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Protection of repetitive DNA borders from self-induced meiotic instability


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.

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Figure 1: Ribosomal-DNA-associated DSB formation and recombination.
Figure 2: Association of the meiotic DSB machinery near the rDNA.
Figure 3: Orc1 and Pch2 collaborate to suppress DSB formation.
Figure 4: Ribosomal-DNA chromatin promotes DSB formation.

Accession codes

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Gene Expression Omnibus

Data deposits

All data sets in this publication are available in the NCBI Gene Expression Omnibus (, accession number GSE30073.


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We thank S. P. Bell, A. Shinohara, N. Hunter, N. Hollingsworth and F. Klein for sharing reagents and data. We thank I. Cheeseman, M. Gehring and V. Subramanian for discussions and critical reading of the manuscript. This work was supported by NIH grant GM088248 to A.H. and by fellowships from the Netherlands Organisation for Scientific Research (NWO Rubicon-825.08.009 and NWO VENI-016.111.004) to G.V.; L.C. was supported by an HHMI Institutional Undergraduate Education Grant to MIT (grant 52005879).

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G.V., H.G.B. and A.H. designed and performed experiments and analysed the data. M.A.T. performed the yeast two-hybrid analysis. J.E.F., L.C. and A.H. performed recombination mapping. G.V., H.G.B. and A.H. wrote the paper.

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Correspondence to Andreas Hochwagen.

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The authors declare no competing financial interests.

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Vader, G., Blitzblau, H., Tame, M. et al. Protection of repetitive DNA borders from self-induced meiotic instability. Nature 477, 115–119 (2011).

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