Protection of repetitive DNA borders from self-induced meiotic instability

Abstract

DNA double strand breaks (DSBs) in repetitive sequences are a potent source of genomic instability, due 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 recombination 1. Within the budding yeast repetitive ribosomal (r)DNA array, meiotic DSB formation is prevented in part through Sir2-dependent heterochromatin 2,3. Here, we demonstrate that the edges of the rDNA array are exceptionally susceptible to meiotic DSBs, revealing an inherent heterogeneity within the rDNA array. We find that this localised 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 specifically increased in the outermost rDNA repeats, leading to NAHR and rDNA instability. Strikingly, the Sir2-dependent heterochromatin of the rDNA itself was responsible for the induction of DSBs at the rDNA borders in pch2Δ cells. Thus, while Sir2 activity globally prevents meiotic DSBs within the rDNA, it creates a highly permissive environment for DSB formation at the heterochromatin/euchromatin junctions. Heterochromatinised repetitive DNA arrays are abundantly present in most eukaryotic genomes. Our data define the borders of such chromatin domains as distinct high-risk regions for meiotic NAHR, whose protection may be a universal requirement to prevent meiotic genome rearrangements associated with genomic diseases and birth defects.

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

“…Pch2 is a conserved AAA+ ATPase that maintains the nonuniform pattern of Hop1 occupancy along meiotic chromosomes (Bö rner et al, 2008;Joshi et al, 2009). The different Hop1 occupancies seen in wild type were preserved early in meiosis in pch2D mutants ( Figure 4A, Figure 4-figure supplement 1A), consistent with previous findings that, in pch2 cells, Spo11-DSB patterns are not altered in most regions of the genome (Vader et al, 2011). By contrast, at later times (4-5 hr after initiation of meiosis), pch2D mutants displayed reduced Hop1 occupancy at HIS4, more closely approaching the lower occupancy levels seen throughout meiosis at URA3 ( Figure 4A; Figure 4-figure supplement 1A).…”

Great majority of recombination events in Arabidopsis are gene conversion events

“…The abundant gene conversions in Arabidopsis suggest that plants are more like mammals (7) than yeast, the latter having relatively common crossing-over compared with gene conversion (6). This difference between taxa we suggest may reflect differences in repeat content, as repetitive sequences are a source of genomic instability during meiosis (27), owing to nonallelic homologous recombination (28). Compared with COs, non-CO [e.g., via SDSA (2)], which yields the most gene conversions, poses the least genomic threat among mechanisms that repair DSBs (29).…”

Mechanism of siRNA production from repetitive DNA

“…Repetitive DNA is known to be a major source of genome instability in various organisms due to hyperrecombination events as a result of replication stress (Bzymek and Lovett 2001;Vader et al 2011). In Neurospora, the repetitive rDNA locus is a site of frequent chromosome breakage (Butler 1992), and we previously showed that the replication process is required for qiRNA production ).…”