database showed that overall identity makes little or no contribution to determining whether the expression of a particular gene will be affected by a given siRNA, except for near-perfect matches. Instead, off-targeting is associated with the presence of one or more perfect 3' untranslated region (UTR) matches with the hexamer or heptamer seed region (positions 2-7 or 2-8) of the antisense strand of the siRNA. These findings have strong implications for future siRNA design and the application of RNAi in high-throughput screening and therapeutic development.
脱靶基因沉默可能会给大规模RNA干扰（RNAi）筛选数据的解读带来显著挑战。我们对通过转染小干扰RNA（siRNA）的人类细胞表达谱鉴定出的脱靶基因进行了详细分析。与通常的假设相反，对后续脱靶基因数据库的分析表明，除了近乎完美的匹配外，总体序列一致性对确定特定基因的表达是否会受到给定siRNA的影响几乎没有贡献。相反，脱靶与siRNA反义链的六聚体或七聚体种子区域（第2 - 7位或2 - 8位）与一个或多个完美的3'非翻译区（UTR）匹配有关。这些发现对未来的siRNA设计以及RNAi在高通量筛选和治疗开发中的应用具有重要意义。
