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  • Review Article
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Maintaining genome stability at the replication fork

Nature Reviews Molecular Cell Biology volume 11, pages 208–219 (2010)Cite this article

Subjects

Key Points

  • Problems in DNA replication can induce chromosome rearrangements that are often associated with pathological disorders.

  • Natural elements such as unusual DNA structures, fragile zones and DNA-binding proteins impede replication and can impact on replication fork stability and progression.

  • Replication induces changes in DNA topology, which affect replication and replication-associated repair processes.

  • Replication checkpoints have key roles in promoting replication fork stability.

  • Different types of DNA lesions elicit the action of diverse damage-tolerance pathways that restore replication fork progression or promote DNA repair.

  • Together with the checkpoint-mediated pathway, small ubiquitin-related modifier (SUMO) and ubiquitin modifications are crucial in regulating the stability and activity of key components of DNA replication and repair machineries.

Abstract

Aberrant DNA replication is a major source of the mutations and chromosome rearrangements that are associated with pathological disorders. When replication is compromised, DNA becomes more prone to breakage. Secondary structures, highly transcribed DNA sequences and damaged DNA stall replication forks, which then require checkpoint factors and specialized enzymatic activities for their stabilization and subsequent advance. These mechanisms ensure that the local DNA damage response, which enables replication fork progression and DNA repair in S phase, is coupled with cell cycle transitions. The mechanisms that operate in eukaryotic cells to promote replication fork integrity and coordinate replication with other aspects of chromosome maintenance are becoming clear.

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Figure 1: Replication initiation and progression.
Figure 2: Topological transitions at the replication fork.
Figure 3: Translesion synthesis- and template switch-mediated damage bypass mechanisms.
Figure 4: Regulation of the Fanconi protein complex in response to DNA damage and a model for interstrand cross link repair.

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References

  1. Schwob, E. Flexibility and governance in eukaryotic DNA replication. Curr. Opin. Microbiol. 7, 680–690 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Kearsey, S. E. & Cotterill, S. Enigmatic variations: divergent modes of regulating eukaryotic DNA replication. Mol. Cell 12, 1067–1075 (2003).

    Article  CAS  PubMed  Google Scholar 

  3. Zegerman, P. & Diffley, J. F. DNA replication as a target of the DNA damage checkpoint. DNA Repair (Amst.) 8, 1077–1088 (2009).

    Article  CAS  Google Scholar 

  4. Raghuraman, M. K. et al. Replication dynamics of the yeast genome. Science 294, 115–121 (2001).

    Article  CAS  PubMed  Google Scholar 

  5. Yabuki, N., Terashima, H. & Kitada, K. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7, 781–789 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Wyrick, J. J. et al. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294, 2357–2360 (2001). References 5 and 6 map replication origins and identify their replication time.

    Article  CAS  PubMed  Google Scholar 

  7. Dershowitz, A. & Newlon, C. S. The effect on chromosome stability of deleting replication origins. Mol. Cell. Biol. 13, 391–398 (1993). Analyzes the consequences of ablating origins and suggests that origins are present in excess.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Woodward, A. M. et al. Excess Mcm2–7 license dormant origins of replication that can be used under conditions of replicative stress. J. Cell Biol. 173, 673–683 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ibarra, A., Schwob, E. & Mendez, J. Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication. Proc. Natl Acad. Sci. USA 105, 8956–8961 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Okuno, Y., McNairn, A. J., den Elzen, N., Pines, J. & Gilbert, D. M. Stability, chromatin association and functional activity of mammalian pre-replication complex proteins during the cell cycle. EMBO J. 20, 4263–4277 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Laskey, R. A. & Harland, R. M. Replication origins in the eukaryotic chromosome. Cell 24, 283–284 (1981).

    Article  CAS  PubMed  Google Scholar 

  12. Ivessa, A. S. et al. The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol. Cell 12, 1525–1536 (2003).

    Article  CAS  PubMed  Google Scholar 

  13. Cha, R. S. & Kleckner, N. ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science 297, 602–606 (2002). Shows the crucial role of the replication checkpoint in preventing breakage at replication slow zones.

    Article  CAS  PubMed  Google Scholar 

  14. Ivessa, A. S., Zhou, J. Q., Schulz, V. P., Monson, E. K. & Zakian, V. A. Saccharomyces Rrm3p, a 5′ to 3′ DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev. 16, 1383–1396 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ivessa, A. S., Zhou, J. Q. & Zakian, V. A. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100, 479–489 (2000).

    Article  CAS  PubMed  Google Scholar 

  16. Shore, D. & Bianchi, A. Telomere length regulation: coupling DNA end processing to feedback regulation of telomerase. EMBO J. 28, 2309–2322 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Gilson, E. & Geli, V. How telomeres are replicated. Nature Rev. Mol. Cell Biol. 8, 825–838 (2007).

