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Recombination-restarted replication makes inverted chromosome fusions at inverted repeats


Impediments to DNA replication are known to induce gross chromosomal rearrangements (GCRs) and copy-number variations (CNVs). GCRs and CNVs underlie human genomic disorders1 and are a feature of cancer2. During cancer development, environmental factors and oncogene-driven proliferation promote replication stress. Resulting GCRs and CNVs are proposed to contribute to cancer development and therapy resistance3. When stress arrests replication, the replisome remains associated with the fork DNA (stalled fork) and is protected by the inter-S-phase checkpoint. Stalled forks efficiently resume when the stress is relieved. However, if the polymerases dissociate from the fork (fork collapse) or the fork structure breaks (broken fork), replication restart can proceed either by homologous recombination or microhomology-primed re-initiation4,5. Here we ascertain the consequences of replication with a fork restarted by homologous recombination in fission yeast. We identify a new mechanism of chromosomal rearrangement through the observation that recombination-restarted forks have a considerably high propensity to execute a U-turn at small inverted repeats (up to 1 in 40 replication events). We propose that the error-prone nature of restarted forks contributes to the generation of GCRs and gene amplification in cancer, and to non-recurrent CNVs in genomic disorders.

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Figure 1: Alternative mechanism for inverted chromosomal fusion.
Figure 2: Rearrangement frequency is dependent on the repeat size and interrupting-sequence size.
Figure 3: Fidelity of HR-restarted fork improves with distance.
Figure 4: U-turn at palindrome centre is chief mechanism for inverted fusion in double- RTS1 constructs.


  1. 1

    Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14, 417–422 (1998)

    CAS  Article  Google Scholar 

  2. 2

    Liu, P., Carvalho, C. M., Hastings, P. & Lupski, J. R. Mechanisms for recurrent and complex human genomic rearrangements. Curr. Opin. Genet. Dev. 22, 211–220 (2012)

    CAS  Article  Google Scholar 

  3. 3

    Mondello, C., Smirnova, A. & Giulotto, E. Gene amplification, radiation sensitivity and DNA double-strand breaks. Mutat. Res. 704, 29–37 (2010)

    CAS  Article  Google Scholar 

  4. 4

    Lee, J. A., Carvalho, C. M. & Lupski, J. R. A. DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235–1247 (2007)

    CAS  Article  Google Scholar 

  5. 5

    Hastings, P. J., Ira, G. & Lupski, J. R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 5, e1000327 (2009)

    CAS  Article  Google Scholar 

  6. 6

    Petermann, E. & Helleday, T. Pathways of mammalian replication fork restart. Nature Rev. Mol. Cell Biol. 11, 683–687 (2010)

    CAS  Article  Google Scholar 

  7. 7

    Blow, J. J., Ge, X. Q. & Jackson, D. A. How dormant origins promote complete genome replication. Trends Biochem. Sci. 36, 405–414 (2011)

    CAS  Article  Google Scholar 

  8. 8

    Letessier, A. et al. Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature 470, 120–123 (2011)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Ozeri-Galai, E. et al. Failure of origin activation in response to fork stalling leads to chromosomal instability at fragile sites. Mol. Cell 43, 122–131 (2011)

    CAS  Article  Google Scholar 

  10. 10

    Murray, J. M. & Carr, A. M. Smc5/6: a link between DNA repair and unidirectional replication? Nature Rev. Mol. Cell Biol. 9, 177–182 (2008)

    CAS  Article  Google Scholar 

  11. 11

    Lambert, S., Watson, A., Sheedy, D. M., Martin, B. & Carr, A. M. Gross chromosomal rearrangements and elevated recombination at an inducible site-specific replication fork barrier. Cell 121, 689–702 (2005)

    CAS  Article  Google Scholar 

  12. 12

    Mizuno, K., Lambert, S., Baldacci, G., Murray, J. M. & Carr, A. M. Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism. Genes Dev. 23, 2876–2886 (2009)

    CAS  Article  Google Scholar 

  13. 13

    Lambert, S. et al. Homologous recombination restarts blocked replication forks at the expense of genome rearrangements by template exchange. Mol. Cell 39, 346–359 (2010)

