Letter | Published:

Protection of repetitive DNA borders from self-induced meiotic instability

Nature volume 477, pages 115119 (01 September 2011) | Download Citation

Abstract

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

All data sets in this publication are available in the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), accession number GSE30073.

References

  1. 1.

    , & Genome destabilization by homologous recombination in the germ line. Nature Rev. Mol. Cell Biol. 11, 182–195 (2010)

  2. 2.

    & A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56, 771–776 (1989)

  3. 3.

    et al. Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 104, 3955–3960 (2007)

  4. 4.

    & Pch2 links chromatin silencing to meiotic checkpoint control. Cell 97, 313–324 (1999)

  5. 5.

    & Two distinct surveillance mechanisms monitor meiotic chromosome metabolism in budding yeast. Curr. Biol. 16, 2473–2479 (2006)

  6. 6.

    et al. Mapping of meiotic single-stranded DNA reveals double-stranded-break hotspots near centromeres and telomeres. Curr. Biol. 17, 2003–2012 (2007)

  7. 7.

    et al. Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 97, 11383–11390 (2000)

  8. 8.

    Meiotic recombination hot spots and cold spots. Nature Rev. Genet. 2, 360–369 (2001)

  9. 9.

    Mechanism and control of meiotic recombination initiation. Curr. Top. Dev. Biol. 52, 1–53 (2001)

  10. 10.

    et al. A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 16, 2755–2760 (2002)

  11. 11.

    , , & Antiviral protein Ski8 is a direct partner of Spo11 in meiotic DNA break formation, independent of its cytoplasmic role in RNA metabolism. Mol. Cell 13, 549–559 (2004)

  12. 12.

    & Initiation of meiotic recombination by formation of DNA double-strand breaks: mechanism and regulation. Biochem. Soc. Trans. 34, 523–525 (2006)

  13. 13.

    , & Yeast Pch2 promotes domainal axis organization, timely recombination progression, and arrest of defective recombinosomes during meiosis. Proc. Natl Acad. Sci. USA 105, 3327–3332 (2008)

  14. 14.

    et al. Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. EMBO J. 28, 99–111 (2009)

  15. 15.

    The origin recognition complex: from simple origins to complex functions. Genes Dev. 16, 659–672 (2002)

  16. 16.

    , & Cell cycle execution point analysis of ORC function and characterization of the checkpoint response to ORC inactivation in Saccharomyces cerevisiae. Genes Cells 11, 557–573 (2006)

  17. 17.

    et al. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 83, 563–568 (1995)

  18. 18.

    & AAA+ proteins: have engine, will work. Nature Rev. Mol. Cell Biol. 6, 519–529 (2005)

  19. 19.

    , , & Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403, 795–800 (2000)

  20. 20.

    & Chromosome segregation: taking the passenger seat. Curr. Biol. 20, R879–R881 (2010)

  21. 21.

    Common themes in mechanisms of gene silencing. Mol. Cell 8, 489–498 (2001)

  22. 22.

    et al. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. PLoS Genet. 6, e1001228 (2010)

  23. 23.

    , & Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997)

  24. 24.

    et al. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 83, 563–568 (1995)

  25. 25.

    Strategies to maintain the stability of the ribosomal RNA gene repeats—collaboration of recombination, cohesion, and condensation. Genes Genet. Syst. 81, 155–161 (2006)

  26. 26.

    , & Mutations in eukaryotic 18S ribosomal RNA affect translational fidelity and resistance to aminoglycoside antibiotics. EMBO J. 13, 906–913 (1994)

  27. 27.

    et al. Close, stable homolog juxtaposition during meiosis in budding yeast is dependent on meiotic recombination, occurs independently of synapsis, and is distinct from DSB-independent pairing contacts. Genes Dev. 16, 1682–1695 (2002)

  28. 28.

    , & Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144, 1425–1436 (1996)

  29. 29.

    et al. Mapping of meiotic single-stranded DNA reveals double-stranded-break hotspots near centromeres and telomeres. Curr. Biol. 17, 2003 (2007)

  30. 30.

    & Genome-wide detection of meiotic DNA double-strand break hotspots using single-stranded DNA. Methods Mol. Biol. 745, 47–63 (2011)

  31. 31.

    , & Meiotic chromosome synapsis in a haploid yeast. Chromosoma 100, 221–228 (1991)

  32. 32.

    & The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination. Cell 106, 59–70 (2001)

Download references

Acknowledgements

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).

Author information

Author notes

    • Gerben Vader
    •  & Hannah G. Blitzblau

    These authors contributed equally to this work.

    • Jill E. Falk
    •  & Andreas Hochwagen

    Present addresses: David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA (J.E.F.) ; Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA (A.H.).

Affiliations

  1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA

    • Gerben Vader
    • , Hannah G. Blitzblau
    • , Mihoko A. Tame
    • , Jill E. Falk
    • , Lisa Curtin
    •  & Andreas Hochwagen
  2. Somerville High School, Somerville, Massachusetts 02143, USA

    • Lisa Curtin

Authors

  1. Search for Gerben Vader in:

  2. Search for Hannah G. Blitzblau in:

  3. Search for Mihoko A. Tame in:

  4. Search for Jill E. Falk in:

  5. Search for Lisa Curtin in:

  6. Search for Andreas Hochwagen in:

Contributions

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Andreas Hochwagen.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figures 1-5 with legends, Supplementary Tables 1-3 and additional references.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature10331

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.