    Article  CAS  Google Scholar 

  18. Dulev, S. et al. Essential global role of CDC14 in DNA synthesis revealed by chromosome underreplication unrecognized by checkpoints in cdc14 mutants. Proc. Natl Acad. Sci. USA 106, 14466–14471 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Aguilera, A. & Gomez-Gonzalez, B. Genome instability: a mechanistic view of its causes and consequences. Nature Rev. Genet. 9, 204–217 (2008).

    Article  CAS  PubMed  Google Scholar 

  20. Kolodner, R. D., Putnam, C. D. & Myung, K. Maintenance of genome stability in Saccharomyces cerevisiae. Science 297, 552–557 (2002).

    Article  CAS  PubMed  Google Scholar 

  21. Bochman, M. L. & Schwacha, A. The Mcm2–7 complex has in vitro helicase activity. Mol. Cell 31, 287–293 (2008).

    Article  CAS  PubMed  Google Scholar 

  22. Labib, K., Tercero, J. A. & Diffley, J. F. Uninterrupted MCM2–7 function required for DNA replication fork progression. Science 288, 1643–1647 (2000).

    Article  CAS  PubMed  Google Scholar 

  23. Dowell, S. J., Romanowski, P. & Diffley, J. F. Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science 265, 1243–1246 (1994).

    Article  CAS  PubMed  Google Scholar 

  24. Bell, S. P. Eukaryotic replicators and associated protein complexes. Curr. Opin. Genet. Dev. 5, 162–167 (1995).

    Article  CAS  PubMed  Google Scholar 

  25. Aparicio, O. M., Weinstein, D. M. & Bell, S. P. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997).

    Article  CAS  PubMed  Google Scholar 

  26. Toone, W. M., Aerne, B. L., Morgan, B. A. & Johnston, L. H. Getting started: regulating the initiation of DNA replication in yeast. Annu. Rev. Microbiol 51, 125–149 (1997).

    Article  CAS  PubMed  Google Scholar 

  27. Gambus, A. et al. GINS maintains association of Cdc45 with MCM in replisome progression complexes at eukaryotic DNA replication forks. Nature Cell Biol. 8, 358–366 (2006).

    CAS  PubMed  Google Scholar 

  28. Katou, Y. et al. S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424, 1078–1083 (2003).

    Article  CAS  PubMed  Google Scholar 

  29. Cobb, J. A., Bjergbaek, L., Shimada, K., Frei, C. & Gasser, S. M. DNA polymerase stabilization at stalled replication forks requires Mec1 and the RecQ helicase Sgs1. EMBO J. 22, 4325–4336 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Lucca, C. et al. Checkpoint-mediated control of replisome-fork association and signalling in response to replication pausing. Oncogene 23, 1206–1213 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Postow, L., Crisona, N. J., Peter, B. J., Hardy, C. D. & Cozzarelli, N. R. Topological challenges to DNA replication: conformations at the fork. Proc. Natl Acad. Sci. USA 98, 8219–8226 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Wang, J. C. Cellular roles of DNA topoisomerases: a molecular perspective. Nature Rev. Mol. Cell. Biol. 3, 430–440 (2002).

    Article  CAS  Google Scholar 

  33. Bermejo, R. et al. Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation. Genes Dev. 21, 1921–1936 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Fields-Berry, S. C. & DePamphilis, M. L. Sequences that promote formation of catenated intertwines during termination of DNA replication. Nucleic Acids Res. 17, 3261–3273 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mirkin, E. V. & Mirkin, S. M. Replication fork stalling at natural impediments. Microbiol Mol. Biol. Rev. 71, 13–35 (2007). A comprehensive review on the natural elements that lead to RF stalling.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Casper, A. M., Nghiem, P., Arlt, M. F. & Glover, T. W. ATR regulates fragile site stability. Cell 111, 779–789 (2002). Documents the role of the replication checkpoint in preventing the expression of fragile sites.

    Article  CAS  PubMed  Google Scholar 

  37. Deshpande, A. M. & Newlon, C. S. DNA replication fork pause sites dependent on transcription. Science 272, 1030–1033 (1996). Shows that tRNA transcription causes RF pausing.

    Article  CAS  PubMed  Google Scholar 

  38. Azvolinsky, A., Giresi, P. G., Lieb, J. D. & Zakian, V. A. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol. Cell 34, 722–734 (2009). Provides a genome-wide analysis of replication pausing elements.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Cook, P. R. The organization of replication and transcription. Science 284, 1790–1795 (1999).

