Pooled‐matrix protein interaction screens using Barcode Fusion Genetics
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 requir...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2016-04-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20156660 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849234285052035072 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Nozomu Yachie |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-0a18ae4d6e6e47358d45bf840a728d90 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2016-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-0a18ae4d6e6e47358d45bf840a728d902025-08-20T04:03:12ZengSpringer NatureMolecular Systems Biology1744-42922016-04-0112411710.15252/msb.20156660Pooled‐matrix protein interaction screens using Barcode Fusion GeneticsNozomu Yachie0Evangelia Petsalaki1Joseph C Mellor2Jochen Weile3Yves Jacob4Marta Verby5Sedide B Ozturk6Siyang Li7Atina G Cote8Roberto Mosca9Jennifer J Knapp10Minjeong Ko11Analyn Yu12Marinella Gebbia13Nidhi Sahni14Song Yi15Tanya Tyagi16Dayag Sheykhkarimli17Jonathan F Roth18Cassandra Wong19Louai Musa20Jamie Snider21Yi‐Chun Liu22Haiyuan Yu23Pascal Braun24Igor Stagljar25Tong Hao26Michael A Calderwood27Laurence Pelletier28Patrick Aloy29David E Hill30Marc Vidal31Frederick P Roth32Donnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDépartement de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut PasteurDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoJoint IRB‐BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona)Donnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoDonnelly Centre, University of TorontoWeill Institute for Cell and Molecular Biology, Cornell UniversityCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteDonnelly Centre, University of TorontoCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteLunenfeld‐Tanenbaum Research Institute, Mt. Sinai HospitalJoint IRB‐BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona)Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana‐Farber Cancer InstituteDonnelly Centre, University of TorontoAbstract 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.https://doi.org/10.15252/msb.20156660DNA barcodeinteractomenext‐generation sequencingprotein interactionyeast two‐hybrid |
| spellingShingle | 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 Pooled‐matrix protein interaction screens using Barcode Fusion Genetics Molecular Systems Biology DNA barcode interactome next‐generation sequencing protein interaction yeast two‐hybrid |
| title | Pooled‐matrix protein interaction screens using Barcode Fusion Genetics |
| title_full | Pooled‐matrix protein interaction screens using Barcode Fusion Genetics |
| title_fullStr | Pooled‐matrix protein interaction screens using Barcode Fusion Genetics |
| title_full_unstemmed | Pooled‐matrix protein interaction screens using Barcode Fusion Genetics |
| title_short | Pooled‐matrix protein interaction screens using Barcode Fusion Genetics |
| title_sort | pooled matrix protein interaction screens using barcode fusion genetics |
| topic | DNA barcode interactome next‐generation sequencing protein interaction yeast two‐hybrid |
| url | https://doi.org/10.15252/msb.20156660 |
| work_keys_str_mv | AT nozomuyachie pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT evangeliapetsalaki pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT josephcmellor pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT jochenweile pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT yvesjacob pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT martaverby pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT sedidebozturk pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT siyangli pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT atinagcote pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT robertomosca pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT jenniferjknapp pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT minjeongko pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT analynyu pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT marinellagebbia pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT nidhisahni pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT songyi pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT tanyatyagi pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT dayagsheykhkarimli pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT jonathanfroth pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT cassandrawong pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT louaimusa pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT jamiesnider pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT yichunliu pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT haiyuanyu pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT pascalbraun pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT igorstagljar pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT tonghao pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT michaelacalderwood pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT laurencepelletier pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT patrickaloy pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT davidehill pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT marcvidal pooledmatrixproteininteractionscreensusingbarcodefusiongenetics AT frederickproth pooledmatrixproteininteractionscreensusingbarcodefusiongenetics |