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Detecting ATM-Dependent Chromatin Modification in DNA Damage Response

  • Protocol
Chromatin Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1288))

Abstract

Loss of function or mutation of the ataxia–telangiectasia mutated gene product (ATM) results in inherited genetic disorders characterized by neurodegeneration, immunodeficiency, and cancer. Ataxia-telangiectasia mutated (ATM) gene product belongs to the PI3K-like protein kinase (PIKKs) family and is functionally implicated in mitogenic signal transduction, chromosome condensation, meiotic recombination, cell-cycle control, and telomere maintenance. The ATM protein kinase is primarily activated in response to DNA double strand breaks (DSBs), the most deleterious form of DNA damage produced by ionizing radiation (IR) or radiomimetic drugs. It is detected at DNA damage sites, where ATM autophosphorylation causes dissociation of the inactive homodimeric form to the activated monomeric form. Interestingly, heat shock can activate ATM independent of the presence of DNA strand breaks. ATM is an integral part of the sensory machinery that detects DSBs during meiosis, mitosis, or DNA breaks mediated by free radicals. These DNA lesions can trigger higher order chromatin reorganization fuelled by posttranslational modifications of histones and histone binding proteins. Our group, and others, have shown that ATM activation is tightly regulated by chromatin modifications. This review summarizes the multiple approaches used to discern the role of ATM and other associated proteins in chromatin modification in response to DNA damage.

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References

  1. Scott SP, Pandita TK (2006) The cellular control of DNA double-strand breaks. J Cell Biochem 99(6):1463–1475

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Richardson C, Horikoshi N, Pandita TK (2004) The role of the DNA double-strand break response network in meiosis. DNA Repair (Amst) 3:1149–1164

    Article  CAS  Google Scholar 

  3. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER III, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y et al (2007) ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316:1160–1166

    Article  CAS  PubMed  Google Scholar 

  4. Pandita TK (2003) A multifaceted role for ATM in genome maintenance. Expert Rev Mol Med 5:1–21

    Article  PubMed  Google Scholar 

  5. Pandita TK (2002) ATM function and telomere stability. Oncogene 21:611–618

    Article  CAS  PubMed  Google Scholar 

  6. Pandita TK, Pathak S, Geard CR (1995) Chromosome end associations, telomeres and telomerase activity in ataxia telangiectasia cells. Cytogenet Cell Genet 71:86–93

    Article  CAS  PubMed  Google Scholar 

  7. Wood LD, Halvorsen TL, Dhar S, Baur JA, Pandita RK, Wright WE, Hande MP, Calaf G, Hei TK, Levine F et al (2001) Characterization of ataxia telangiectasia fibroblasts with extended life-span through telomerase expression. Oncogene 20:278–288

    Article  CAS  PubMed  Google Scholar 

  8. Pandita TK, Hittelman WN (1992) Initial chromosome damage but not DNA damage is greater in ataxia telangiectasia cells. Radiat Res 130:94–103

    Article  CAS  PubMed  Google Scholar 

  9. Pandita TK, Hittelman WN (1992) The contribution of DNA and chromosome repair deficiencies to the radiosensitivity of ataxia-telangiectasia. Radiat Res 131:214–223

    Article  CAS  PubMed  Google Scholar 

  10. Morgan SE, Lovly C, Pandita TK, Shiloh Y, Kastan MB (1997) Fragments of ATM which have dominant-negative or complementing activity. Mol Cell Biol 17:2020–2029

    PubMed Central  CAS  PubMed  Google Scholar 

  11. Hunt CR, Pandita RK, Laszlo A, Higashikubo R, Agarwal M, Kitamura T, Gupta A, Rief N, Horikoshi N, Baskaran R et al (2007) Hyperthermia activates a subset of ataxia-telangiectasia mutated effectors independent of DNA strand breaks and heat shock protein 70 status. Cancer Res 67:3010–3017

    Article  CAS  PubMed  Google Scholar 

  12. Price BD, D’Andrea AD (2013) Chromatin remodeling at DNA double-strand breaks. Cell 152:1344–1354

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Soria G, Polo SE, Almouzni G (2012) Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol Cell 46:722–734

