Analyzing Genome Rearrangements in Saccharomyces cerevisiae

  • Anjana Srivatsan
  • Christopher D. Putnam
  • Richard D. KolodnerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1672)


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.

Key words

Genome instability Deletion Monocentric translocation Dicentric translocation De novo telomere addition Genetics GCR rates Whole-genome sequencing 



This work was supported by NIH grant GM26017 and the Ludwig Institute for Cancer Research.


  1. 1.
    Chan JE, Kolodner RD (2011) A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements. PLoS Genet 7:e1002089CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Chen C, Kolodner RD (1999) Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants. Nat Genet 23:81–85CrossRefPubMedGoogle Scholar
  3. 3.
    Putnam CD, Hayes TK, Kolodner RD (2009) Specific pathways prevent duplication-mediated genome rearrangements. Nature 460:984–989CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Myung K, Chen C, Kolodner RD (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411:1073–1076CrossRefPubMedGoogle Scholar
  5. 5.
    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
  6. 6.
    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
  7. 7.
    Pennaneach V, Kolodner RD (2009) Stabilization of dicentric translocations through secondary rearrangements mediated by multiple mechanisms in S. cerevisiae. PLoS One 4:e6389CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    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
  9. 9.
    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
  10. 10.
    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
  11. 11.
    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
  12. 12.
    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
  13. 13.
    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
  14. 14.
    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
  15. 15.
    Chan JE, Kolodner RD (2012) Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification. PLoS Genet 8:e1002539CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    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
  17. 17.
    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
  18. 18.
    Lea DE, Coulson CA (1949) The distribution of the numbers of mutants in bacterial populations. J Genet 49:264–285CrossRefPubMedGoogle Scholar
  19. 19.
    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Guan P, Sung WK (2016) Structural variation detection using next-generation sequencing data: a comparative technical review. Methods 102:36–49CrossRefPubMedGoogle Scholar
  22. 22.
    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

Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Anjana Srivatsan
    • 1
  • Christopher D. Putnam
    • 1
    • 2
  • Richard D. Kolodner
    • 1
    • 3
    • 4
    • 5
    Email author
  1. 1.Ludwig Institute for Cancer ResearchUniversity of California School of Medicine, San DiegoLa JollaUSA
  2. 2.Department of MedicineUniversity of California School of Medicine, San DiegoLa JollaUSA
  3. 3.Department of Cellular and Molecular MedicineUniversity of California School of Medicine, San DiegoLa JollaUSA
  4. 4.Moores-UCSD Cancer CenterUniversity of California School of Medicine, San DiegoLa JollaUSA
  5. 5.Institute of Genomic MedicineUniversity of California School of Medicine, San DiegoLa JollaUSA

Personalised recommendations