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A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens

2012; Nature Portfolio; Volume: 9; Issue: 4 Linguagem: Inglês

10.1038/nmeth.1898

1548-7105

Frederic Sigoillot, Susan K. Lyman, Jeremy F. Huckins, Britt Adamson, Eunah Chung, Brian Quattrochi, Randall W. King,

RNA Interference and Gene Delivery

Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens. Because off-target effects hamper interpretation and validation of RNAi screen data, we developed a bioinformatics method, genome-wide enrichment of seed sequence matches (GESS), to identify candidate off-targeted transcripts in primary screening data. GESS analysis revealed a prominent off-targeted transcript in several screens, including MAD2 (MAD2L1) in a screen for genes required for the spindle assembly checkpoint. GESS analysis results can enhance the validation rate in RNAi screens.