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Novarina D, Rosas Bringas FR, Rosas Bringas OG, Chang M. High-throughput replica-pinning approach to screen for yeast genes controlling low-frequency events. STAR Protoc 2022; 3:101082. [PMID: 35059655 PMCID: PMC8760548 DOI: 10.1016/j.xpro.2021.101082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Saccharomyces cerevisiae is a leading model system for genome-wide screens, but low-frequency events (e.g., point mutations, recombination events) are difficult to detect with existing approaches. Here, we describe a high-throughput screening technique to detect low-frequency events using high-throughput replica pinning of high-density arrays of yeast colonies. This approach can be used to screen genes that control any process involving low-frequency events for which genetically selectable reporters are available, e.g., spontaneous mutations, recombination, and transcription errors. For complete details on the use and execution of this protocol, please refer to (Novarina et al., 2020a, 2020b).
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Affiliation(s)
- Daniele Novarina
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Fernando R. Rosas Bringas
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Omar G. Rosas Bringas
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
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Novarina D, Janssens GE, Bokern K, Schut T, Oerle NC, Kazemier HG, Veenhoff LM, Chang M. A genome-wide screen identifies genes that suppress the accumulation of spontaneous mutations in young and aged yeast cells. Aging Cell 2020; 19:e13084. [PMID: 31854076 PMCID: PMC6996960 DOI: 10.1111/acel.13084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/27/2019] [Accepted: 11/10/2019] [Indexed: 12/24/2022] Open
Abstract
To ensure proper transmission of genetic information, cells need to preserve and faithfully replicate their genome, and failure to do so leads to genome instability, a hallmark of both cancer and aging. Defects in genes involved in guarding genome stability cause several human progeroid syndromes, and an age-dependent accumulation of mutations has been observed in different organisms, from yeast to mammals. However, it is unclear whether the spontaneous mutation rate changes during aging and whether specific pathways are important for genome maintenance in old cells. We developed a high-throughput replica-pinning approach to screen for genes important to suppress the accumulation of spontaneous mutations during yeast replicative aging. We found 13 known mutation suppression genes, and 31 genes that had no previous link to spontaneous mutagenesis, and all acted independently of age. Importantly, we identified PEX19, encoding an evolutionarily conserved peroxisome biogenesis factor, as an age-specific mutation suppression gene. While wild-type and pex19Δ young cells have similar spontaneous mutation rates, aged cells lacking PEX19 display an elevated mutation rate. This finding suggests that functional peroxisomes may be important to preserve genome integrity specifically in old cells.
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Affiliation(s)
- Daniele Novarina
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Georges E. Janssens
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Koen Bokern
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Tim Schut
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Noor C. Oerle
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Hinke G. Kazemier
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Michael Chang
- European Research Institute for the Biology of Ageing University Medical Center Groningen University of Groningen Groningen The Netherlands
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Peter JJ, Watson TL, Walker ME, Gardner JM, Lang TA, Borneman A, Forgan A, Tran T, Jiranek V. Use of a wine yeast deletion collection reveals genes that influence fermentation performance under low-nitrogen conditions. FEMS Yeast Res 2018; 18:4841842. [DOI: 10.1093/femsyr/foy009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 02/05/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Josephine J Peter
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tommaso L Watson
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Jennifer M Gardner
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tom A Lang
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Angus Forgan
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tina Tran
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Australian Research Council Training Centre for Innovative Wine Production, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
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