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PMID: 19277046 Published · ppublish English Journal Article Research Support, N.I.H., Intramural Review

The emerging role of nuclear architecture in DNA repair and genome maintenance.

Nature reviews. Molecular cell biology ·Vol. 10 ·No. 4 ·2009-04-00 ·Pages 243-54

Misteli T, Soutoglou E

Abstract

DNA repair and maintenance of genome stability are crucial to cellular and organismal function, and defects in these processes have been implicated in cancer and ageing. Detailed molecular, biochemical and genetic analyses have outlined the molecular framework involved in cellular DNA-repair pathways, but recent cell-biological approaches have revealed important roles for the spatial and temporal organization of the DNA-repair machinery during the recognition of DNA lesions and the assembly of repair complexes. It has also become clear that local higher-order chromatin structure, chromatin dynamics and non-random global genome organization are key factors in genome maintenance. These cell-biological features of DNA repair illustrate an emerging role for nuclear architecture in multiple aspects of genome maintenance.

MeSH Terms
Animals Cell Nucleus/genetics Chromatin/metabolism DNA Damage DNA Repair Genome Humans Models, Biological
Chemicals
Chromatin
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Misteli Tom
National Cancer Institute, NIH, Bethesda, Maryland 20892, USA. [email protected]
Soutoglou Evi
References (124)
124 references, click to expand
  1. DNA double-strand break repair: all's well that ends well.
    Annu Rev Genet. 2006;40:363-83 PMID: 16895466
  2. Spatial genome organization in the formation of chromosomal translocations.
    Semin Cancer Biol. 2007 Feb;17(1):80-90 PMID: 17137790
  3. Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair.
    Genes Dev. 2005 Jul 15;19(14):1656-61 PMID: 16024655
  4. Recruitment of the type B histone acetyltransferase Hat1p to chromatin is linked to DNA double-strand breaks.
    Mol Cell Biol. 2006 May;26(9):3649-58 PMID: 16612003
  5. Quality control of DNA break metabolism: in the 'end', it's a good thing.
    EMBO J. 2008 Feb 20;27(4):581-8 PMID: 18285819
  6. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage.
    Genes Dev. 2006 Sep 1;20(17):2437-49 PMID: 16951256
  7. Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair.
    Mol Cell Biol. 2005 Jun;25(12):4903-13 PMID: 15923609
  8. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions.
    Science. 2004 Dec 17;306(5704):2084-7 PMID: 15528408
  9. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response.
    Nature. 2005 Jul 14;436(7048):294-8 PMID: 16015338
  10. Mre11 assembles linear DNA fragments into DNA damage signaling complexes.
    PLoS Biol. 2004 May;2(5):E110 PMID: 15138496
  11. Chromatin remodeling in DNA double-strand break repair.
    Curr Opin Genet Dev. 2007 Apr;17(2):126-31 PMID: 17320375
  12. The RCAF complex mediates chromatin assembly during DNA replication and repair.
    Nature. 1999 Dec 2;402(6761):555-60 PMID: 10591219
  13. H2AX haploinsufficiency modifies genomic stability and tumor susceptibility.
    Cell. 2003 Aug 8;114(3):371-383 PMID: 12914701
  14. DNA damage-induced G2-M checkpoint activation by histone H2AX and 53BP1.
    Nat Cell Biol. 2002 Dec;4(12):993-7 PMID: 12447390
  15. A role for Saccharomyces cerevisiae histone H2A in DNA repair.
    Nature. 2000 Dec 21-28;408(6815):1001-4 PMID: 11140636
  16. ATM activation and signaling under hypoxic conditions.
    Mol Cell Biol. 2009 Jan;29(2):526-37 PMID: 18981219
  17. Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response.
    Science. 2007 May 25;316(5828):1194-8 PMID: 17525340
  18. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin.
    Mol Cell. 2008 Jul 25;31(2):167-77 PMID: 18657500
  19. A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
    Nature. 2006 Jan 26;439(7075):497-501 PMID: 16299494
  20. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer.
    Nat Genet. 2004 Apr;36(4):331-4 PMID: 15054488
  21. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
    Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13513-8 PMID: 15353583
  22. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.
    Cell. 2004 Dec 17;119(6):767-75 PMID: 15607974
  23. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin.
    PLoS Biol. 2004 May;2(5):E131 PMID: 15045029
  24. SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging.
    Cell. 2008 Nov 28;135(5):907-18 PMID: 19041753
  25. Involvement of human MOF in ATM function.
    Mol Cell Biol. 2005 Jun;25(12):5292-305 PMID: 15923642
  26. Tissue-specific spatial organization of genomes.
    Genome Biol. 2004;5(7):R44 PMID: 15239829
  27. H2AX is required for recombination between immunoglobulin switch regions but not for intra-switch region recombination or somatic hypermutation.
