3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

  title={3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets},
  author={Amanda Birmingham and Emily M. Anderson and Angela Reynolds and Diane Ilsley-Tyree and Devin Leake and Yuriy Fedorov and Scott Baskerville and Elena M Maksimova and Kathryn Robinson and Jon M. Karpilow and William S. Marshall and Anastasia Khvorova},
  journal={Nature Methods},
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… 

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A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

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The discovery is revealed that the specificity of an siRNA can be affected by the location of its target site, and siRNA had greatly elevated tolerance towards mismatches in target sites in the 3′-UTR of the mRNA compared with the same target sites cloned in the coding region.



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It is shown that most functional siRNAs have characteristic sequence features and there is a 99.9% chance of designing an effective siRNA in a set of three with more than 50% knockdown efficiency in a biological readout.

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Asymmetry in the Assembly of the RNAi Enzyme Complex

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