Puddu F~Jackson SP, 2019

Pubmed ID 31511699
Title Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.
Authors Fabio Puddu, Mareike Herzog, Alexandra Selivanova, Siyue Wang, Jin Zhu, Shir Klein-Lavi, Molly Gordon, Roi Meirman, Gonzalo Millan-Zambrano, I├▒igo Ayestaran, Israel Salguero, Roded Sharan, Rong Li, Martin Kupiec, Stephen P Jackson
Abstract 4-6, 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.
Citation Nature 2019; 573:416-420

Datasets

Download the list of datasets
Paper Phenotype Condition Medium Collection Tested mutants Data Details
Puddu F~Jackson SP, 2019 rDNA copy number standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 genome instability (CUP1 copy number) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 mtDNA copy number standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 2micron copy number standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 transposable element copy number (Ty1) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 transposable element copy number (Ty2) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 transposable element copy number (Ty3) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 transposable element copy number (Ty4) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 transposable element copy number (Ty5) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 telomere length standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 1) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 2) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 3) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 4) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 5) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 6) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 7) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 8) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 9) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 10) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 11) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 12) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 13) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 14) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 15) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 chromosome ploidy (chromosome 16) standard hom 4,395 Quantitative
Puddu F~Jackson SP, 2019 genome instability (number of subchromosomal deletions/amplifications) standard hom 4,395 Quantitative

Curation history

Data

Nov. 8, 2019 Ready to load.
Nov. 27, 2019 Loaded.

Tested strains

Nov. 8, 2019 Ready to load.
Nov. 27, 2019 Loaded.