    Article  CAS  PubMed  Google Scholar 

  40. Olavarrieta, L., Hernandez, P., Krimer, D. B. & Schvartzman, J. B. DNA knotting caused by head-on collision of transcription and replication. J. Mol. Biol. 322, 1–6 (2002). Documents the topological consequences of RFs clashing with transcription units.

    Article  CAS  PubMed  Google Scholar 

  41. Tuduri, S. et al. Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nature Cell Biol. 11, 1315–1324 (2009).

    Article  CAS  PubMed  Google Scholar 

  42. Bermejo, R. et al. Genome-organizing factors Top2 and Hmo1 prevent chromosome fragility at sites of S phase transcription. Cell 138, 870–884 (2009).

    Article  CAS  PubMed  Google Scholar 

  43. Lindahl, T. Instability and decay of the primary structure of DNA. Nature 362, 709–715 (1993).

    Article  CAS  PubMed  Google Scholar 

  44. Mirkin, S. M. DNA structures, repeat expansions and human hereditary disorders. Curr. Opin. Struct. Biol. 16, 351–358 (2006).

    Article  CAS  PubMed  Google Scholar 

  45. Lόpez Castel, A., Cleary, J. D & Pearson, C. E. Repeat instability as the basis for human diseases and as a potential target for therapy. Nature Rev. Mol. Cell Biol. 11, 165–170 (2010).

    Article  CAS  Google Scholar 

  46. Orr, H. T. & Zoghbi, H. Y. Trinucleotide repeat disorders. Annu. Rev. Neurosci. 30, 575–621 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Durkin, S. G. & Glover, T. W. Chromosome fragile sites. Annu. Rev. Genet. 41, 169–192 (2007).

    Article  CAS  PubMed  Google Scholar 

  48. Sutherland, G. R. Fragile sites on human chromosomes: demonstration of their dependence on the type of tissue culture medium. Science 197, 265–266 (1977).

    Article  CAS  PubMed  Google Scholar 

  49. Roeder, G. S. & Fink, G. R. DNA rearrangements associated with a transposable element in yeast. Cell 21, 239–249 (1980).

    Article  CAS  PubMed  Google Scholar 

  50. Argueso, J. L. et al. Double-strand breaks associated with repetitive DNA can reshape the genome. Proc. Natl Acad. Sci. USA 105, 11845–11850 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Lemoine, F. J., Degtyareva, N. P., Lobachev, K. & Petes, T. D. Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. Cell 120, 587–598 (2005). Shows that limiting the amounts of DNA polymerases can lead to fragile site expression.

    Article  CAS  PubMed  Google Scholar 

  52. Admire, A. et al. Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast. Genes Dev. 20, 159–173 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Peter, B. J., Ullsperger, C., Hiasa, H., Marians, K. J. & Cozzarelli, N. R. The structure of supercoiled intermediates in DNA replication. Cell 94, 819–827 (1998).

    Article  CAS  PubMed  Google Scholar 

  54. Trinh, T. Q. & Sinden, R. R. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352, 544–547 (1991).

    Article  CAS  PubMed  Google Scholar 

  55. Rosche, W. A., Trinh, T. Q. & Sinden, R. R. Differential DNA secondary structure-mediated deletion mutation in the leading and lagging strands. J. Bacteriol. 177, 4385–4391 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Hansen, R. S., Canfield, T. K., Lamb, M. M., Gartler, S. M. & Laird, C. D. Association of fragile X syndrome with delayed replication of the FMR1 gene. Cell 73, 1403–1409 (1993).

    Article  CAS  PubMed  Google Scholar 

  57. Lu, J., Kobayashi, R. & Brill, S. J. Characterization of a high mobility group 1/2 homolog in yeast. J. Biol. Chem. 271, 33678–33685 (1996).

    Article  CAS  PubMed  Google Scholar 

  58. Kim, H. & Livingston, D. M. Suppression of a DNA polymerase δ mutation by the absence of the high mobility group protein Hmo1 in Saccharomyces cerevisiae. Curr. Genet. 55, 127–138 (2009).

    Article  CAS  PubMed  Google Scholar 

  59. Prado, F. & Aguilera, A. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J. 24, 1267–1276 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Pomerantz, R. T. & O'Donnell, M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762–766 (2008). In vitro study proposing that mRNAs can be used as primers by the leading-strand polymerase.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Dalgaard, J. Z. & Klar, A. J. A DNA replication-arrest site RTS1 regulates imprinting by determining the direction of replication at mat1 in S. pombe. Genes Dev. 15, 2060–2068 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. 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). Describes the consequences of RF collapse in the triggering of recombination and genome instability.

