Kittler Ralf, Surendranath Vineeth, Heninger Anne-Kristin, Slabicki Mikolaj, Theis Mirko, Putz Gabriele, Franke Kristin, Caldarelli Antonio, Grabner Hannes, Kozak Karol, Wagner Jan, Rees Effi, Korn Bernd, Frenzel Corina, Sachse Christoph, Sönnichsen Birte, Guo Jie, Schelter Janell, Burchard Julja, Linsley Peter S, Jackson Aimee L, Habermann Bianca, Buchholz Frank
Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
Nat Methods. 2007 Apr;4(4):337-44. doi: 10.1038/nmeth1025. Epub 2007 Mar 11.
RNA interference (RNAi) has become an important technique for loss-of-gene-function studies in mammalian cells. To achieve reliable results in an RNAi experiment, efficient and specific silencing triggers are required. Here we present genome-wide data sets for the production of endoribonuclease-prepared short interfering RNAs (esiRNAs) for human, mouse and rat. We used an algorithm to predict the optimal region for esiRNA synthesis for every protein-coding gene of these three species. We created a database, RiDDLE, for retrieval of target sequences and primer information. To test this in silico resource experimentally, we generated 16,242 esiRNAs that can be used for RNAi screening in human cells. Comparative analyses with chemically synthesized siRNAs demonstrated a high silencing efficacy of esiRNAs and a 12-fold reduction of downregulated off-target transcripts as detected by microarray analysis. Hence, the presented esiRNA libraries offer an efficient, cost-effective and specific alternative to presently available mammalian RNAi resources.
RNA干扰（RNAi）已成为哺乳动物细胞中基因功能缺失研究的一项重要技术。为了在RNAi实验中获得可靠的结果，需要高效且特异的沉默触发因子。在此，我们展示了针对人类、小鼠和大鼠产生核糖核酸内切酶制备的小干扰RNA（esiRNA）的全基因组数据集。我们使用一种算法来预测这三个物种每个蛋白质编码基因的esiRNA合成最佳区域。我们创建了一个数据库RiDDLE，用于检索靶序列和引物信息。为了通过实验测试这种计算机资源，我们生成了16242个可用于人类细胞RNAi筛选的esiRNA。与化学合成的小干扰RNA（siRNA）的比较分析表明，esiRNA具有很高的沉默效率，并且通过微阵列分析检测到下调的脱靶转录本减少了12倍。因此，所展示的esiRNA文库为目前可用的哺乳动物RNAi资源提供了一种高效、经济且特异的替代方案。
