Meiotic recombination is the hallmark of sexual reproduction, allowing parental genes to be mixed and shuffled for the next generation. However, homologous recombination events might be too dangerous in some regions of the genome. For instance, repetitive DNA sequences are prone to nonallelic homologous recombination. These events can result in copy number variations in the progeny as well as catastrophic genomic rearrangements that are associated with diseases and birth defects. To prevent such events, budding yeast Saccharomyces cerevisiae blocks the formation of meiotic double-strand breaks (DSBs) within the repetitive ribosomal DNA (rDNA) array, partly through formation of heterochromatin in a Sir2-dependent manner. The meiosis-specific AAA-ATPase Pch2 was also known to suppress recombination at the rDNA site, though its exact role was unclear. Now, Hochwagen and colleagues examine these issues in detail and find that the borders of the rDNA array are actually highly susceptible to meiotic DSBs and that yeast cells have a mechanism to specifically protect those regions. This border protection system uses Pch2 and the protein Orc1, a subunit of the origin recognition complex involved in initiation of DNA replication. Deficiencies of Pch2 or Orc1 led to higher rates of DSBs and nonallelic recombination at the rDNA borders, resulting in changes in the number of rDNA repeats in the progeny. Moreover, chromatin immunoprecipitation (ChIP) analyses revealed that Pch2 blocks the recruitment of DSB factors Rec114, Mer2 and Mre11 to the rDNA borders. The effects of the pch2 mutation could be largely suppressed by mutation of histone deacetylase Sir2, indicating that though Sir2 protects the bulk of the rDNA from meiotic DSBs, it induces their formation at the junction of heterochromatic and euchromatic regions. The reasons for this remain unknown, and, though heterochromatin marks vary between organisms, it will be interesting to see whether similar mechanisms operate in higher eukaryotes. (Nature doi:10.1038/nature10331, published online 7 August 2011)