Noise amidst the silence: off-target effects of siRNAs?

RNA interference (RNAi), mediated by short interfering RNAs (siRNAs), is widely used to silence gene expression and to define gene function in mammalian cells. Initially, this gene silencing via transcript degradation was believed to be exquisitely specific, requiring near-identity between the siRNA and the target mRNA. However, several recent reports have suggested that non-specific effects can be induced by siRNAs, both at the level of mRNA and protein. These findings suggest that siRNAs can regulate the expression of unintended targets, and argue for further experiments on the mechanism and extent of off-target gene regulation(s). In the meantime, caution is warranted in interpreting gene function and phenotypes resulting from RNAi experiments.

[1]  Robert H. Silverman,et al.  Activation of the interferon system by short-interfering RNAs , 2003, Nature Cell Biology.

[2]  R. Iggo,et al.  Determinants of interferon-stimulated gene induction by RNAi vectors. , 2004, Differentiation; research in biological diversity.

[3]  R. Iggo,et al.  Induction of an interferon response by RNAi vectors in mammalian cells , 2003, Nature Genetics.

[4]  K. Ui-Tei,et al.  Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. , 2004, Nucleic acids research.

[5]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

[6]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[7]  Serge Batalov,et al.  Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. , 2003, Molecular cell.

[8]  S. Fesik,et al.  Specificity of short interfering RNA determined through gene expression signatures , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Tyra G. Wolfsberg,et al.  Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Anindya Dutta,et al.  Small RNAs with Imperfect Match to Endogenous mRNA Repress Translation , 2003, Journal of Biological Chemistry.

[11]  J. Manola,et al.  A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. , 2004, Nucleic acids research.

[12]  A. Reynolds,et al.  Rational siRNA design for RNA interference , 2004, Nature Biotechnology.

[13]  Michael R. Green,et al.  Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). , 2004, RNA.

[14]  Howard Y. Chang,et al.  Genomewide view of gene silencing by small interfering RNAs , 2003, Proceedings of the National Academy of Sciences of the United States of America.