Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

Wuming Gong,Yejun Wang,Tongbin Li,Yongliang Ren,Dong Lin,Qiqi Xu,Haiyan Zhou

doi:10.1186/1471-2105-7-516

Abstract

BackgroundShort interfering RNAs have allowed the development of clean and easily regulated methods for disruption of gene expression. However, while these methods continue to grow in popularity, designing effective siRNA experiments can be challenging. The various existing siRNA design guidelines suffer from two problems: they differ considerably from each other, and they produce high levels of false-positive predictions when tested on data of independent origins.ResultsUsing a distinctly large set of siRNA efficacy data assembled from a vast diversity of origins (the siRecords data, containing records of 3,277 siRNA experiments targeting 1,518 genes, derived from 1,417 independent studies), we conducted extensive analyses of all known features that have been implicated in increasing RNAi effectiveness. A number of features having positive impacts on siRNA efficacy were identified. By performing quantitative analyses on cooperative effects among these features, then applying a disjunctive rule merging (DRM) algorithm, we developed a bundle of siRNA design rule sets with the false positive problem well curbed. A comparison with 15 online siRNA design tools indicated that some of the rule sets we developed surpassed all of these design tools commonly used in siRNA design practice in positive predictive values (PPVs).ConclusionThe availability of the large and diverse siRNA dataset from siRecords and the approach we describe in this report have allowed the development of highly effective and generally applicable siRNA design rule sets. Together with ever improving RNAi lab techniques, these design rule sets are expected to make siRNAs a more useful tool for molecular genetics, functional genomics, and drug discovery studies.

Highlights

Short interfering RNAs have allowed the development of clean and regulated methods for disruption of gene expression
We identified a bundle of highly effective and generally applicable rule sets for siRNA design
This was accomplished by applying a simple strategy in which we analyzed a large number of candidate features for association with increased siRNA efficacies, used quantitative analyses of the joint effects of these significant features to identify positive cooperativity among these features

Summary

Introduction

Short interfering RNAs have allowed the development of clean and regulated methods for disruption of gene expression While these methods continue to grow in popularity, designing effective siRNA experiments can be challenging. Short interfering RNAs (siRNAs) are double-stranded RNAs typically of length between 19 and 25 with 2 nucleotide overhangs on the 3' ends, and they are capable of inducing sequence-specific, post-transcriptional deletion of gene products, leading to the silencing of the gene activity. The siRNA-based gene knock-down techniques are preferred by many because of their ability to disrupt individual gene's function without affecting related genes [9] These techniques are attractive for gene silencing studies in mammalian cells, because, unlike longer double-stranded RNAs, siRNAs are not likely to trigger interferon responses which lead to non-specific mRNA degradation [5]

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Conclusion