Use of RNA Interference to Study DNA Repair

DNA repair pathways maintain the integrity of the genome and thereby help prevent the onset of cancer, disease, and aging phenotypes [DNA Repair and Mutagenesis, ASM, Washington, DC]. As such, the critical requirement for DNA repair proteins and pathways in response to radiation and genotoxic chemotherapeutics implicates DNA repair proteins as prime targets for improving response to currently available anticancer regimens. Although defects in critical DNA repair pathways or proteins can predispose to cancer onset [FASEB J 26:2094–2104, 2012], such cancer-specifi c DNA repair defects offer novel approaches for tumor-selective therapy. To effectively evaluate the functional role of a specifi c DNA repair protein with regard to cell survival, response to genotoxins, and genome stability, it has become standard practice to employ select genetic tools to alter expression of the gene of interest and/or reexpress a mutant transgene [Cancer Res 71:2308–2317, 2011; Mol Cancer Res 8:67–79, 2010; Neuro Oncol 13:471–486, 2011]. A useful approach to reduce or suppress a specifi c gene of interest in cells is RNA interference. Briefl y, RNA interference is a posttranscriptional gene-silencing biological mechanism whereby RNA molecules inhibit gene expression either by translational suppression or by the targeted degradation of specifi c mRNA molecules. Once the gene of interest is suppressed in this manner and validated for gene expression loss, the resulting knockdown (KD) cells can be used for functional analysis to defi ne the cellular impact of gene loss and provide a resource for evaluating mutants of the gene, such as somatic or germ-line mutations, for impact on function [PLoS Genet 8:e1003086, 2012]. Herein, we describe methods to modify human cells via RNA interference as well as methods to validate gene KD and some measures of cellular response to genotoxins to uncover functional DNA repair defects in the absence of the gene.