    Article  CAS  PubMed  Google Scholar 

  63. Inagawa, T. et al. Schizosaccharomyces pombe Rtf2 mediates site-specific replication termination by inhibiting replication restart. Proc. Natl Acad. Sci. USA 106, 7927–7932 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Doe, C. L. & Whitby, M. C. The involvement of Srs2 in post-replication repair and homologous recombination in fission yeast. Nucleic Acids Res. 32, 1480–1491 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Fabre, F., Chan, A., Heyer, W. D. & Gangloff, S. Alternate pathways involving Sgs1/Top3, Mus81/Mms4, and Srs2 prevent formation of toxic recombination intermediates from single-stranded gaps created by DNA replication. Proc. Natl Acad. Sci. USA 99, 16887–16892 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Pfander, B., Moldovan, G. L., Sacher, M., Hoege, C. & Jentsch, S. SUMO-modified PCNA recruits Srs2 to prevent recombination during S phase. Nature 436, 428–433 (2005).

    Article  CAS  PubMed  Google Scholar 

  67. Papouli, E. et al. Crosstalk between SUMO and ubiquitin on PCNA is mediated by recruitment of the helicase Srs2p. Mol. Cell 19, 123–133 (2005).

    Article  CAS  PubMed  Google Scholar 

  68. Branzei, D., Vanoli, F. & Foiani, M. SUMOylation regulates Rad18-mediated template switch. Nature 456, 915–920 (2008). Provides physical evidence for a role of the Rad18 pathway in promoting recombination structures that involve sister chromatids during replication of damaged templates.

    Article  CAS  PubMed  Google Scholar 

  69. Branzei, D. et al. Ubc9- and Mms21-mediated sumoylation counteracts recombinogenic events at damaged replication forks. Cell 127, 509–522 (2006). Documents the role of sumoylation in the resolution of recombination intermediates formed during the replication of damaged templates.

    Article  CAS  PubMed  Google Scholar 

  70. Zhao, X. & Blobel, G. A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc. Natl Acad. Sci. USA 102, 4777–4782 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Sollier, J. et al. The Saccharomyces cerevisiae Esc2 and Smc5–6 proteins promote sister chromatid junction-mediated intra-S repair. Mol. Biol. Cell 20, 1671–1682 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Stegmeier, F. & Amon, A. Closing mitosis: the functions of the Cdc14 phosphatase and its regulation. Annu. Rev. Genet. 38, 203–232 (2004).

    Article  CAS  PubMed  Google Scholar 

  73. Lopes, M. et al. The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412, 557–561 (2001).

    Article  CAS  PubMed  Google Scholar 

  74. Sogo, J. M., Lopes, M. & Foiani, M. Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297, 599–602 (2002). References 73 and74 document the role of the replication checkpoint in preventing the regression of stalled RFs.

    Article  CAS  PubMed  Google Scholar 

  75. Doksani, Y., Bermejo, R., Fiorani, S., Haber, J. E. & Foiani, M. Replicon dynamics, dormant origin firing, and terminal fork integrity after double-strand break formation. Cell 137, 247–258 (2009). Addresses the consequences of RFs encountering DSBs, and the pathways promoting the integrity of such terminal RFs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Lahiri, M., Gustafson, T. L., Majors, E. R. & Freudenreich, C. H. Expanded CAG repeats activate the DNA damage checkpoint pathway. Mol. Cell 15, 287–293 (2004).

    Article  CAS  PubMed  Google Scholar 

  77. Freudenreich, C. H. & Lahiri, M. Structure-forming CAG/CTG repeat sequences are sensitive to breakage in the absence of Mrc1 checkpoint function and S-phase checkpoint signaling: implications for trinucleotide repeat expansion diseases. Cell Cycle 3, 1370–1374 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. 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).

    Article  PubMed  PubMed Central  Google Scholar 

  79. Voineagu, I., Surka, C. F., Shishkin, A. A., Krasilnikova, M. M. & Mirkin, S. M. Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility. Nature Struct. Mol. Biol. 16, 226–228 (2009).

    Article  CAS  Google Scholar 

  80. Postow, L. et al. Positive torsional strain causes the formation of a four-way junction at replication forks. J. Biol. Chem. 276, 2790–2796 (2001). In vitro study showing that RF reversal can be induced by positive supercoiling.

    Article  CAS  PubMed  Google Scholar 

  81. Fierro-Fernandez, M., Hernandez, P., Krimer, D. B., Stasiak, A. & Schvartzman, J. B. Topological locking restrains replication fork reversal. Proc. Natl Acad. Sci. USA 104, 1500–1505 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Cotta-Ramusino, C. et al. Exo1 processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells. Mol. Cell 17, 153–159 (2005).

