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PMID: 19361851 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Replicon dynamics, dormant origin firing, and terminal fork integrity after double-strand break formation.

Cell ·Vol. 137 ·No. 2 ·2009-04-17 ·Pages 247-58

Doksani Y, Bermejo R, Fiorani S, Haber JE, Foiani M

Abstract

In response to replication stress, the Mec1/ATR and SUMO pathways control stalled- and damaged-fork stability. We investigated the S phase response at forks encountering a broken template (termed the terminal fork). We show that double-strand break (DSB) formation can locally trigger dormant origin firing. Irreversible fork resolution at the break does not impede progression of the other fork in the same replicon (termed the sister fork). The Mre11-Tel1/ATM response acts at terminal forks, preventing accumulation of cruciform DNA intermediates that tether sister chromatids and can undergo nucleolytic processing. We conclude that sister forks can be uncoupled during replication and that, after DSB-induced fork termination, replication is rescued by dormant origin firing or adjacent replicons. We have uncovered a Tel1/ATM- and Mre11-dependent response controlling terminal fork integrity. Our findings have implications for those genome instability syndromes that accumulate DNA breaks during S phase and for forks encountering eroding telomeres.

MeSH Terms
DNA Repair DNA Replication Endodeoxyribonucleases/genetics,metabolism Endonucleases Exodeoxyribonucleases/genetics,metabolism Intracellular Signaling Peptides and Proteins/genetics,metabolism Protein Serine-Threonine Kinases/genetics,metabolism Replication Origin Replicon Saccharomyces cerevisiae/cytology,genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism
Chemicals
Intracellular Signaling Peptides and Proteins SAE2 protein, S cerevisiae Saccharomyces cerevisiae Proteins Protein Serine-Threonine Kinases TEL1 protein, S cerevisiae Endodeoxyribonucleases Endonucleases Exodeoxyribonucleases MRE11 protein, S cerevisiae
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Doksani Ylli
FIRC Institute of Molecular Oncology Foundation (IFOM-IEO Campus) and DSBB-Università degli Studi di Milano, Via Adamello 16, 20139 Milan, Italy.
Bermejo Rodrigo
Fiorani Simona
Haber James E
Foiani Marco
References (89)
89 references, click to expand
  1. Localization of a DNA replication origin and termination zone on chromosome III of Saccharomyces cerevisiae.
    Mol Cell Biol. 1992 Oct;12(10):4733-41 PMID: 1406657
  2. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae.
    Yeast. 1996 Mar 15;12(3):259-65 PMID: 8904338
  3. Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage.
    Cell. 1998 Aug 7;94(3):399-409 PMID: 9708741
  4. The DNA replication checkpoint response stabilizes stalled replication forks.
    Nature. 2001 Aug 2;412(6846):557-61 PMID: 11484058
  5. Double-strand breaks trigger MRX- and Mec1-dependent, but Tel1-independent, checkpoint activation.
    FEMS Yeast Res. 2006 Aug;6(5):836-47 PMID: 16879433
  6. Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication.
    Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8956-61 PMID: 18579778
  7. The arrest of replication forks in the rDNA of yeast occurs independently of transcription.
    Cell. 1992 Oct 16;71(2):267-76 PMID: 1423594
  8. Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses.
    Cell. 2007 Aug 10;130(3):499-511 PMID: 17693258
  9. Telomere shortening triggers senescence of human cells through a pathway involving ATM, p53, and p21(CIP1), but not p16(INK4a).
    Mol Cell. 2004 May 21;14(4):501-13 PMID: 15149599
  10. Loss of a yeast telomere: arrest, recovery, and chromosome loss.
    Cell. 1993 Nov 19;75(4):729-39 PMID: 8242745
  11. Physical monitoring of mating type switching in Saccharomyces cerevisiae.
    Mol Cell Biol. 1988 Jun;8(6):2342-9 PMID: 2841579
  12. Topoisomerase II can unlink replicating DNA by precatenane removal.
    EMBO J. 2001 Nov 15;20(22):6509-19 PMID: 11707421
  13. Cellular machineries for chromosomal DNA repair.
    Genes Dev. 2004 Mar 15;18(6):602-16 PMID: 15075289
  14. Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication.
