Molecular Systems Biology (Apr 2016)
Pooled‐matrix protein interaction screens using Barcode Fusion Genetics
- Nozomu Yachie,
- Evangelia Petsalaki,
- Joseph C Mellor,
- Jochen Weile,
- Yves Jacob,
- Marta Verby,
- Sedide B Ozturk,
- Siyang Li,
- Atina G Cote,
- Roberto Mosca,
- Jennifer J Knapp,
- Minjeong Ko,
- Analyn Yu,
- Marinella Gebbia,
- Nidhi Sahni,
- Song Yi,
- Tanya Tyagi,
- Dayag Sheykhkarimli,
- Jonathan F Roth,
- Cassandra Wong,
- Louai Musa,
- Jamie Snider,
- Yi‐Chun Liu,
- Haiyuan Yu,
- Pascal Braun,
- Igor Stagljar,
- Tong Hao,
- Michael A Calderwood,
- Laurence Pelletier,
- Patrick Aloy,
- David E Hill,
- Marc Vidal,
- Frederick P Roth
Affiliations
- Nozomu Yachie
- Donnelly Centre University of Toronto Toronto ON Canada
- Evangelia Petsalaki
- Donnelly Centre University of Toronto Toronto ON Canada
- Joseph C Mellor
- Donnelly Centre University of Toronto Toronto ON Canada
- Jochen Weile
- Donnelly Centre University of Toronto Toronto ON Canada
- Yves Jacob
- Département de Virologie Unité de Génétique Moléculaire des Virus à ARN Institut Pasteur Paris France
- Marta Verby
- Donnelly Centre University of Toronto Toronto ON Canada
- Sedide B Ozturk
- Donnelly Centre University of Toronto Toronto ON Canada
- Siyang Li
- Donnelly Centre University of Toronto Toronto ON Canada
- Atina G Cote
- Donnelly Centre University of Toronto Toronto ON Canada
- Roberto Mosca
- Joint IRB‐BSC Program in Computational Biology Institute for Research in Biomedicine (IRB Barcelona) Barcelona Spain
- Jennifer J Knapp
- Donnelly Centre University of Toronto Toronto ON Canada
- Minjeong Ko
- Donnelly Centre University of Toronto Toronto ON Canada
- Analyn Yu
- Donnelly Centre University of Toronto Toronto ON Canada
- Marinella Gebbia
- Donnelly Centre University of Toronto Toronto ON Canada
- Nidhi Sahni
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Song Yi
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Tanya Tyagi
- Donnelly Centre University of Toronto Toronto ON Canada
- Dayag Sheykhkarimli
- Donnelly Centre University of Toronto Toronto ON Canada
- Jonathan F Roth
- Donnelly Centre University of Toronto Toronto ON Canada
- Cassandra Wong
- Donnelly Centre University of Toronto Toronto ON Canada
- Louai Musa
- Donnelly Centre University of Toronto Toronto ON Canada
- Jamie Snider
- Donnelly Centre University of Toronto Toronto ON Canada
- Yi‐Chun Liu
- Donnelly Centre University of Toronto Toronto ON Canada
- Haiyuan Yu
- Weill Institute for Cell and Molecular Biology Cornell University Ithaca NY USA
- Pascal Braun
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Igor Stagljar
- Donnelly Centre University of Toronto Toronto ON Canada
- Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Michael A Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Laurence Pelletier
- Lunenfeld‐Tanenbaum Research Institute Mt. Sinai Hospital Toronto ON Canada
- Patrick Aloy
- Joint IRB‐BSC Program in Computational Biology Institute for Research in Biomedicine (IRB Barcelona) Barcelona Spain
- David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology Dana‐Farber Cancer Institute Boston MA USA
- Frederick P Roth
- Donnelly Centre University of Toronto Toronto ON Canada
- DOI
- https://doi.org/10.15252/msb.20156660
- Journal volume & issue
-
Vol. 12,
no. 4
pp. n/a – n/a
Abstract
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