Nature Communications (Apr 2023)
Next-generation large-scale binary protein interaction network for Drosophila melanogaster
- Hong-Wen Tang,
- Kerstin Spirohn,
- Yanhui Hu,
- Tong Hao,
- István A. Kovács,
- Yue Gao,
- Richard Binari,
- Donghui Yang-Zhou,
- Kenneth H. Wan,
- Joel S. Bader,
- Dawit Balcha,
- Wenting Bian,
- Benjamin W. Booth,
- Atina G. Coté,
- Steffi de Rouck,
- Alice Desbuleux,
- Kah Yong Goh,
- Dae-Kyum Kim,
- Jennifer J. Knapp,
- Wen Xing Lee,
- Irma Lemmens,
- Cathleen Li,
- Mian Li,
- Roujia Li,
- Hyobin Julianne Lim,
- Yifang Liu,
- Katja Luck,
- Dylan Markey,
- Carl Pollis,
- Sudharshan Rangarajan,
- Jonathan Rodiger,
- Sadie Schlabach,
- Yun Shen,
- Dayag Sheykhkarimli,
- Bridget TeeKing,
- Frederick P. Roth,
- Jan Tavernier,
- Michael A. Calderwood,
- David E. Hill,
- Susan E. Celniker,
- Marc Vidal,
- Norbert Perrimon,
- Stephanie E. Mohr
Affiliations
- Hong-Wen Tang
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Kerstin Spirohn
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Tong Hao
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- István A. Kovács
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
- Yue Gao
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Donghui Yang-Zhou
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Kenneth H. Wan
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory
- Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University
- Dawit Balcha
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Wenting Bian
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Benjamin W. Booth
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory
- Atina G. Coté
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
- Steffi de Rouck
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology
- Alice Desbuleux
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Kah Yong Goh
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School
- Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center
- Jennifer J. Knapp
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto
- Wen Xing Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School
- Irma Lemmens
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology
- Cathleen Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Mian Li
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Roujia Li
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
- Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center
- Yifang Liu
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Katja Luck
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Dylan Markey
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Carl Pollis
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Sudharshan Rangarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Sadie Schlabach
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Yun Shen
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Dayag Sheykhkarimli
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
- Bridget TeeKing
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Frederick P. Roth
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
- Jan Tavernier
- Cytokine Receptor Lab, VIB Center for Medical Biotechnology
- Michael A. Calderwood
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- David E. Hill
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Susan E. Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory
- Marc Vidal
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School
- DOI
- https://doi.org/10.1038/s41467-023-37876-0
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 16
Abstract
Abstract Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