    Nature. 2006 Nov 30;444(7119):638-42 PMID: 17136094
  15. Activation of Rad53 kinase in response to DNA damage and its effect in modulating phosphorylation of the lagging strand DNA polymerase.
    EMBO J. 1999 Nov 15;18(22):6561-72 PMID: 10562568
  16. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated.
    Mol Cell Biol. 1992 Mar;12(3):1292-303 PMID: 1545810
  17. Ubc9- and mms21-mediated sumoylation counteracts recombinogenic events at damaged replication forks.
    Cell. 2006 Nov 3;127(3):509-22 PMID: 17081974
  18. Elevated recombination rates in transcriptionally active DNA.
    Cell. 1989 Feb 24;56(4):619-30 PMID: 2645056
  19. The yeast Xrs2 complex functions in S phase checkpoint regulation.
    Genes Dev. 2001 Sep 1;15(17):2238-49 PMID: 11544181
  20. Anatomy and dynamics of DNA replication fork movement in yeast telomeric regions.
    Mol Cell Biol. 2004 May;24(9):4019-31 PMID: 15082794
  21. ATR regulates fragile site stability.
    Cell. 2002 Dec 13;111(6):779-89 PMID: 12526805
  22. Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV.
    Genes Dev. 2008 Sep 1;22(17):2426-33 PMID: 18765793
  23. ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones.
    Science. 2002 Jul 26;297(5581):602-6 PMID: 12142538
  24. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage.
    Nature. 2005 Mar 31;434(7033):605-11 PMID: 15758953
  25. Human CtIP promotes DNA end resection.
    Nature. 2007 Nov 22;450(7169):509-14 PMID: 17965729
  26. Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint.
    Nature. 2001 Aug 2;412(6846):553-7 PMID: 11484057
  27. Replication initiates at multiple locations on an autonomously replicating plasmid in human cells.
    Mol Cell Biol. 1991 Mar;11(3):1464-72 PMID: 1996103
  28. The product of the HO gene is a nuclease: purification and characterization of the enzyme.
    Cold Spring Harb Symp Quant Biol. 1984;49:89-96 PMID: 6099261
  29. Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase.
    Mol Cell. 2002 Aug;10(2):373-85 PMID: 12191482
  30. Activation of a yeast replication origin near a double-stranded DNA break.
    Genes Dev. 1994 Mar 1;8(5):554-62 PMID: 7926750
  31. Mechanisms of common fragile site instability.
    Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R197-205 PMID: 16244318
  32. Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes.
    Science. 2003 Jun 6;300(5625):1542-8 PMID: 12791985
  33. Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions.
    Mol Cell. 2006 Jan 6;21(1):15-27 PMID: 16387650
  34. Chromosome fragmentation after induction of a double-strand break is an active process prevented by the RMX repair complex.
    Curr Biol. 2004 Dec 14;14(23):2107-12 PMID: 15589152
  35. The localization of replication origins on ARS plasmids in S. cerevisiae.
    Cell. 1987 Nov 6;51(3):463-71 PMID: 2822257
  36. Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex.
    Mol Cell. 2007 Nov 30;28(4):638-51 PMID: 18042458
  37. Replication fork reactivation downstream of a blocked nascent leading strand.
    Nature. 2006 Feb 2;439(7076):557-62 PMID: 16452972
  38. DNA breaks promote genomic instability by impeding proper chromosome segregation.
    Curr Biol. 2004 Dec 14;14(23):2096-106 PMID: 15589151
  39. Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals.
