Pooled-matrix protein interaction screens using Barcode Fusion Genetics.
Nozomu YachieEvangelia PetsalakiJoseph C MellorJochen WeileYves JacobMarta VerbySedide B OzturkSiyang LiAtina G CoteRoberto MoscaJennifer J KnappMinjeong KoAnalyn YuMarinella GebbiaNidhi SahniSong YiTanya TyagiDayag SheykhkarimliJonathan F RothCassandra WongLouai MusaJamie SniderYi-Chun LiuHaiyuan YuPascal BraunIgor StagljarTong HaoMichael A CalderwoodLaurence PelletierPatrick AloyDavid E HillMarc VidalFrederick P RothPublished in: Molecular systems biology (2016)
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.