High-throughput selection of effective RNAi probes for gene silencing

Kumar, Rajeev, Conklin, Douglas S., Mittal, Vivek (October 2003) High-throughput selection of effective RNAi probes for gene silencing. Genome Research, 13 (10). pp. 2333-2340. ISSN 1088-9051

URL: http://www.ncbi.nlm.nih.gov/pubmed/14525931
DOI: 10.1101/gr.1575003

Abstract

RNA interference (RNAi) is a process of sequence-specific posttranscriptional gene silencing mediated by double-stranded RNA. RNA! has recently emerged as a powerful genetic tool to analyze gene function in mammalian cells. The power of this method is limited however, by the uncertainty in predicting the efficacy of small interfering RNAs (siRNAs) in silencing a gene. This has imposed serious limitations not only for small-scale but also for high-throughput RNAi screening initiatives in mammalian systems. We have developed a reliable and quantitative approach for the rapid and efficient identification of the most effective siRNA against any gene. The efficacy of siRNA sequences is monitored by their ability to reduce the expression of cognate target-reporter fusions with easily quantified readouts. Finally, using microarray-based cell transfections, we demonstrate an unlimited potential of this approach in high-throughput screens for identifying effective siRNA probes for silencing genes in mammalian systems. This approach is likely to have implications in the use of RNAi as a reverse genetic tool for analyzing mammalian gene function on a genome-wide scale.

Item Type: Paper
Uncontrolled Keywords: SHORT-INTERFERING RNAS CULTURED-MAMMALIAN-CELLS HAIRPIN RNAS EXPRESSION INDUCTION DUPLEXES REPLICATION INITIATION EMBRYOS MICE
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
Investigative techniques and equipment > RNAI
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNAi
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene silencing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > siRNA
CSHL Authors:
Communities: CSHL labs > Mittal lab
Depositing User: Matt Covey
Date: October 2003
Date Deposited: 01 Apr 2013 21:02
Last Modified: 01 Apr 2013 21:02
PMCID: PMC403718
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27989

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