siRNA off-target effects in genome-wide screens identify signaling pathway members.

Methods Development

Abstract

We introduce a method for analyzing small interfering RNA (siRNA) genetic screens based entirely on off-target effects. Using a screen for members of the Wnt pathway, we demonstrate that this method identifies known pathway components, some of which are not present in the screening library. This technique can be applied to siRNA screen results retroactively to confirm positives and identify genes missed using conventional methods for on-target gene selection.

Authors

Buehler, Eugen; Khan, Aly A; Marine, Shane; Rajaram, Misha; Bahl, Amit; Burchard, Julja; Ferrer-Alegre, Marc;

Keywords

  • 3' Untranslated Regions/ genetics
  • Algorithms
  • Animals
  • Base Sequence
  • Computational Biology/ methods
  • Gene Expression Profiling
  • Gene Library
  • Genome/ genetics
  • Genomics/ methods
  • Humans
  • Models, Genetic
  • RNA Interference
  • RNA, Small Interfering/ genetics
  • Reproducibility of Results
  • Signal Transduction/ genetics
  • Wnt Signaling Pathway/ genetics

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