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Cell Syst. 2016 Sep 28;3(3):264-277.e10. doi: 10.1016/j.cels.2016.08.008. Epub 2016 Sep 8.

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.

Author information

1
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.
2
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Sciences, University of Toronto, Toronto, ON M5S 3E1, Canada.
3
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada.
4
Department of Molecular Biology, NCCR Program "Frontiers in Genetics", Institute of Genetics, Genomics, Geneva (iGE3), University of Geneva, 30, quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
5
Laboratory of Computational Systems Biology, Ecole Polytéchnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
6
Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA.
7
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
8
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
9
Dipartimento di Bioscienze, Universita' degli Studi di Milano, 20122 Milano, Italy.
10
Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz 55128, Germany.
11
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address: charlie.boone@utoronto.ca.
12
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address: brenda.andrews@utoronto.ca.

Abstract

A significant challenge of functional genomics is to develop methods for genome-scale acquisition and analysis of cell biological data. Here, we present an integrated method that combines genome-wide genetic perturbation of Saccharomyces cerevisiae with high-content screening to facilitate the genetic description of sub-cellular structures and compartment morphology. As proof of principle, we used a Rad52-GFP marker to examine DNA damage foci in ∼20 million single cells from ∼5,000 different mutant backgrounds in the context of selected genetic or chemical perturbations. Phenotypes were classified using a machine learning-based automated image analysis pipeline. 345 mutants were identified that had elevated numbers of DNA damage foci, almost half of which were identified only in sensitized backgrounds. Subsequent analysis of Vid22, a protein implicated in the DNA damage response, revealed that it acts together with the Sgs1 helicase at sites of DNA damage and preferentially binds G-quadruplex regions of the genome. This approach is extensible to numerous other cell biological markers and experimental systems.

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