Pooled-matrix Protein Interaction Screens Using Barcode Fusion Genetics

Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

Abstract

High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods.

Keywords: DNA barcode; interactome; next‐generation sequencing; protein interaction; yeast two‐hybrid.

Publication types

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

MeSH terms

  • Centrosome / metabolism*
  • Chromosomes, Human / metabolism
  • Gene Library
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Proteome / metabolism*
  • Saccharomyces cerevisiae / genetics*
  • Two-Hybrid System Techniques

Substances

  • Proteome