    Article  CAS  PubMed  Google Scholar 

  83. Feng, W. et al. Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nature Cell Biol. 8, 148–155 (2006).

    Article  CAS  PubMed  Google Scholar 

  84. Alcasabas, A. A. et al. Mrc1 transduces signals of DNA replication stress to activate Rad53. Nature Cell Biol. 3, 958–965 (2001).

    Article  CAS  PubMed  Google Scholar 

  85. Osborn, A. J. & Elledge, S. J. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Genes Dev. 17, 1755–1767 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Foss, E. J. Tof1p regulates DNA damage responses during S phase in Saccharomyces cerevisiae. Genetics 157, 567–577 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Branzei, D. & Foiani, M. The checkpoint response to replication stress. DNA Repair (Amst.) 8, 1038–1046 (2009).

    Article  CAS  Google Scholar 

  88. Shishkin, A. A. et al. Large-scale expansions of Friedreich's ataxia GAA repeats in yeast. Mol. Cell 35, 82–92 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Kai, M. & Wang, T. S. Checkpoint activation regulates mutagenic translesion synthesis. Genes Dev. 17, 64–76 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Sabbioneda, S. et al. The 9-1-1 checkpoint clamp physically interacts with polζ and is partially required for spontaneous polζ-dependent mutagenesis in Saccharomyces cerevisiae. J. Biol. Chem. 280, 38657–38665 (2005).

    Article  CAS  PubMed  Google Scholar 

  91. Liberi, G. et al. Rad51-dependent DNA structures accumulate at damaged replication forks in sgs1 mutants defective in the yeast ortholog of BLM RecQ helicase. Genes Dev. 19, 339–350 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Lopes, M., Foiani, M. & Sogo, J. M. Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol. Cell 21, 15–27 (2006). Shows physical evidence that gaps form during DNA replication without affecting RF progression.

    Article  CAS  PubMed  Google Scholar 

  93. Sancar, A., Lindsey-Boltz, L. A., Unsal-Kacmaz, K. & Linn., S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73, 39–85 (2004).

    Article  CAS  PubMed  Google Scholar 

  94. Higgins, N. P., Kato, K. & Strauss, B. A model for replication repair in mammalian cells. J. Mol. Biol. 101, 417–425 (1976).

    Article  CAS  PubMed  Google Scholar 

  95. Heller, R. C. & Marians, K. J. Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439, 557–562 (2006). In vitro study showing that leading strands can also restart by re-priming downstream of the blocking lesions.

    Article  CAS  PubMed  Google Scholar 

  96. Amado, L. & Kuzminov, A. The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision. J. Biol. Chem. 281, 22635–22646 (2006).

    Article  CAS  PubMed  Google Scholar 

  97. Kogoma, T. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol Mol. Biol. Rev. 61, 212–238 (1997). Comprehensive review on the DNA metabolism processes operating during DNA replication.

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Barbour, L., Ball, L. G., Zhang, K. & Xiao, W. DNA damage checkpoints are involved in postreplication repair. Genetics 174, 1789–1800 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Paulovich, A. G., Margulies, R. U., Garvik, B. M. & Hartwell, L. H. RAD9, RAD17, and RAD24 are required for S phase regulation in Saccharomyces cerevisiae in response to DNA damage. Genetics 145, 45–62 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Kai, M., Furuya, K., Paderi, F., Carr, A. M. & Wang, T. S. Rad3-dependent phosphorylation of the checkpoint clamp regulates repair-pathway choice. Nature Cell Biol. 9, 691–697 (2007).

    Article  CAS  PubMed  Google Scholar 

  101. Prakash, L. Characterization of postreplication repair in Saccharomyces cerevisiae and effects of rad6, rad18, rev3 and rad52 mutations. Mol. Gen. Genet. 184, 471–478 (1981).

    Article  CAS  PubMed  Google Scholar 

  102. Zhang, H. & Lawrence, C. W. The error-free component of the RAD6/RAD18 DNA damage tolerance pathway of budding yeast employs sister-strand recombination. Proc. Natl Acad. Sci. USA 102, 15954–15959 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Gangavarapu, V., Prakash, S. & Prakash, L. Requirement of RAD52 group genes for postreplication repair of UV-damaged DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 27, 7758–7764 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Hoege, C., Pfander, B., Moldovan, G. L., Pyrowolakis, G. & Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419, 135–141 (2002). This study was the first to identify PCNA modifications by ubiquitin and SUMO, and to suggest their role in DNA repair.

