Development and application of a DNA microarray-based yeast two-hybrid system


  • B. Suter
  • J.F. Fontaine
  • R. Yildirimman
  • T. Raskó
  • M.H. Schaefer
  • A. Rasche
  • P. Porras
  • B.M. Vázquez-Álvarez
  • J. Russ
  • K. Rau
  • R. Foulle
  • M. Zenkner
  • K. Saar
  • R. Herwig
  • M.A. Andrade-Navarro
  • E.E. Wanker


  • Nucleic Acids Research


  • Nucleic Acids Res 41 (3): 1496-507


  • The yeast two-hybrid (Y2H) system is the most widely applied methodology for systematic protein-protein interaction (PPI) screening and the generation of comprehensive interaction networks. We developed a novel Y2H interaction screening procedure using DNA microarrays for high-throughput quantitative PPI detection. Applying a global pooling and selection scheme to a large collection of human open reading frames, proof-of-principle Y2H interaction screens were performed for the human neurodegenerative disease proteins huntingtin and ataxin-1. Using systematic controls for unspecific Y2H results and quantitative benchmarking, we identified and scored a large number of known and novel partner proteins for both huntingtin and ataxin-1. Moreover, we show that this parallelized screening procedure and the global inspection of Y2H interaction data are uniquely suited to define specific PPI patterns and their alteration by disease-causing mutations in huntingtin and ataxin-1. This approach takes advantage of the specificity and flexibility of DNA microarrays and of the existence of solid-related statistical methods for the analysis of DNA microarray data, and allows a quantitative approach toward interaction screens in human and in model organisms.