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

• Published in: Nucleic acids research Vol. 41; no. 3; pp. 1496 - 1507
• Main Authors: Suter, Bernhard, Fontaine, Jean-Fred, Yildirimman, Reha, Raskó, Tamás, Schaefer, Martin H, Rasche, Axel, Porras, Pablo, Vázquez-Álvarez, Blanca M, Russ, Jenny, Rau, Kirstin, Foulle, Raphaele, Zenkner, Martina, Saar, Kathrin, Herwig, Ralf, Andrade-Navarro, Miguel A, Wanker, Erich E
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.02.2013
• Subjects: Ataxin-1; Ataxins; Computational Biology; Humans; Huntingtin Protein; Mutation; Nerve Tissue Proteins - genetics; Nerve Tissue Proteins - metabolism; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Oligonucleotide Array Sequence Analysis - methods; Open Reading Frames; Protein Interaction Maps; Two-Hybrid System Techniques; Yeasts - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gks1329

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.