RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.
Drosophila (fly)
Genomic screening with RNAi: results and challenges.” Annu Rev Biochem, 79, Pp. 37-64.Abstract
. 2010. “
High-content chemical and RNAi screens for suppressors of neurotoxicity in a Huntington's disease model.” PLoS One, 6, 8, Pp. e23841.Abstract
. 2011. “
The evolutionarily conserved protein CG9186 is associated with lipid droplets, required for their positioning and for fat storage.” J Cell Sci, 126, Pt 10, Pp. 2198-212.Abstract
. 2013. “
Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis.” BMC Bioinformatics, 15, Pp. 192.Abstract
. 2014. “
Genome-wide RNAi analysis of growth and viability in Drosophila cells.” Science, 303, 5659, Pp. 832-5.Abstract
. 2004. “
Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays.” Nat Methods, 3, 10, Pp. 833-8.Abstract
. 2006. “
ESCRT factors restrict mycobacterial growth.” Proc Natl Acad Sci U S A, 105, 8, Pp. 3070-5.Abstract
. 2008. “
Bili inhibits Wnt/beta-catenin signaling by regulating the recruitment of axin to LRP6.” PLoS One, 4, 7, Pp. e6129.Abstract
. 2009. “
Where gene discovery turns into systems biology: genome-scale RNAi screens in Drosophila.” Wiley Interdiscip Rev Syst Biol Med, 3, 4, Pp. 471-8.Abstract
. 2011. “
Control of proinflammatory gene programs by regulated trimethylation and demethylation of histone H4K20.” Mol Cell, 48, 1, Pp. 28-38.Abstract
. 2012. “
The Hippo signaling pathway interactome.” Science, 342, 6159, Pp. 737-40.Abstract
. 2013. “
In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila.” Genetics, 201, 2, Pp. 433-42.Abstract
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FlyRNAi: the Drosophila RNAi screening center database.” Nucleic Acids Res, 34, Database issue, Pp. D489-94.Abstract
. 2006. “
A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila.” Genome Biol, 8, 9, Pp. R203.Abstract
. 2007. “
Comparative analysis of argonaute-dependent small RNA pathways in Drosophila.” Mol Cell, 32, 4, Pp. 592-9.Abstract
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