Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays.

Published

Journal Article

To evaluate the specificity of long dsRNAs used in high-throughput RNA interference (RNAi) screens performed at the Drosophila RNAi Screening Center (DRSC), we performed a global analysis of their activity in 30 genome-wide screens completed at our facility. Notably, our analysis predicts that dsRNAs containing > or = 19-nucleotide perfect matches identified in silico to unintended targets may contribute to a significant false positive error rate arising from off-target effects. We confirmed experimentally that such sequences in dsRNAs lead to false positives and to efficient knockdown of a cross-hybridizing transcript, raising a cautionary note about interpreting results based on the use of a single dsRNA per gene. Although a full appreciation of all causes of false positive errors remains to be determined, we suggest simple guidelines to help ensure high-quality information from RNAi high-throughput screens.

Full Text

Duke Authors

Cited Authors

  • Kulkarni, MM; Booker, M; Silver, SJ; Friedman, A; Hong, P; Perrimon, N; Mathey-Prevot, B

Published Date

  • October 2006

Published In

Volume / Issue

  • 3 / 10

Start / End Page

  • 833 - 838

PubMed ID

  • 16964256

Pubmed Central ID

  • 16964256

International Standard Serial Number (ISSN)

  • 1548-7091

Digital Object Identifier (DOI)

  • 10.1038/nmeth935

Language

  • eng

Conference Location

  • United States