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 ), 20kb distal toYCR048, with similar intensity as to the hotspot, despite the absence of DSBs in this region.