    Article  CAS  PubMed  Google Scholar 

  105. Stelter, P. & Ulrich, H. D. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425, 188–191 (2003).

    Article  CAS  PubMed  Google Scholar 

  106. Kannouche, P. L., Wing, J. & Lehmann, A. R. Interaction of human DNA polymerase ɛ with monoubiquitinated PCNA: a possible mechanism for the polymerase switch in response to DNA damage. Mol. Cell 14, 491–500 (2004).

    Article  CAS  PubMed  Google Scholar 

  107. Torres-Ramos, C. A., Prakash, S. & Prakash, L. Requirement of RAD5 and MMS2 for postreplication repair of UV-damaged DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 22, 2419–2426 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Haracska, L., Torres-Ramos, C. A., Johnson, R. E., Prakash, S. & Prakash, L. Opposing effects of ubiquitin conjugation and SUMO modification of PCNA on replicational bypass of DNA lesions in Saccharomyces cerevisiae. Mol. Cell. Biol. 24, 4267–4274 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Falbo, K. B. et al. Involvement of a chromatin remodeling complex in damage tolerance during DNA replication. Nature Struct. Mol. Biol. 16, 1167–1172 (2009).

    Article  CAS  Google Scholar 

  110. Wu, L. & Hickson, I. D. The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 426, 870–874 (2003).

    Article  CAS  PubMed  Google Scholar 

  111. Mankouri, H. W. & Hickson, I. D. Top3 processes recombination intermediates and modulates checkpoint activity after DNA damage. Mol. Biol. Cell 17, 4473–4483 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Mankouri, H. W., Ngo, H. P. & Hickson, I. D. Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae. Mol. Biol. Cell 20, 1683–1694 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Goldfless, S. J., Morag, A. S., Belisle, K. A., Sutera, V. A., Jr. & Lovett, S. T. DNA repeat rearrangements mediated by DnaK-dependent replication fork repair. Mol. Cell 21, 595–604 (2006).

    Article  CAS  PubMed  Google Scholar 

  114. Johnson, R. E. et al. Saccharomyces cerevisiae RAD5-encoded DNA repair protein contains DNA helicase and zinc-binding sequence motifs and affects the stability of simple repetitive sequences in the genome. Mol. Cell. Biol. 12, 3807–3818 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Branzei, D. & Foiani, M. Template switching: from replication fork repair to genome rearrangements. Cell 131, 1228–1230 (2007).

    Article  CAS  PubMed  Google Scholar 

  116. 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). Proposes that template switching involving microhomology elements and different RFs is responsible for the complex genome rearrangements associated with certain genomic disorders.

    Article  CAS  PubMed  Google Scholar 

  117. Paek, A. L. et al. Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. Genes Dev. 23, 2861–2875 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. 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). References 117 and 118 propose that template switching at nearby inverted repeats generates dicentric chromosomes without a DSB intermediate.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Scharer, O. D. DNA interstrand crosslinks: natural and drug-induced DNA adducts that induce unique cellular responses. Chembiochem 6, 27–32 (2005).

    Article  CAS  PubMed  Google Scholar 

  120. Niedzwiedz, W. et al. The Fanconi anaemia gene FANCC promotes homologous recombination and error-prone DNA repair. Mol. Cell 15, 607–620 (2004).

    Article  CAS  PubMed  Google Scholar 

  121. Wang, W. Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. Nature Rev. Genet. 8, 735–748 (2007).

    Article  CAS  PubMed  Google Scholar 

  122. Sobeck, A. et al. Fanconi anemia proteins are required to prevent accumulation of replication-associated DNA double-strand breaks. Mol. Cell. Biol. 26, 425–437 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Meetei, A. R., Yan, Z. & Wang, W. FANCL replaces BRCA1 as the likely ubiquitin ligase responsible for FANCD2 monoubiquitination. Cell Cycle 3, 179–181 (2004).

    Article  CAS  PubMed  Google Scholar 

  124. Smogorzewska, A. et al. Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell 129, 289–301 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Ciccia, A. et al. Identification of FAAP24, a Fanconi anemia core complex protein that interacts with FANCM. Mol. Cell 25, 331–343 (2007).

    Article  CAS  PubMed  Google Scholar 

  126. Xia, B. et al. Fanconi anemia is associated with a defect in the BRCA2 partner PALB2. Nature Genet. 39, 159–161 (2007).

    Article  CAS  PubMed  Google Scholar 

  127. Sung, P. & Klein, H. Mechanism of homologous recombination: mediators and helicases take on regulatory functions. Nature Rev. Mol. Cell Biol. 7, 739–750 (2006).

    Article  CAS  Google Scholar 

  128. Litman, R. et al. BACH1 is critical for homologous recombination and appears to be the Fanconi anemia gene product FANCJ. Cancer Cell 8, 255–265 (2005).

