Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method

• Published in: Genome research Vol. 23; no. 2; pp. 300 - 311
• Main Authors: Makanae, Koji, Kintaka, Reiko, Makino, Takashi, Kitano, Hiroaki, Moriya, Hisao
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.02.2013
• Subjects: Gene Dosage; Gene Expression; Gene Regulatory Networks; Genes, Fungal; Genome, Fungal; Molecular Sequence Annotation; Open Reading Frames; Protein Interaction Maps; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.146662.112

Gene overexpression beyond a permissible limit causes defects in cellular functions. However, the permissible limits of most genes are unclear. Previously, we developed a genetic method designated genetic tug-of-war (gTOW) to measure the copy number limit of overexpression of a target gene. In the current study, we applied gTOW to the analysis of all protein-coding genes in the budding yeast Saccharomyces cerevisiae. We showed that the yeast cellular system was robust against an increase in the copy number by up to 100 copies in >80% of the genes. After frameshift and segmentation analyses, we isolated 115 dosage-sensitive genes (DSGs) with copy number limits of 10 or less. DSGs contained a significant number of genes involved in cytoskeletal organization and intracellular transport. DSGs tended to be highly expressed and to encode protein complex members. We demonstrated that the protein burden caused the dosage sensitivity of highly expressed genes using a gTOW experiment in which the open reading frame was replaced with GFP. Dosage sensitivities of some DSGs were rescued by the simultaneous increase in the copy numbers of partner genes, indicating that stoichiometric imbalances among complexes cause dosage sensitivity. The results obtained in this study will provide basic knowledge about the physiology of chromosomal abnormalities and the evolution of chromosomal composition.