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12Design and Application of a shRNA-Based GeneReplacement RetrovirusRugang Zhang, Peter D. Adams, and Xiaofen YeSummaryTo perform structure/function analyses of a protein in vivo, ideally one should be able tosimultaneously abolish expression of the endogenous wild-type protein, substitute it with a formof the protein containing a targeted mutation, and analyze the functional consequences. Untilrecently, this was a highly challenging and/or laborious approach in mammalian systems, requiringa targeted gene knockin in a human cell line or mouse. Herein is described a RNA interference(RNAi)-based approach to achieve this much more simply in mammalian cells. A single retrovirushas been constructed, which directs expression of a short hairpin RNA (shRNA) to knockdownexpression of the endogenous protein of interest; a cDNA coding for a wild-type or mutantversion of the same protein that also contains “silent mutations” that do not affect the proteinsequence, but do make the mRNA resistant to the shRNA; and a puromycin-resistance gene toallow rapid drug selection of the virus-infected cells. Using this virus, expression of the endogenousAnti-Silencing Function 1a (ASF1a) histone chaperone has been efficiently replaced in primaryhuman cells, by an ectopically expressed epitope-tagged version. Moreover, the virus isdesigned so that other shRNA and shRNA-resistant cDNA cassettes can easily be substituted,making the approach readily applicable to other protein targets.Key Words: Gene replacement; retrovirus; shRNA; silent mutations; shRNA-resistant cDNA;U6 promoter.1. IntroductionRNAi-based technologies have revolutionized the molecular and cellularapproaches taken to understand biological processes in mammalian cells. Forexample, when studying gene function at the cellular level, researchers can useRNAi technology to quickly generate cells lacking the gene of interest andexamine its “loss-of-function” phenotype (1). Furthermore, it is becomingfeasible to perform RNAi-based “genetic screens” in mammalian cells for geneproducts whose inactivation confers a specific cellular phenotype (2–6).From: Methods in Molecular Biology, vol. 408: Gene Function AnalysisEdited by: M. Ochs © Humana Press Inc., Totowa, NJ211

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