    J Cell Biol. 2007 Jul 16;178(2):209-18 PMID: 17635934
  40. ATM- and cell cycle-dependent regulation of ATR in response to DNA double-strand breaks.
    Nat Cell Biol. 2006 Jan;8(1):37-45 PMID: 16327781
  41. SUMOylation regulates Rad18-mediated template switch.
    Nature. 2008 Dec 18;456(7224):915-20 PMID: 19092928
  42. A DNA damage response pathway controlled by Tel1 and the Mre11 complex.
    Mol Cell. 2001 Jun;7(6):1255-66 PMID: 11430828
  43. Requirement of the Mre11 complex and exonuclease 1 for activation of the Mec1 signaling pathway.
    Mol Cell Biol. 2004 Nov;24(22):10016-25 PMID: 15509802
  44. Overlapping functions of the Saccharomyces cerevisiae Mre11, Exo1 and Rad27 nucleases in DNA metabolism.
    Genetics. 2001 Dec;159(4):1423-33 PMID: 11779786
  45. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break.
    Curr Biol. 2004 Oct 5;14(19):1703-11 PMID: 15458641
  46. Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines.
    Yeast. 1999 Jul;15(10B):963-72 PMID: 10407276
  47. Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects.
    Science. 2002 Jul 26;297(5581):599-602 PMID: 12142537
  48. Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae.
    Cold Spring Harb Symp Quant Biol. 1993;58:415-23 PMID: 7956055
  49. Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint.
    Genes Dev. 2005 May 1;19(9):1040-52 PMID: 15833913
  50. Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress.
    Genes Dev. 2007 Dec 15;21(24):3331-41 PMID: 18079179
  51. A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication.
    Nature. 1998 Oct 8;395(6702):615-8 PMID: 9783589
  52. Characterization of the activation domain of the Rad53 checkpoint kinase.
    Cell Cycle. 2008 Feb 15;7(4):493-9 PMID: 18287812
  53. A replication map of a 61-kb circular derivative of Saccharomyces cerevisiae chromosome III.
    Mol Biol Cell. 1992 Sep;3(9):999-1013 PMID: 1330093
  54. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories.
    Cell. 2006 Jun 30;125(7):1297-308 PMID: 16814716
  55. A novel mre11 mutation impairs processing of double-strand breaks of DNA during both mitosis and meiosis.
    Mol Cell Biol. 1998 Jan;18(1):260-8 PMID: 9418873
  56. ATM regulates ATR chromatin loading in response to DNA double-strand breaks.
    J Exp Med. 2006 Feb 20;203(2):297-303 PMID: 16461339
  57. Branch migrating sister chromatid junctions form at replication origins through Rad51/Rad52-independent mechanisms.
    Mol Cell. 2003 Dec;12(6):1499-510 PMID: 14690603
  58. Initiation at closely spaced replication origins in a yeast chromosome.
    Science. 1993 Dec 10;262(5140):1728-31 PMID: 8259517
  59. The stability of nucleosomes at the replication fork.
    J Mol Biol. 1996 May 3;258(2):224-39 PMID: 8627621
  60. The DNA damage response during DNA replication.
    Curr Opin Cell Biol. 2005 Dec;17(6):568-75 PMID: 16226452
  61. Completion of replication map of Saccharomyces cerevisiae chromosome III.
    Mol Biol Cell. 2001 Nov;12(11):3317-27 PMID: 11694569
  62. Break dosage, cell cycle stage and DNA replication influence DNA double strand break response.
    EMBO J. 2008 Jul 9;27(13):1875-85 PMID: 18511906
  63. Minichromosome maintenance proteins are direct targets of the ATM and ATR checkpoint kinases.
    Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10078-83 PMID: 15210935
  64. The Drosophila Mre11/Rad50 complex is required to prevent both telomeric fusion and chromosome breakage.
    Curr Biol. 2004 Aug 10;14(15):1360-6 PMID: 15296753
  65. The yeast CDK inhibitor Sic1 prevents genomic instability by promoting replication origin licensing in late G(1).
    Mol Cell. 2002 May;9(5):1067-78 PMID: 12049742
  66. Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand annealing mode of DNA repair in budding yeast.
    Mol Cell Biol. 2007 Sep;27(18):6433-45 PMID: 17636031
  67. Exonuclease activity is required for sequence addition and Cdc13p loading at a de novo telomere.
    Curr Biol. 2001 Sep 4;11(17):1336-40 PMID: 11553326
  68. Histone acetylation regulates the time of replication origin firing.
    Mol Cell. 2002 Nov;10(5):1223-33 PMID: 12453428
  69. An oncogene-induced DNA damage model for cancer development.
    Science. 2008 Mar 7;319(5868):1352-5 PMID: 18323444
  70. Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template.
