Protection of repetitive DNA borders from self-induced meiotic instability

Abstract

Breakages in repetitive ribosomal DNA (rDNA) sequences can lead to rearrangements through non-allelic homologous recombination, a common source of genomic instability and human disease. Programmed breaks are an essential event in meiosis, however. Vader et al. have identified two proteins, Pch2 and Orc1, that protect the repetitive rDNA array from inappropriate breakages. Surprisingly, Sir2, which establishes the protective heterochromatin environment at rDNA, also makes the border between this heterochromatin and the neighbouring euchromatin susceptible to breaks. Such junctions are therefore at high risk for non-allelic homologous recombination in meiosis. DNA double strand breaks (DSBs) in repetitive sequences are a potent source of genomic instability, owing to the possibility of non-allelic homologous recombination (NAHR). Repetitive sequences are especially at risk during meiosis, when numerous programmed DSBs are introduced into the genome to initiate meiotic recombination1. In the repetitive ribosomal DNA (rDNA) array of the budding yeast Saccharomyces cerevisiae, meiotic DSB formation is prevented in part through Sir2-dependent heterochromatin formation2,3. Here we show that the edges of the rDNA array are exceptionally susceptible to meiotic DSBs, revealing an inherent heterogeneity in the rDNA array. We find that this localized DSB susceptibility necessitates a border-specific protection system consisting of the meiotic ATPase Pch2 and the origin recognition complex subunit Orc1. Upon disruption of these factors, DSB formation and recombination increased specifically in the outermost rDNA repeats, leading to NAHR and rDNA instability. Notably, the Sir2-dependent heterochromatin of the rDNA itself was responsible for the induction of DSBs at the rDNA borders in pch2Δ cells. Thus, although the activity of Sir2 globally prevents meiotic DSBs in the rDNA, it creates a highly permissive environment for DSB formation at the junctions between heterochromatin and euchromatin. Heterochromatinized repetitive DNA arrays are abundant in most eukaryotic genomes. Our data define the borders of such chromatin domains as distinct high-risk regions for meiotic NAHR, the protection of which may be a universal requirement to prevent meiotic genome rearrangements that are associated with genomic diseases and birth defects.