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Nat Commun. 2019 Aug 29;10(1):3907. doi: 10.1038/s41467-019-11809-2.

Maximizing binary interactome mapping with a minimal number of assays.

Author information

1
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA.
2
Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
3
Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
4
Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, Groupe Interdisciplinaire de Génomique Appliquée (GIGA Institute), University of Liège, 7 Place du 20 Août, 4000, Liège, Belgium.
5
Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France.
6
Équipe Chimie, Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), UMR8601, CNRS, Université Paris Descartes, 45 rue des Saints-Pères, 75006, Paris, France.
7
Center for Medical Biotechnology, Vlaams Instituut voor Biotechnologie (VIB), 3 Albert Baertsoenkaai, 9000, Ghent, Belgium.
8
Cytokine Receptor Laboratory (CRL), Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 3 Albert Baertsoenkaai, 9000, Ghent, Belgium.
9
Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, 28 rue du Docteur Roux, 75015, Paris, France.
10
Département de Biologie Structurale et Chimie, Unité de Chimie et Biocatalyse, Institut Pasteur, UMR3523, CNRS, 28 rue du Docteur Roux, 75015, Paris, France.
11
Neuroproteomics, Max Delbrück Center for Molecular Medicine, 10 Robert-Rössle-Str., 13125, Berlin, Germany.
12
Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 3 Dr. Bohr-Gasse, 1030, Vienna, Austria.
13
Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), Campus Miguel de Unamuno, 37007, Salamanca, Spain.
14
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. marc_vidal@dfci.harvard.edu.
15
Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. marc_vidal@dfci.harvard.edu.
16
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. michael_calderwood@dfci.harvard.edu.
17
Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. michael_calderwood@dfci.harvard.edu.
18
Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA. michael_calderwood@dfci.harvard.edu.
19
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), 450 Brookline Avenue, Boston, MA, 02215, USA. yves.jacob@pasteur.fr.
20
Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot, Sorbonne Paris Cité, 28 rue du Docteur Roux, 75015, Paris, France. yves.jacob@pasteur.fr.

Abstract

Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose a framework for binary protein-protein interaction (PPI) mapping based on optimally combining assays and/or assay versions to maximize detection of true positive interactions, while avoiding detection of random protein pairs. We have engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions, differing by protein expression systems and tagging configurations. The resulting union of N2H versions recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our findings should be applicable to systematic mapping of other biological landscapes.

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