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Nature. 2019 Sep;573(7774):416-420. doi: 10.1038/s41586-019-1549-9. Epub 2019 Sep 11.

Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.

Author information

1
The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK. f.puddu@gurdon.cam.ac.uk.
2
Department of Biochemistry, University of Cambridge, Cambridge, UK. f.puddu@gurdon.cam.ac.uk.
3
Wellcome Sanger Institute, Hinxton, UK. f.puddu@gurdon.cam.ac.uk.
4
The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
5
Department of Biochemistry, University of Cambridge, Cambridge, UK.
6
Wellcome Sanger Institute, Hinxton, UK.
7
Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
8
School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.
9
Department of Pathology, University of Cambridge, Cambridge, UK.
10
School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
11
The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK. s.jackson@gurdon.cam.ac.uk.
12
Department of Biochemistry, University of Cambridge, Cambridge, UK. s.jackson@gurdon.cam.ac.uk.

Abstract

Despite major progress in defining the functional roles of genes, a complete understanding of their influences is far from being realized, even in relatively simple organisms. A major milestone in this direction arose via the completion of the yeast Saccharomyces cerevisiae gene-knockout collection (YKOC), which has enabled high-throughput reverse genetics, phenotypic screenings and analyses of synthetic-genetic interactions1-3. Ensuing experimental work has also highlighted some inconsistencies and mistakes in the YKOC, or genome instability events that rebalance the effects of specific knockouts4-6, but a complete overview of these is lacking. The identification and analysis of genes that are required for maintaining genomic stability have traditionally relied on reporter assays and on the study of deletions of individual genes, but whole-genome-sequencing technologies now enable-in principle-the direct observation of genome instability globally and at scale. To exploit this opportunity, we sequenced the whole genomes of nearly all of the 4,732 strains comprising the homozygous diploid YKOC. Here, by extracting information on copy-number variation of tandem and interspersed repetitive DNA elements, we describe-for almost every single non-essential gene-the genomic alterations that are induced by its loss. Analysis of this dataset reveals genes that affect the maintenance of various genomic elements, highlights cross-talks between nuclear and mitochondrial genome stability, and shows how strains have genetically adapted to life in the absence of individual non-essential genes.

PMID:
31511699
PMCID:
PMC6774800
[Available on 2020-03-11]
DOI:
10.1038/s41586-019-1549-9

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