Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress
| Autor: | Stephane Flibotte, Jennifer Chiang, Guri Giaever, Patrick Flaherty, Mauricio Neira, Pei Jun Zhao, Amy S. Lee, Erica Acton, Corey Nislow, Sunita Sinha |
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| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
prototrophy Genotype Auxotrophy Immunology Saccharomyces cerevisiae Biology General Biochemistry Genetics and Molecular Biology Plasmid maintenance 03 medical and health sciences Gene Knockout Techniques Stress Physiological gene–environment correlation lcsh:QH301-705.5 yeast deletion collection Genetics genome-wide fitness assay General Neuroscience Strain (biology) Research Gene Annotation Phenotype 030104 developmental biology lcsh:Biology (General) Backcrossing Functional genomics functional genomics Research Article Genome-Wide Association Study |
| Zdroj: | Open Biology Open Biology, Vol 7, Iss 6 (2017) |
| ISSN: | 2046-2441 |
| Popis: | The Yeast Knockout (YKO) collection has provided a wealth of functional annotations from genome-wide screens. An unintended consequence is that 76% of gene annotations derive from one genotype. The nutritional auxotrophies in the YKO, in particular, have phenotypic consequences. To address this issue, ‘prototrophic’ versions of the YKO collection have been constructed, either by introducing a plasmid carrying wild-type copies of the auxotrophic markers (Plasmid-Borne, PB prot ) or by backcrossing (Backcrossed, BC prot ) to a wild-type strain. To systematically assess the impact of the auxotrophies, genome-wide fitness profiles of prototrophic and auxotrophic collections were compared across diverse drug and environmental conditions in 250 experiments. Our quantitative profiles uncovered broad impacts of genotype on phenotype for three deletion collections, and revealed genotypic and strain-construction-specific phenotypes. The PB prot collection exhibited fitness defects associated with plasmid maintenance, while BC prot fitness profiles were compromised due to strain loss from nutrient selection steps during strain construction. The repaired prototrophic versions of the YKO collection did not restore wild-type behaviour nor did they clarify gaps in gene annotation resulting from the auxotrophic background. To remove marker bias and expand the experimental scope of deletion libraries, construction of a bona fide prototrophic collection from a wild-type strain will be required. |
| Databáze: | OpenAIRE |
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