Meiosis pp 55-63 | Cite as

Measurement of Spatial Proximity and Accessibility of Chromosomal Loci in Saccharomyces cerevisiae Using Cre /loxP Site-Specific Recombination

  • Doris Lui
  • Sean M. Burgess
Part of the Methods in Molecular Biology book series (MIMB, volume 557)


Several methods have been developed to measure interactions between homologous chromosomes during meiosis in budding yeast. These include cytological analysis of fixed, spread nuclei using fluorescence in situ hybridization (FISH) (1, 2), visualization of GFP-labeled chromosomal loci in living cells (3), and Chromosome-Conformation Capture (3C) (4). Here we describe a quantitative genetic assay that uses exogenous site-specific recombination to monitor the level of homolog associations between two defined loci in living cells of budding yeast (5). We have used the Cre/loxP assay to genetically dissect nuclear architecture and meiotic homolog pairing in budding yeast. Data obtained from this assay report on the relative spatial proximity or accessibility of two chromosomal loci located within the same strain and can be compared to measurements from different mutated strains.

Key words

budding yeast meiosis homolog pairing chromosome collision assay site-specific recombination Cre/loxP 



The authors would like to give a special thanks to Tamara Peoples-Holst, Eric Dean, and Joshua Chang Mell for their contribution to the optimization of this protocol over the years. This work has been supported by the National Institutes of Health (NIH) grant NIH R01 GM075119 (S.M.B), the American Cancer Society RSG-01-053-01-CCG (S.M.B), and the NIH-Environmental Health Sciences training grant NIH T 32 ES07059 (D.Y.L).


  1. 1.
    Weiner, B. M., and Kleckner, N. (1994) Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell 77, 977–991.PubMedCrossRefGoogle Scholar
  2. 2.
    Loidl, J., Scherthan, H., and Kaback, D. B. (1994) Physical association between nonhomologous chromosomes precedes distributive disjunction in yeast. Proc. Natl. Acad. Sci. USA 91, 331–334.PubMedCrossRefGoogle Scholar
  3. 3.
    Aragon-Alcaide, L., and Strunnikov, A. V. (2000) Functional dissection of in vivo interchromosome association in Saccharomyces cerevisiae. Nat. Cell Biol. 2, 812–818.PubMedCrossRefGoogle Scholar
  4. 4.
    Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002) Capturing chromosome conformation. Science 295, 1306–1311.PubMedCrossRefGoogle Scholar
  5. 5.
    Burgess, S. M., and Kleckner, N. (1999) Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. Genes & Dev. 13, 1871–1883.CrossRefGoogle Scholar
  6. 6.
    Peoples, T. L., Dean, E., Gonzalez, O., Lambourne, L., and Burgess, S. M. (2002) Close, stable homolog juxtaposition during meiosis in budding yeast is dependent on meiotic recombination, occurs independently of synapsis, and is distinct from DSB-independent pairing contacts. Genes & Dev. 16, 1682–1695.CrossRefGoogle Scholar
  7. 7.
    Peoples-Holst, T. L., and Burgess, S. M. (2005) Multiple branches of the meiotic recombination pathway contribute independently to homolog pairing and stable juxtaposition during meiosis in budding yeast. Genes & Dev. 19, 863–874.CrossRefGoogle Scholar
  8. 8.
    Lui, D. Y., Peoples-Holst, T. L., Mell, J. C., Wu, H. Y., Dean, E. W., and Burgess, S. M. (2006) Analysis of close stable homolog juxtaposition during meiosis in mutants of Saccharomyces cerevisiae. Genetics 173, 1207–1222.PubMedCrossRefGoogle Scholar
  9. 9.
    Xu, L., Ajimura, M., Padmore, R., Klein, C., and Kleckner, N. (1995) NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae. Mol. Cell. Biol. 15, 6572–6581.PubMedGoogle Scholar
  10. 10.
    Allers, T., and Lichten, M. (2001) Differential timing and control of noncrossover and crossover recombination during meiosis. Cell 106, 47–57.PubMedCrossRefGoogle Scholar
  11. 11.
    Sherman, F., and Roman, H. (1963) Evidence for two types of allelic recombination in yeast. Genetics 48, 255–261.PubMedGoogle Scholar
  12. 12.
    Esposito, R. E., and Esposito, M. S. (1974) Genetic recombination and commitment to meiosis in Saccharomyces. Proc. Natl. Acad. Sci. USA 71, 3172–3176.PubMedCrossRefGoogle Scholar
  13. 13.
    Zenvirth, D., Loidl, J., Klein, S., Arbel, A., Shemesh, R., and Simchen, G. (1997) Switching yeast from meiosis to mitosis: double-strand break repair, recombination and synaptonemal complex. Genes Cells 2, 487–498.PubMedCrossRefGoogle Scholar
  14. 14.
    Mell, J. C., Komachi, K., Hughes, O., and Burgess, S. (2008) Cooperative interactions between pairs of homologous chromatids during meiosis in Saccharomyces cerevisiae. Genetics 179, 1125–1127.Google Scholar
  15. 15.
    Kane, S. M., and Roth, R. (1974) Carbohydrate metabolism during ascospore development in yeast. J. Bacteriol. 118, 8–14.PubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Doris Lui
    • 1
  • Sean M. Burgess
    • 1
  1. 1.Section of Molecular and Cellular BiologyCollege of Biological Sciences, University of CaliforniaDavisUSA

Personalised recommendations