Genome architecture and stability in the Saccharomyces cerevisiae knockout collection

Fabio Puddu (), Mareike Herzog, Alexandra Selivanova, Siyue Wang, Jin Zhu, Shir Klein-Lavi, Molly Gordon, Roi Meirman, Gonzalo Millan-Zambrano, Iñigo Ayestaran, Israel Salguero, Roded Sharan, Rong Li, Martin Kupiec and Stephen P. Jackson ()
Additional contact information
Fabio Puddu: University of Cambridge
Mareike Herzog: University of Cambridge
Alexandra Selivanova: University of Cambridge
Siyue Wang: University of Cambridge
Jin Zhu: Johns Hopkins University School of Medicine
Shir Klein-Lavi: Tel Aviv University
Molly Gordon: Johns Hopkins University School of Medicine
Roi Meirman: Tel Aviv University
Gonzalo Millan-Zambrano: University of Cambridge
Iñigo Ayestaran: University of Cambridge
Israel Salguero: University of Cambridge
Roded Sharan: Tel Aviv University
Rong Li: Johns Hopkins University School of Medicine
Martin Kupiec: Tel Aviv University
Stephen P. Jackson: University of Cambridge

Nature, 2019, vol. 573, issue 7774, 416-420

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41586-019-1549-9

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