Genome rearrangements underlie different human diseases including many cancers. Determining the rates at which genome rearrangements arise and isolating unique, independent genome rearrangements is critical to understanding the genes and pathways that prevent or promote genome rearrangements. Here, we describe quantitative S. cerevisiae genetic assays for measuring the rates of accumulating genome rearrangements including deletions, translocations, and broken chromosomes healed by de novo telomere addition that result in the deletion of two counter-selectable genes, CAN1 and URA3, placed in the nonessential regions of the S. cerevisiae genome. The assays also allow for the isolation of individual genome rearrangements for structural studies, and a method for analyzing genome rearrangements by next-generation DNA sequencing is provided.
Genome instability Deletion Monocentric translocation Dicentric translocation De novo telomere addition Genetics GCR rates Whole-genome sequencing
This is a preview of subscription content, log in to check access.
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
This work was supported by NIH grant GM26017 and the Ludwig Institute for Cancer Research.
Myung K, Chen C, Kolodner RD (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411:1073–1076CrossRefPubMedGoogle Scholar
Pennaneach V, Kolodner RD (2004) Recombination and the Tel1 and Mec1 checkpoints differentially effect genome rearrangements driven by telomere dysfunction in yeast. Nat Genet 36:612–617CrossRefPubMedGoogle Scholar
Chen C, Umezu K, Kolodner RD (1998) Chromosomal rearrangements occur in S. cerevisiae rfa1 mutator mutants due to mutagenic lesions processed by double-strand-break repair. Mol Cell 2:9–22CrossRefPubMedGoogle Scholar
Pennaneach V, Kolodner RD (2009) Stabilization of dicentric translocations through secondary rearrangements mediated by multiple mechanisms in S. cerevisiae. PLoS One 4:e6389CrossRefPubMedPubMedCentralGoogle Scholar
Putnam CD, Pennaneach V, Kolodner RD (2004) Chromosome healing through terminal deletions generated by de novo telomere additions in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 101:13262–13267CrossRefPubMedPubMedCentralGoogle Scholar
Narayanan V, Mieczkowski PA, Kim HM, Petes TD, Lobachev KS (2006) The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell 125:1283–1296CrossRefPubMedGoogle Scholar
Kanellis P, Gagliardi M, Banath JP, Szilard RK, Nakada S, Galicia S et al (2007) A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet 3:e134CrossRefPubMedPubMedCentralGoogle Scholar
Koszul R, Caburet S, Dujon B, Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 23:234–243CrossRefPubMedGoogle Scholar
Umezu K, Hiraoka M, Mori M, Maki H (2002) Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae: retrotransposon Ty1 plays a crucial role in chromosomal rearrangements. Genetics 160:97–110PubMedPubMedCentralGoogle Scholar
Zhang Y, Saini N, Sheng Z, Lobachev KS (2013) Genome-wide screen reveals replication pathway for quasi-palindrome fragility dependent on homologous recombination. PLoS Genet 9:e1003979CrossRefPubMedPubMedCentralGoogle Scholar
Lemoine FJ, Degtyareva NP, Lobachev K, Petes TD (2005) Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. Cell 120:587–598CrossRefPubMedGoogle Scholar
Chan JE, Kolodner RD (2012) Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification. PLoS Genet 8:e1002539CrossRefPubMedPubMedCentralGoogle Scholar
Putnam CD, Pallis K, Hayes TK, Kolodner RD (2014) DNA repair pathway selection caused by defects in TEL1, SAE2, and de novo telomere addition generates specific chromosomal rearrangement signatures. PLoS Genet 10:e1004277CrossRefPubMedPubMedCentralGoogle Scholar
Serero A, Jubin C, Loeillet S, Legoix-Ne P, Nicolas AG (2014) Mutational landscape of yeast mutator strains. Proc Natl Acad Sci U S A 111:1897–1902Google Scholar
Lea DE, Coulson CA (1949) The distribution of the numbers of mutants in bacterial populations. J Genet 49:264–285CrossRefPubMedGoogle Scholar
Guan P, Sung WK (2016) Structural variation detection using next-generation sequencing data: a comparative technical review. Methods 102:36–49CrossRefPubMedGoogle Scholar
Putnam CD, Srivatsan A, Nene RV, Martinez SL, Clotfelter SP, Bell SN et al (2016) A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. Nat Commun 7:11256CrossRefPubMedPubMedCentralGoogle Scholar