RNA interference (RNAi) leads to sequence-specific knockdown of gene function. The approach can be used in large-scale screens to interrogate function in various model organisms and an increasing number of other species. Genome-scale RNAi screens are routinely performed in cultured or primary cells or in vivo in organisms such as C. elegans. High-throughput RNAi screening is benefitting from the development of sophisticated new instrumentation and software tools for collecting and analyzing data, including high-content image data. The results of large-scale RNAi screens have already proved useful, leading to new understandings of gene function relevant to topics such as infection, cancer, obesity, and aging. Nevertheless, important caveats apply and should be taken into consideration when developing or interpreting RNAi screens. Some level of false discovery is inherent to high-throughput approaches and specific to RNAi screens, false discovery due to off-target effects (OTEs) of RNAi reagents remains a problem. The need to improve our ability to use RNAi to elucidate gene function at large scale and in additional systems continues to be addressed through improved RNAi library design, development of innovative computational and analysis tools and other approaches.
High-throughput data analysis
RNAi screening: new approaches, understandings, and organisms.” Wiley Interdiscip Rev RNA, 3, 2, Pp. 145-58.Abstract
. 2012. “
Definition of global and transcript-specific mRNA export pathways in metazoans.” Genes Dev, 22, 1, Pp. 66-78.Abstract
. 2008. “
RNAi screening comes of age: improved techniques and complementary approaches.” Nat Rev Mol Cell Biol, 15, 9, Pp. 591-600.Abstract
. 2014. “
Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays.” Nat Methods, 3, 10, Pp. 833-8.Abstract
. 2006. “
RNAiCut: automated detection of significant genes from functional genomic screens.” Nat Methods, 6, 7, Pp. 476-7.
. 2009. “
Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen.” PLoS Genet, 8, 5, Pp. e1002667.Abstract
. 2012. “
Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila.” Genes Dev, 19, 16, Pp. 1861-70.Abstract
. 2005. “
Identification of novel genes involved in light-dependent CRY degradation through a genome-wide RNAi screen.” Genes Dev, 22, 11, Pp. 1522-33.Abstract
. 2008. “
Drosophila genome-wide RNAi screen identifies multiple regulators of HIF-dependent transcription in hypoxia.” PLoS Genet, 6, 6, Pp. e1000994.Abstract
. 2010. “
A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression.” Proc Natl Acad Sci U S A, 104, 22, Pp. 9381-6.Abstract
. 2007. “
Genome-wide RNAi screen identifies Letm1 as a mitochondrial Ca2+/H+ antiporter.” Science, 326, 5949, Pp. 144-7.Abstract
. 2009. “
BUHO: a MATLAB script for the study of stress granules and processing bodies by high-throughput image analysis.” PLoS One, 7, 12, Pp. e51495.Abstract
. 2012. “
FlyRNAi: the Drosophila RNAi screening center database.” Nucleic Acids Res, 34, Database issue, Pp. D489-94.Abstract
. 2006. “