Meiosis pp 267-283 | Cite as

Analysis of Protein–DNA Interactions During Meiosis by Quantitative Chromatin Immunoprecipitation (qChIP)

Part of the Methods in Molecular Biology book series (MIMB, volume 557)


During meiotic prophase a number of important events require recombination between maternal and paternal chromosomes, which is initiated through the introduction of DNA double-strand breaks (DSBs). The majority of DSBs, which mostly occur at so-called hotspots, have been located between cohesin binding sites. qChIP (chromatin immunoprecipitation quantified by real-time PCR) is a sensitive, accurate, and cost-efficient alternative to ChIP-on-Chip for the analysis of noncovalent protein–DNA interactions at defined binding sites in vivo. Here we use qChIP to study Mre11 binding to three chromosomal loci during meiosis. We show that Mre11 interacts with a known hotspot region (YCR048) in the R-band of chromosome III, but not with a cold region in the G-band (YCR011). Interestingly Mre11 binds to a cohesin binding site (YCR067 ), 20 kb distal to YCR048, with similar intensity as to the hotspot, despite the absence of DSBs in this region.

Key words

ChIP qChIP real-time PCR qPCR DNA binding Mre11 meiotic recombination double-strand break repair 



We thank Marie Therese Hauser, Kim Nasmyth, and Katsuhiko Shirahige for helping us to set up, or improve parts of the technique and former lab member Silvia Prieler for tagging Mre11. This work was supported by FWF grant P18847 to F.K.


  1. 1.
    Tanaka, T., Knapp, D., and Nasmyth, K. (1997) Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell 90, 649–660.PubMedCrossRefGoogle Scholar
  2. 2.
    Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K., and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424, 1078–1083.PubMedCrossRefGoogle Scholar
  3. 3.
    Prieler, S., Penkner, A., Borde, V., and Klein, F. (2005) The control of Spo11’s interaction with meiotic recombination hotspots. Genes Dev. 19, 255–269.PubMedCrossRefGoogle Scholar
  4. 4.
    Katou, Y., Kaneshiro, K., Aburatani, H., and Shirahige, K. (2006) Genomic approach for the understanding of dynamic aspect of chromosome behavior. Methods Enzymol. 409, 389–410.PubMedCrossRefGoogle Scholar
  5. 5.
    Nairz, K. and Klein, F. (1997) mre11S - a yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis. Genes Dev. 11, 2272–2290.PubMedCrossRefGoogle Scholar
  6. 6.
    Borde, V., Lin, W., Novikov, E., Petrini, J. H., Lichten, M., and Nicolas, A. (2004) Association of Mre11p with double-strand break sites during yeast meiosis. Mol. Cell 13, 389–401.PubMedCrossRefGoogle Scholar
  7. 7.
    Baudat, F. and Nicolas, A. (1997) Clustering of meiotic double-strand breaks on yeast chromosome III. Proc. Natl. Acad. Sci. U. S. A. 94, 5213–5218.PubMedCrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Max F. Perutz Laboratories of the University of ViennaAustria

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