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Cell. 2013 Feb 14;152(4):909-22. doi: 10.1016/j.cell.2013.01.030. Epub 2013 Feb 8.

A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.

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  • 1Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research and Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94122, USA. bassik@cmp.ucsf.edu

Abstract

Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.

Copyright © 2013 Elsevier Inc. All rights reserved.

PMID:
23394947
[PubMed - indexed for MEDLINE]
PMCID:
PMC3652613
Free PMC Article
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