    Article  CAS  PubMed  Google Scholar 

  129. Nojima, K. et al. Multiple repair pathways mediate tolerance to chemotherapeutic cross-linking agents in vertebrate cells. Cancer Res. 65, 11704–11711 (2005).

    Article  CAS  PubMed  Google Scholar 

  130. Gari, K., Decaillet, C., Delannoy, M., Wu, L. & Constantinou, A. Remodeling of DNA replication structures by the branch point translocase FANCM. Proc. Natl Acad. Sci. USA 105, 16107–16112 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  131. Gari, K., Decaillet, C., Stasiak, A. Z., Stasiak, A. & Constantinou, A. The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks. Mol. Cell 29, 141–148 (2008).

    Article  CAS  PubMed  Google Scholar 

  132. Sun, W. et al. The FANCM ortholog Fml1 promotes recombination at stalled replication forks and limits crossing over during DNA double-strand break repair. Mol. Cell 32, 118–128 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Chen, Y. H. et al. Interplay between the Smc5/6 complex and the Mph1 helicase in recombinational repair. Proc. Natl Acad. Sci. USA 106, 21252–21257 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Raschle, M. et al. Mechanism of replication-coupled DNA interstrand crosslink repair. Cell 134, 969–980 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Knipscheer, P. et al. The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair. Science 326, 1698–1701 (2009). References 134 and 135 propose, based on in vitro studies, a new mechanism through which Fanconi anaemia proteins promote ICL repair.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Lou, Z., Minter-Dykhouse, K. & Chen, J. BRCA1 participates in DNA decatenation. Nature Struct. Mol. Biol. 12, 589–593 (2005).

    Article  CAS  Google Scholar 

  137. Andreassen, P. R., D'Andrea, A. D. & Taniguchi, T. ATR couples FANCD2 monoubiquitination to the DNA-damage response. Genes Dev. 18, 1958–1963 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Luke-Glaser, S., Luke, B., Grossi, S. & Constantinou, A. FANCM regulates DNA chain elongation and is stabilized by S-phase checkpoint signalling. EMBO J. 10 Dec 2009 (doi: 10.1038/emboj.2009.371).

  139. Wang, J. C. DNA topoisomerases. Annu. Rev. Biochem. 65, 635–692 (1996).

    Article  CAS  PubMed  Google Scholar 

  140. Koster, D. A., Palle, K., Bot., E. S., Bjornsti, M. A. & Dekker, N. H. Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature 448, 213–217 (2007).

    Article  CAS  PubMed  Google Scholar 

  141. Branzei, D. & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nature Rev. Mol. Cell Biol. 9, 297–308 (2008).

    Article  CAS  Google Scholar 

  142. Sonoda, E., Hochegger, H., Saberi, A., Taniguchi, Y. & Takeda, S. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst.) 5, 1021–1029 (2006).

    Article  CAS  Google Scholar 

  143. Tsao, Y. P., Russo, A., Nyamuswa, G., Silber, R. & Liu, L. F. Interaction between replication forks and topoisomerase I-DNA cleavable complexes: studies in a cell-free SV40 DNA replication system. Cancer Res. 53, 5908–5914 (1993).

    CAS  PubMed  Google Scholar 

  144. Bartek, J. & Lukas, J. DNA damage checkpoints: from initiation to recovery or adaptation. Curr. Opin. Cell Biol. 19, 238–245 (2007).

    Article  CAS  PubMed  Google Scholar 

  145. Segurado, M. & Diffley, J. F. Separate roles for the DNA damage checkpoint protein kinases in stabilizing DNA replication forks. Genes Dev. 22, 1816–1827 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Champoux, J. J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369–413 (2001).

    Article  CAS  PubMed  Google Scholar 

  147. Geiss-Friedlander, R. & Melchior, F. Concepts in sumoylation: a decade on. Nature Rev. Mol. Cell Biol. 8, 947–956 (2007).

    Article  CAS  Google Scholar 

  148. Mimura, S., Komata, M., Kishi, T., Shirahige, K. & Kamura, T. SCFDia2 regulates DNA replication forks during S-phase in budding yeast. EMBO J. 28, 3693–3705 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Morohashi, H., Maculins, T. & Labib, K. The amino-terminal TPR domain of Dia2 tethers SCF(Dia2) to the replisome progression complex. Curr. Biol. 19, 1943–1949 (2009). References 148 and 149 identifiy the replisome components Mrc1 and Ctf4 as targets for the F-box ubiquitin ligase Dia2.

    Article  CAS  PubMed  Google Scholar 

  150. Zhong, W., Feng, H., Santiago, F. E. & Kipreos, E. T. CUL-4 ubiquitin ligase maintains genome stability by restraining DNA-replication licensing. Nature 423, 885–889 (2003).

