Mapping of Crossover Sites Using DNA Microarrays

  • Stacy Y. Chen
  • Jennifer C. FungEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 745)


Crossovers (COs) play an essential role in promoting successful chromosome segregation during meiosis. Crossing over generates chiasmata, which are physical bridges between homologs that provide the appropriate tension to properly align chromosomes on the meiosis I spindle. Homolog pairs that fail to cross over can result in meiosis I nondisjunction, leading to aneuploid gametes. Therefore, the number and distribution of crossovers are tightly regulated to ensure that each chromosome pair receives at least one CO. Here, we describe a DNA microarray-based method to map CO distribution genome-wide, on a cell-by-cell basis, allowing for rapid and accurate analysis of multiple aspects of CO control.

Key words

Meiosis, recombination crossover noncrossover direct allelic scanning crossover interference crossover homeostasis S96 YJM789 



We thank Carol Anderson for optimizing an alternative yeast inoculation method for genomic DNA extraction. We thank Ashwini Oke for her assistance in performing the DNase I digestion for this publication. We also thank Mike Pollard for critical reading of the manuscript. S.Y.C. is supported by a Genentech Fellowship. J.C.F. is supported by the American Cancer Society Research Scholar Award (RSG CCG 110688).


  1. 1.
    Roeder, G.S. (1997) Meiotic chromosomes: it takes two to tango. Genes Dev 11, 2600–2621.PubMedCrossRefGoogle Scholar
  2. 2.
    Zickler, D., and Kleckner, N. (1999) Meiotic chromosomes: integrating structure and function. Annu Rev Genet 33, 603–754.PubMedCrossRefGoogle Scholar
  3. 3.
    Whitby, M.C. (2005) Making crossovers during meiosis. Biochem Soc Trans 33, 1451–1455.PubMedCrossRefGoogle Scholar
  4. 4.
    Hassold, T. (2007) The origin of human aneuploidy: where we have been, where we are going. Hum Mol Genet 16, 203–208.CrossRefGoogle Scholar
  5. 5.
    Hillers, K.J. (2004) Crossover interference. Curr Biol 14, R1036–R1037.PubMedCrossRefGoogle Scholar
  6. 6.
    Jones, G.H. (1984) The control of chiasma distribution. Symp Soc Exp Biol 38, 293–320.PubMedGoogle Scholar
  7. 7.
    Muller, H. (1916) The mechanism of crossing over. Am Nat 50, 193–434.CrossRefGoogle Scholar
  8. 8.
    Martini, E., Diaz, R.L., Hunter, N., and Keeney, S. (2006) Crossover homeostasis in yeast meiosis. Cell 126, 285–295.PubMedCrossRefGoogle Scholar
  9. 9.
    Winzeler, E.A., Richards, D.R., Conway, A.R., Goldstein, A.L., Kalman, S., McCullough, M.J., McCusker, J.H., Stevens, D.A., Wodicka, L., Lockhart, D.J., and Davis, R.W. (1998) Direct allelic variation scanning of the yeast genome. Science 281, 1194–1197.PubMedCrossRefGoogle Scholar
  10. 10.
    Chen, S.Y., Tsubouchi, T., Rockmill, B., Sandler, J.S., Richards, D.R., Vader, G., Hochwagen, A., Roeder, G.S., and Fung, J.C. (2008) Global analysis of the meiotic crossover landscape. Dev Cell 15, 401–415.PubMedCrossRefGoogle Scholar
  11. 11.
    McPeek, M.S., and Speed, T.P. (1995) Modeling interference in genetic recombination. Genetics 139, 1031–1044.PubMedGoogle Scholar
  12. 12.
    Zhao, H., Speed, T.P., and McPeek, M.S. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics 139, 1045–1056.PubMedGoogle Scholar
  13. 13.
    Affymetrix. (2005) GeneChip expression analysis technical manual with specific protocols for using the GeneChip hybridization, wash, and stain kit.Google Scholar
  14. 14.
    Richards, D. (2004) Allelescan users manual.
  15. 15.
    Okimoto, R., and Dodgson, J.B. (1996) Improved PCR amplification of multiple specific alleles (PAMSA) using internally mismatched primers. Biotechniques 21, 20–22, 24, 26.PubMedGoogle Scholar
  16. 16.
    Qiagen. (2001) Qiagen Genomic DNA handbook.Google Scholar
  17. 17.
  18. 18.
    Mancera, E., Bourgon, R., Brozzi, A., Huber, W., and Steinmetz, L.M. (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454, 479–485.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan FranciscoUSA

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