    CAS  Article  Google Scholar 

  14. 14

    Sánchez-Gorostiaga, A., Lopez-Estrano, C., Krimer, D. B., Schvartzman, J. B. & Hernandez, P. Transcription termination factor reb1p causes two replication fork barriers at its cognate sites in fission yeast ribosomal DNA in vivo. Mol. Cell. Biol. 24, 398–406 (2004)

    Article  Google Scholar 

  15. 15

    Krings, G. & Bastia, D. swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe. Proc. Natl Acad. Sci. USA 101, 14085–14090 (2004)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Williams, W. L. & Muller, U. R. Effects of palindrome size and sequence on genetic stability in the bacteriophage ϕX174 genome. J. Mol. Biol. 196, 743–755 (1987)

    CAS  Article  Google Scholar 

  17. 17

    Voineagu, I., Narayanan, V., Lobachev, K. S. & Mirkin, S. M. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc. Natl Acad. Sci. USA 105, 9936–9941 (2008)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Lydeard, J. R. et al. Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly. Genes Dev. 24, 1133–1144 (2010)

    CAS  Article  Google Scholar 

  19. 19

    Deem, A. et al. Break-induced replication is highly inaccurate. PLoS Biol. 9, e1000594 (2011)

    CAS  Article  Google Scholar 

  20. 20

    Smith, C. E., Llorente, B. & Symington, L. S. Template switching during break-induced replication. Nature 447, 102–105 (2007)

    ADS  CAS  Article  Google Scholar 

  21. 21

    Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011)

    MathSciNet  CAS  Article  Google Scholar 

  22. 22

    Zuffardi, O., Bonaglia, M., Ciccone, R. & Giorda, R. Inverted duplications deletions: underdiagnosed rearrangements? Clin. Genet. 75, 505–513 (2009)

    CAS  Article  Google Scholar 

  23. 23

    Arlt, M. F., Wilson, T. E. & Glover, T. W. Replication stress and mechanisms of CNV formation. Curr. Opin. Genet. Dev. 22, 204–210 (2012)

    CAS  Article  Google Scholar 

  24. 24

    Liu, P. et al. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146, 889–903 (2011)

    CAS  Article  Google Scholar 

  25. 25

    Kloosterman, W. P. et al. Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep. 1, 648–655 (2012)

    CAS  Article  Google Scholar 

  26. 26

    Iraqui, I. et al. Recovery of arrested replication forks by homologous recombination is error-prone. PLoS Genet. 8, e1002976 (2012)

    CAS  Article  Google Scholar 

  27. 27

    Pelliccia, F., Bosco, N. & Rocchi, A. Breakages at common fragile sites set boundaries of amplified regions in two leukemia cell lines K562 - Molecular characterization of FRA2H and localization of a new CFS FRA2S. Cancer Lett. 299, 37–44 (2010)

    CAS  Article  Google Scholar 

  28. 28

    Blumrich, A. et al. The FRA2C common fragile site maps to the borders of MYCN amplicons in neuroblastoma and is associated with gross chromosomal rearrangements in different cancers. Hum. Mol. Genet. 20, 1488–1501 (2011)

    CAS  Article  Google Scholar 

  29. 29

    Carvalho, C. M. et al. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. Nature Genet. 43, 1074–1081 (2011)

    CAS  Article  Google Scholar 

  30. 30

    Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795–823 (1991)

    CAS  Article  Google Scholar 

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We thank E. Hoffman, J. Baxter, M. Neale and members of the Carr and Murray laboratories for discussions. J.M.M. acknowledges Cancer Research UK (CRUK) grant C9601/A9484: A.M.C. acknowledges Medical Research Council (MRC) grant G0600233.

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I.M., K.M. and S.A.S. performed experiments. J.M.M., K.M. and A.M.C. wrote the manuscript. All authors contributed to experimental design.

Corresponding author

Correspondence to Antony M. Carr.

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The authors declare no competing financial interests.

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Mizuno, K., Miyabe, I., Schalbetter, S. et al. Recombination-restarted replication makes inverted chromosome fusions at inverted repeats. Nature 493, 246–249 (2013).

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