    Article  CAS  PubMed  Google Scholar 

  151. Zhang, Y. W. et al. Genotoxic stress targets human Chk1 for degradation by the ubiquitin-proteasome pathway. Mol. Cell 19, 607–618 (2005).

    Article  CAS  PubMed  Google Scholar 

  152. Leung-Pineda, V., Huh, J. & Piwnica-Worms, H. DDB1 targets Chk1 to the Cul4 E3 ligase complex in normal cycling cells and in cells experiencing replication stress. Cancer Res. 69, 2630–2637 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Whitcomb, E. A., Dudek, E. J., Liu, Q. & Taylor, A. Novel control of S phase of the cell cycle by ubiquitin-conjugating enzyme H7. Mol. Biol. Cell 20, 1–9 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Taniguchi, T. et al. S-phase-specific interaction of the Fanconi anemia protein, FANCD2, with BRCA1 and RAD51. Blood 100, 2414–2420 (2002).

    Article  CAS  PubMed  Google Scholar 

  155. Das-Bradoo, S. et al. Defects in DNA ligase I trigger PCNA ubiquitylation at Lys 107. Nature Cell Biol. 12, 74–79 (2010).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank all members of our laboratories for helpful discussions. The work in D.B's laboratory is supported by the European Research Council grant 242928 and the Associazione Italiana per la Ricerca sul Cancro. The work in M.F's laboratory is supported by grants from Telethon, the Associazione Italiana per la Ricerca sul Cancro and the European Community.

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Authors and Affiliations

  1. Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, Milan, 20139, Italy

    Dana Branzei & Marco Foiani

  2. Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy

    Marco Foiani

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Glossary

Autonomously replicating sequence

A DNA element in the yeast genome that contains origins of replication.

Replication fork

The branch point structure that forms during DNA replication between two template DNA strands, at which nascent DNA synthesis is ongoing.

GINS complex

An essential complex for DNA replication that promotes polymerase-ε loading and the activity of the MCM helicase.

Precatenane

A cruciform junction that is formed by the intertwining of sister duplexes in the replicated portion of a replicon.

Supercoil

A contortion in DNA that is important for DNA packaging and DNA and RNA synthesis. Topoisomerases sense supercoiling and act to either generate or dissipate it by changing DNA topology.

Catenane

An interlocked DNA molecule.

Late replication zone

A DNA region that replicates late during S phase.

Triplex H-DNA

A DNA structure in which a DNA duplex associates with another DNA single strand, in either a parallel or antiparallel orientation.

Left-handed Z-DNA

One of the three biologically active double helical structures of DNA. The others are A- and B-DNA.

Slipped-strand S-DNA

A homoduplex DNA formed between two strands that have either the same number or a different number of repeats (usually triple repeats).

Replication slow zone

A genetically encoded region that causes slower fork progression and also tends to accumulate convergent RFs and, thus, to represent the positions of preferential RF termination.

Ty element

A eukaryotic transposable element that resembles retroviruses, with long terminal repeats at both ends in a direct orientation. The RNA intermediate formed by transcription of the Ty element is copied as DNA by a reverse transcriptase encoded by the Tyb gene of the Ty element. This DNA copy is then inserted into a new site in the yeast genome.

Transfer RNA

A small RNA molecule that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.

Homologous recombination

A type of genetic recombination in which DNA sequences are exchanged between two similar or identical strands of DNA.

Heterochromatization

The formation of a tightly packed form of DNA, which makes the DNA less accessible to protein factors that usually bind. Certain DNA elements, such as centromeres and telomeres, are heterochromatic.

Bulky lesion

A DNA lesion in which the nucleotides carry bulky groups. Methylated DNA and thymine dimers caused by UV irradiation are examples.

DNA adduct

A piece of DNA that is covalently bonded to a chemical.

Homologous duplex

A DNA duplex that shows homology with another DNA region or sequence and usually contains a DSB.

Presynaptic filament

A nucleoprotein filament consisting of Rad51 molecules bound to ssDNA.

Hemicatenane

A cruciform junction of two dsDNA molecules, in which one of the strands of one duplex passes between the two strands of the other duplex, and vice versa.

Microhomology

Refers to homologous sequences that are extremely small, usually just a few base pairs long.

Dicentric chromosome intermediate

An unstable chromosome that has two centromeres.

DNA decatenation

The unknotting of catenated structures.

Camptothecin

A natural alkaloid that inhibits TOP1. Camptothecin analogues are often used in cancer chemotherapy.

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Branzei, D., Foiani, M. Maintaining genome stability at the replication fork. Nat Rev Mol Cell Biol 11, 208–219 (2010). https://doi.org/10.1038/nrm2852

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