A challenge for authentic mechanistic interpretation of large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling that can result from short regions (approximately six nucleotides) of oligonucleotide complementarity to many different mRNAs.
To help defend against this, we have developed a computational approach, Deconvolution Analysis of RNAi Screening data (DecoRNAi), for automated quantitation and annotation of microRNA-like off-target effects in primary RNAi screening data sets. Substantial reduction of off-target rates was experimentally validated in five distinct biological screens across different genome-wide siRNA libraries.
A public-access graphical user interface has been built to allow application of this algorithm by the functional genomics community.