A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Atorvastatin
  • Biological Transport*
  • Carrier Proteins / metabolism
  • Cell Line, Tumor
  • Coat Protein Complex I / metabolism
  • Endoplasmic Reticulum / metabolism
  • Epistasis, Genetic*
  • Heptanoic Acids / pharmacology
  • Humans
  • Membrane Proteins / metabolism
  • Proto-Oncogene Proteins / metabolism
  • Pyrroles / pharmacology
  • RNA, Small Interfering
  • Ribosomal Proteins / metabolism
  • Ricin / toxicity*
  • Vesicular Transport Proteins / metabolism


  • C17orf75 protein, human
  • Carrier Proteins
  • Coat Protein Complex I
  • Heptanoic Acids
  • Membrane Proteins
  • Proto-Oncogene Proteins
  • Pyrroles
  • RNA, Small Interfering
  • RPS25 protein, human
  • Ribosomal Proteins
  • Vesicular Transport Proteins
  • WDR11 protein, human
  • transport protein particle, TRAPP
  • Ricin
  • Atorvastatin