    J Exp Med. 2003 Jun 16;197(12):1767-78 PMID: 12810694
  28. Phosphorylation of histone H2B at DNA double-strand breaks.
    J Exp Med. 2004 Jun 21;199(12):1671-7 PMID: 15197225
  29. Cell biology: chromosome territories.
    Nature. 2007 Jan 25;445(7126):379-781 PMID: 17251970
  30. Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability.
    J Biol Chem. 2008 Jul 11;283(28):19478-88 PMID: 18480059
  31. Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9.
    Mol Cell Biol. 2005 Oct;25(19):8430-43 PMID: 16166626
  32. Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair.
    Nat Cell Biol. 2007 Jun;9(6):683-90 PMID: 17486112
  33. Phospho-dependent interactions between NBS1 and MDC1 mediate chromatin retention of the MRN complex at sites of DNA damage.
    EMBO Rep. 2008 Aug;9(8):795-801 PMID: 18583988
  34. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.
    Mol Cell. 2004 Dec 22;16(6):979-90 PMID: 15610740
  35. ATR signaling can drive cells into senescence in the absence of DNA breaks.
    Genes Dev. 2008 Feb 1;22(3):297-302 PMID: 18245444
  36. The Mre11/Rad50/Nbs1 complex and its role as a DNA double-strand break sensor for ATM.
    Cell Cycle. 2005 Jun;4(6):737-40 PMID: 15908798
  37. RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites.
    Science. 2007 May 25;316(5828):1198-202 PMID: 17525341
  38. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase.
    Science. 2008 Oct 24;322(5901):597-602 PMID: 18948542
  39. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.
    Cell. 2006 Dec 29;127(7):1361-73 PMID: 17190600
  40. RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly.
    Cell. 2007 Nov 30;131(5):901-14 PMID: 18001825
  41. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex.
    Science. 2004 Jan 16;303(5656):343-8 PMID: 14645854
  42. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks.
    J Cell Biol. 2006 Mar 13;172(6):823-34 PMID: 16520385
  43. Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage.
    EMBO J. 2002 Apr 15;21(8):2030-7 PMID: 11953322
  44. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation.
    Nature. 2003 Jan 30;421(6922):499-506 PMID: 12556884
  45. Abnormal rearrangement within the alpha/delta T-cell receptor locus in lymphomas from Atm-deficient mice.
    Blood. 2000 Sep 1;96(5):1940-6 PMID: 10961898
  46. Histone H2AX phosphorylation is dispensable for the initial recognition of DNA breaks.
    Nat Cell Biol. 2003 Jul;5(7):675-9 PMID: 12792649
  47. In situ visualization of DNA double-strand break repair in human fibroblasts.
    Science. 1998 Apr 24;280(5363):590-2 PMID: 9554850
  48. The nuclear topography of ABL, BCR, PML, and RARalpha genes: evidence for gene proximity in specific phases of the cell cycle and stages of hematopoietic differentiation.
    Blood. 1999 Feb 15;93(4):1197-207 PMID: 9949162
  49. DNA lesions and DNA damage response: even long lasting relationships need a "break".
    Cell Cycle. 2008 Dec;7(23):3653-8 PMID: 19029795
  50. Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals.
    J Cell Biol. 2007 Jul 16;178(2):209-18 PMID: 17635934
  51. The histone methyltransferase SET8 is required for S-phase progression.
    J Cell Biol. 2007 Dec 31;179(7):1337-45 PMID: 18166648
  52. Cell cycle-regulated centers of DNA double-strand break repair.
    Cell Cycle. 2003 Sep-Oct;2(5):479-83 PMID: 12963848
  53. gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair.
    Mol Cell. 2005 Dec 9;20(5):801-9 PMID: 16310392
  54. Tumor formation via loss of a molecular motor protein.
    Curr Biol. 2006 Aug 8;16(15):1559-64 PMID: 16890532
  55. Mammalian cell cycle checkpoints: signalling pathways and their organization in space and time.
    DNA Repair (Amst). 2004 Aug-Sep;3(8-9):997-1007 PMID: 15279786
  56. Imaging of protein movement induced by chromosomal breakage: tiny 'local' lesions pose great 'global' challenges.
    Chromosoma. 2005 Aug;114(3):146-54 PMID: 15988581
  57. H2B (Ser10) phosphorylation is induced during apoptosis and meiosis in S. cerevisiae.
    Cell Cycle. 2005 Jun;4(6):780-3 PMID: 15970663
  58. Genomic instability in mice lacking histone H2AX.
    Science. 2002 May 3;296(5569):922-7 PMID: 11934988
  59. New histone incorporation marks sites of UV repair in human cells.
    Cell. 2006 Nov 3;127(3):481-93 PMID: 17081972
  60. Histone H2AX: a dosage-dependent suppressor of oncogenic translocations and tumors.
    Cell. 2003 Aug 8;114(3):359-70 PMID: 12914700
  61. Schizosaccharomyces pombe Hst4 functions in DNA damage response by regulating histone H3 K56 acetylation.
    Eukaryot Cell. 2008 May;7(5):800-13 PMID: 18344406
  62. Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair.
    Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1644-9 PMID: 14711989
  63. Positional stability of single double-strand breaks in mammalian cells.
    Nat Cell Biol. 2007 Jun;9(6):675-82 PMID: 17486118
  64. MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks.
    Cell. 2005 Dec 29;123(7):1213-26 PMID: 16377563
  65. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway.
    Nat Cell Biol. 2006 Aug;8(8):870-6 PMID: 16862143
  66. Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae.
    Nature. 2005 Nov 17;438(7066):379-83 PMID: 16292314
  67. Chromatin dynamics and the preservation of genetic information.
    Nature. 2007 Jun 21;447(7147):951-8 PMID: 17581578
  68. ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex.
    Science. 2005 Apr 22;308(5721):551-4 PMID: 15790808
  69. Mammalian SWI/SNF complexes facilitate DNA double-strand break repair by promoting gamma-H2AX induction.
    EMBO J. 2006 Sep 6;25(17):3986-97 PMID: 16932743
  70. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase.
    Science. 2007 Dec 7;318(5856):1637-40 PMID: 18006705
  71. Mobility and immobility of chromatin in transcription and genome stability.
    Curr Opin Genet Dev. 2007 Oct;17(5):435-42 PMID: 17905579
  72. The DNA damage response: putting checkpoints in perspective.
    Nature. 2000 Nov 23;408(6811):433-9 PMID: 11100718
  73. MDC1 regulates intra-S-phase checkpoint by targeting NBS1 to DNA double-strand breaks.
    Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11200-5 PMID: 18678890
  74. Constitutive phosphorylation of MDC1 physically links the MRE11-RAD50-NBS1 complex to damaged chromatin.
    J Cell Biol. 2008 Apr 21;181(2):227-40 PMID: 18411308
  75. The impact of a negligent G2/M checkpoint on genomic instability and cancer induction.
    Nat Rev Cancer. 2007 Nov;7(11):861-9 PMID: 17943134
  76. Control of sister chromatid recombination by histone H2AX.
    Mol Cell. 2004 Dec 22;16(6):1017-25 PMID: 15610743
  77. The cellular response to DNA double-strand breaks: defining the sensors and mediators.
    Trends Cell Biol. 2003 Sep;13(9):458-62 PMID: 12946624
  78. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response.
    Nature. 2008 May 29;453(7195):682-6 PMID: 18438399
  79. Global transcription in pluripotent embryonic stem cells.
    Cell Stem Cell. 2008 May 8;2(5):437-47 PMID: 18462694
  80. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair.
    Cell. 2004 Dec 17;119(6):777-88 PMID: 15607975
  81. Phosphorylation of SDT repeats in the MDC1 N terminus triggers retention of NBS1 at the DNA damage-modified chromatin.
    J Cell Biol. 2008 Apr 21;181(2):213-26 PMID: 18411307
  82. A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication.
    Mol Cell. 2008 Jul 11;31(1):33-46 PMID: 18614045
  83. A unified view of the DNA-damage checkpoint.
    Curr Opin Cell Biol. 2002 Apr;14(2):237-45 PMID: 11891124
  84. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins.
    Cell. 2007 Nov 30;131(5):887-900 PMID: 18001824
  85. FACT-mediated exchange of histone variant H2AX regulated by phosphorylation of H2AX and ADP-ribosylation of Spt16.
    Mol Cell. 2008 Apr 11;30(1):86-97 PMID: 18406329
  86. Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response.
    Science. 2007 May 25;316(5828):1202-5 PMID: 17525342
  87. Global chromatin compaction limits the strength of the DNA damage response.
    J Cell Biol. 2007 Sep 24;178(7):1101-8 PMID: 17893239
  88. Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair.
    Cell. 2008 Jul 25;134(2):231-43 PMID: 18662539
  89. Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks.
    J Cell Biol. 2006 Apr 24;173(2):195-206 PMID: 16618811
  90. Modulation of RNA polymerase assembly dynamics in transcriptional regulation.
    Mol Cell. 2008 May 23;30(4):486-97 PMID: 18498750
  91. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins.
    Cell. 2004 Sep 17;118(6):699-713 PMID: 15369670
  92. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks.
    Nature. 2004 Nov 18;432(7015):406-11 PMID: 15525939
  93. Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island.
