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Journal articles
Maximizing binary interactome mapping with a minimal number of assays
Soon Choi
1
Julien Olivet
1, 2
Patricia Cassonnet
3, 4
Pierre-Olivier Vidalain
5
Katja Luck
1, 6
Luke Lambourne
1, 6
Kerstin Spirohn
1, 6
Irma Lemmens
7, 8
Mélanie Santos
3, 4
Caroline Demeret
3, 4
Louis Jones
9
Sudharshan Rangarajan
1, 6
Wenting Bian
1, 6
Eloi Coutant
10
Yves Janin
10
Sylvie van der Werf
3, 4
Philipp Trepte
11
Erich Wanker
11
Javier de las Rivas
12
Jan Tavernier
7, 8
Jean-Claude Twizere
2
Tong Hao
1, 6
David Hill
1, 6
Marc Vidal
1, 6
Michael Calderwood
1, 6
Yves Jacob
3, 1
Soon Gang Choi 1
Author
Julien Olivet 1, 2
Author
Patricia Cassonnet 3, 4
Author IdHAL : patricia-cassonnet
Pierre-Olivier Vidalain 5
Author IdHAL : pierre-olivier-vidalain ORCID : https://orcid.org/0000-0003-3082-7407
Katja Luck 1, 6
Author
Luke Lambourne 1, 6
Author
Kerstin Spirohn 1, 6
Author
Irma Lemmens 7, 8
Author
Mélanie Dos Santos 3, 4
Author
Caroline Demeret 3, 4
Author IdHAL : caroline-demeret ORCID : https://orcid.org/0000-0002-1103-6805
Louis Jones 9
Author
Sudharshan Rangarajan 1, 6
Author
Wenting Bian 1, 6
Author
Eloi P Coutant 10
Author
Yves Louis Janin 10
Author IdHAL : yvesljanin ResearcherId : http://www.researcherid.com/rid/N-5364-2014 ORCID : https://orcid.org/0000-0003-3019-9842
Sylvie van der Werf 3, 4
Author
Philipp Trepte 11
Author
Erich E Wanker 11
Author
Javier de las Rivas 12
Author
Jan Tavernier 7, 8
Author
Michael A Calderwood 1, 6
Author
Yves Jacob 3, 1
Author
1
Dana-Farber Cancer Institute [Boston] (450 Brookline Ave.
Boston, MA 02215 - United States)
2
Université de Liège (Place du 20-Août, 7 4000 Liège - Belgium)
3
GMV-ARN (UMR_3569 / U-Pasteur_2) - Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (Département de Virologie, 25-28 rue du docteur Roux, 75724 Paris cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- UPD7 - Université Paris Diderot - Paris 7 : U-Pasteur_2 (5 rue Thomas-Mann - 75205 Paris cedex 13 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR_3569 (France)
4
USPC - Université Sorbonne Paris Cité (Université Sorbonne Paris Cité | 100-104, avenue de France | 75013 Paris - France)
5
LCBPT - UMR 8601 - Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (45 Rue des Saints-Pères
75270 PARIS CEDEX 06 - France)
- UPD5 - Université Paris Descartes - Paris 5 : UMR 8601 (12, rue de l'École de Médecine - 75270 Paris cedex 06 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR 8601 (France)
6
HMS - Harvard Medical School [Boston] (25 Shattuck Street Boston, MA 02115 - United States)
7
VIB - Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (Falnders Institute for Biotechnology - Rijvisschestraat 120, 9052, Belgique - Belgium)
8
UGENT - Ghent University [Belgium] (St. Pietersnieuwstraat 33, 9000 Gent, - Belgium)
9
C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative (25-28 rue du docteur Roux, 75724 Paris cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : USR3756 (France)
10
Chimie et Biocatalyse (Département de Biologie structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris Cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : UMR3523 (France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
11
MDC - Max Delbrück Center for Molecular Medicine [Berlin] (Robert-Rössle-Straße 10, 13125 Berlin, Allemagne - Germany)
- Helmholtz-Gemeinschaft = Helmholtz Association (Anna-Louisa-Karsch-Straße 2, 10178 Berlin - Germany)
12
Universidad de Salamanca (37008 Salamanca. España - Spain)
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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Journal articles
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https://hal-pasteur.archives-ouvertes.fr/pasteur-02322138
Contributor : Yves Janin <>
Submitted on : Monday, October 21, 2019 - 3:35:24 PM
Last modification on : Monday, January 11, 2021 - 2:30:05 PM
Contributor : Yves Janin <>
Submitted on : Monday, October 21, 2019 - 3:35:24 PM
Last modification on : Monday, January 11, 2021 - 2:30:05 PM
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41467_2019_Article_11809.pdf
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Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-02322138, version 1
- PUBMED : 31467278
- DOI : 10.1038/s41467-019-11809-2
Collections
PASTEUR | CNRS | INC-CNRS | UNIV-PARIS5 | UNIV-PARIS7 | USPC | UNIV-PARIS | UP-SCIENCES
Citation
Soon Choi, Julien Olivet, Patricia Cassonnet, Pierre-Olivier Vidalain, Katja Luck, et al.. Maximizing binary interactome mapping with a minimal number of assays. Nature Communications, Nature Publishing Group, 2019, 10 (1), pp.3907. ⟨10.1038/s41467-019-11809-2⟩. ⟨pasteur-02322138⟩
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