    Biochem Cell Biol. 2007 Aug;85(4):509-20 PMID: 17713585
  71. Transpositions and translocations induced by site-specific double-strand breaks in budding yeast.
    DNA Repair (Amst). 2006 Sep 8;5(9-10):998-1009 PMID: 16807137
  72. Arrest, adaptation, and recovery following a chromosome double-strand break in Saccharomyces cerevisiae.
    Cold Spring Harb Symp Quant Biol. 2000;65:303-14 PMID: 12760044
  73. Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system.
    Nucleic Acids Res. 2005 Dec 06;33(21):6931-41 PMID: 16332696
  74. Endogenous gamma-H2AX-ATM-Chk2 checkpoint activation in Bloom's syndrome helicase deficient cells is related to DNA replication arrested forks.
    Mol Cancer Res. 2007 Jul;5(7):713-24 PMID: 17634426
  75. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis.
    Methods Enzymol. 1995;262:613-27 PMID: 8594382
  76. Early replication of short telomeres in budding yeast.
    Cell. 2007 Mar 23;128(6):1051-62 PMID: 17382879
  77. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1.
    Nature. 2004 Oct 21;431(7011):1011-7 PMID: 15496928
  78. Independent positioning and action of Escherichia coli replisomes in live cells.
    Cell. 2008 Apr 4;133(1):90-102 PMID: 18394992
  79. Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints.
    Nature. 2006 Nov 30;444(7119):633-7 PMID: 17136093
  80. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.
    Yeast. 1999 Oct;15(14):1541-53 PMID: 10514571
  81. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends.
    Cell. 2008 Sep 19;134(6):981-94 PMID: 18805091
  82. Intermediates of recombination during mating type switching in Saccharomyces cerevisiae.
    EMBO J. 1990 Mar;9(3):663-73 PMID: 2178924
  83. Mating-type gene switching in Saccharomyces cerevisiae.
    Annu Rev Genet. 1998;32:561-99 PMID: 9928492
  84. Regulation of DNA-replication origins during cell-cycle progression.
    Nature. 1998 Oct 8;395(6702):618-21 PMID: 9783590
  85. Saccharomyces cerevisiae ATM orthologue suppresses break-induced chromosome translocations.
    Nature. 2008 Jul 24;454(7203):543-6 PMID: 18650924
  86. Functions of the DNA damage response pathway target Ho endonuclease of yeast for degradation via the ubiquitin-26S proteasome system.
    Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10077-82 PMID: 10963670
  87. ATM-related Tel1 associates with double-strand breaks through an Xrs2-dependent mechanism.
    Genes Dev. 2003 Aug 15;17(16):1957-62 PMID: 12923051
  88. A DNA damage checkpoint response in telomere-initiated senescence.
    Nature. 2003 Nov 13;426(6963):194-8 PMID: 14608368
  89. Regulation of Saccharomyces Rad53 checkpoint kinase during adaptation from DNA damage-induced G2/M arrest.
    Mol Cell. 2001 Feb;7(2):293-300 PMID: 11239458
Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2009.02.016
Published
2009-04-17
Epub
2009-00-09
Pages
247-58
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC2789576
Subset
IM
Grants
NIGMS NIH HHS · R01 GM076020 · United States
NIGMS NIH HHS · GM61766 · United States
NIGMS NIH HHS · R01 GM020056-34 · United States
NIGMS NIH HHS · GM20056 · United States
NIGMS NIH HHS · R01 GM061766-09 · United States
NIGMS NIH HHS · R01 GM076020-04 · United States
NIGMS NIH HHS · R01 GM061766 · United States
NIGMS NIH HHS · R37 GM020056 · United States
NIGMS NIH HHS · R01 GM020056 · United States
NIGMS NIH HHS · R01 GM061766-08 · United States
Telethon · GGP08066 · Italy
Corrections
CommentIn
PMID: 19379688
External Links
PubMed source DOI: 10.1016/j.cell.2009.02.016 PMC Full Text View journal details
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