    PLoS Genet. 2008 Aug 15;4(8):e1000155 PMID: 18704159
  94. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions.
    Nat Rev Genet. 2007 Feb;8(2):104-15 PMID: 17230197
  95. DNA damage checkpoint and repair centers.
    Curr Opin Cell Biol. 2004 Jun;16(3):328-34 PMID: 15145359
  96. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56.
    Science. 2007 Feb 2;315(5812):649-52 PMID: 17272722
  97. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks.
    Nat Cell Biol. 2006 Jan;8(1):91-9 PMID: 16341205
  98. Conservation of relative chromosome positioning in normal and cancer cells.
    Curr Biol. 2002 Oct 1;12(19):1692-7 PMID: 12361574
  99. 53BP1 facilitates long-range DNA end-joining during V(D)J recombination.
    Nature. 2008 Nov 27;456(7221):529-33 PMID: 18931658
  100. DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics.
    Mol Cell Biol. 2007 Oct;27(20):7028-40 PMID: 17709392
  101. 53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility.
    Nature. 2008 Nov 27;456(7221):524-8 PMID: 18931659
  102. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre.
    Nat Cell Biol. 2003 Jun;5(6):572-7 PMID: 12766777
  103. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage.
    Cell. 2004 Nov 24;119(5):603-14 PMID: 15550243
  104. Human Rvb1/Tip49 is required for the histone acetyltransferase activity of Tip60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage.
    Mol Cell Biol. 2008 Apr;28(8):2690-700 PMID: 18285460
  105. Dynamics of DNA double-strand breaks revealed by clustering of damaged chromosome domains.
    Science. 2004 Jan 2;303(5654):92-5 PMID: 14704429
  106. The histone chaperone Asf1 at the crossroads of chromatin and DNA checkpoint pathways.
    Chromosoma. 2007 Apr;116(2):79-93 PMID: 17180700
  107. DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain.
    Mol Cell. 2004 Dec 22;16(6):991-1002 PMID: 15610741
  108. Mathematical modeling of nucleotide excision repair reveals efficiency of sequential assembly strategies.
    Mol Cell. 2005 Sep 2;19(5):679-90 PMID: 16137623
  109. Activation of the cellular DNA damage response in the absence of DNA lesions.
    Science. 2008 Jun 13;320(5882):1507-10 PMID: 18483401
  110. Colocalization of sensors is sufficient to activate the DNA damage checkpoint in the absence of damage.
    Mol Cell. 2008 May 9;30(3):267-76 PMID: 18471973
  111. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair.
    Nature. 2002 Sep 26;419(6905):411-5 PMID: 12353039
  112. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations.
    PLoS Biol. 2006 May;4(5):e138 PMID: 16623600
  113. Spatial proximity of translocation-prone gene loci in human lymphomas.
    Nat Genet. 2003 Jul;34(3):287-91 PMID: 12808455
  114. Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair.
    Mol Cell Biol. 2002 Dec;22(23):8353-65 PMID: 12417736
  115. Activation of ATM depends on chromatin interactions occurring before induction of DNA damage.
    Nat Cell Biol. 2009 Jan;11(1):92-6 PMID: 19079244
  116. Histone H4 and the maintenance of genome integrity.
    Genes Dev. 1995 Jul 15;9(14):1716-27 PMID: 7622036
  117. Beyond the sequence: cellular organization of genome function.
    Cell. 2007 Feb 23;128(4):787-800 PMID: 17320514
  118. Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway.
    EMBO Rep. 2002 Apr;3(4):329-34 PMID: 11897662
  119. Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks.
    Genes Dev. 2006 Jun 15;20(12):1583-96 PMID: 16778077
  120. Megabase chromatin domains involved in DNA double-strand breaks in vivo.
    J Cell Biol. 1999 Sep 6;146(5):905-16 PMID: 10477747
  121. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139.
    J Biol Chem. 1998 Mar 6;273(10):5858-68 PMID: 9488723
  122. Orchestration of chromatin-based processes: mind the TRRAP.
    Oncogene. 2007 Aug 13;26(37):5358-72 PMID: 17694078
  123. Mdc1 couples DNA double-strand break recognition by Nbs1 with its H2AX-dependent chromatin retention.
    EMBO J. 2004 Jul 7;23(13):2674-83 PMID: 15201865
  124. Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks.
    EMBO J. 2007 Sep 19;26(18):4113-25 PMID: 17762868
Article Info
Journal
Nature reviews. Molecular cell biology
Abbr.
Nat Rev Mol Cell Biol
ISSN
1471-0080
Published
2009-04-00
Epub
2009-00-11
Pages
243-54
Language
English
Region
England
NLM ID
100962782
PMCID
PMC3478884
Subset
IM
Grants
Intramural NIH HHS · Z01 BC010309-09 · United States
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