    Article  CAS  PubMed  Google Scholar 

  14. Bakkenist CJ, Kastan MB (2003) DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421:499–506

    Article  CAS  PubMed  Google Scholar 

  15. Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (1998) DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 273:5858–5868

    Article  CAS  PubMed  Google Scholar 

  16. Mahadevaiah SK, Turner JM, Baudat F, Rogakou EP, de Boer P, Blanco-Rodriguez J, Jasin M, Keeney S, Bonner WM, Burgoyne PS (2001) Recombinational DNA double-strand breaks in mice precede synapsis. Nat Genet 27:271–276

    Article  CAS  PubMed  Google Scholar 

  17. Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146:905–916

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Bonner WM, Redon CE, Dickey JS, Nakamura AJ, Sedelnikova OA, Solier S, Pommier Y (2008) GammaH2AX and cancer. Nat Rev Cancer 8:957–967

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Bassing CH, Chua KF, Sekiguchi J, Suh H, Whitlow SR, Fleming JC, Monroe BC, Ciccone DN, Yan C, Vlasakova K et al (2002) Increased ionizing radiation sensitivity and genomic instability in the absence of histone H2AX. Proc Natl Acad Sci U S A 99:8173–8178

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Ciccia A, Elledge SJ (2010) The DNA damage response: making it safe to play with knives. Mol Cell 40:179–204

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Jackson SP, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461:1071–1078

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Hari KL, Santerre A, Sekelsky JJ, McKim KS, Boyd JB, Hawley RS (1995) The mei-41 gene of D. melanogaster is a structural and functional homolog of the human ataxia telangiectasia gene. Cell 82:815–821

    Article  CAS  PubMed  Google Scholar 

  23. Kim ST, Xu B, Kastan MB (2002) Involvement of the cohesin protein, Smc1, in ATM-dependent and independent responses to DNA damage. Genes Dev 16:560–570

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Yazdi PT, Wang Y, Zhao S, Patel N, Lee EY, Qin J (2002) SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint. Genes Dev 16:571–582

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Carson CT, Schwartz RA, Stracker TH, Lilley CE, Lee DV, Weitzman MD (2003) The Mre11 complex is required for ATM activation and the G2/M checkpoint. EMBO J 22:6610–6620

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Karlseder J, Hoke K, Mirzoeva OK, Bakkenist C, Kastan MB, Petrini JH, de Lange T (2004) The telomeric protein TRF2 binds the ATM kinase and can inhibit the ATM-dependent DNA damage response. PLoS Biol 2:E240

    Article  PubMed Central  PubMed  Google Scholar 

  27. Lee JH, Paull TT (2005) ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 308:551–554

    Article  CAS  PubMed  Google Scholar 

  28. Pandita TK, Lieberman HB, Lim DS, Dhar S, Zheng W, Taya Y, Kastan MB (2000) Ionizing radiation activates the ATM kinase throughout the cell cycle. Oncogene 19:1386–1391

    Article  CAS  PubMed  Google Scholar 

  29. Smilenov LB, Dhar S, Pandita TK (1999) Altered telomere nuclear matrix interactions and nucleosomal periodicity in ataxia telangiectasia cells before and after ionizing radiation treatment. Mol Cell Biol 19:6963–6971

    PubMed Central  CAS  PubMed  Google Scholar 

  30. Gupta A, Sharma GG, Young CSH, Agarwal M, Smith ER, Paull TT, Lucchesi JC, Khanna KK, Ludwig T, Pandita TK (2005) Involvement of human MOF in ATM function. Mol Cell Biol 25:5292–5305

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Smith ER, Pannuti A, Gu W, Steurnagel A, Cook RG, Allis CD, Lucchesi JC (2000) The Drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol Cell Biol 20:312–318

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Akhtar A, Becker PB (2000) Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol Cell 5:367–375

    Article  CAS  PubMed  Google Scholar 

  33. Tse C, Sera T, Wolffe AP, Hansen JC (1998) Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 18:4629–4638

    PubMed Central  CAS  PubMed  Google Scholar 

  34. Turner BM, Birley AJ, Lavender J (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in Drosophila polytene nuclei. Cell 69:375–384

    Article  CAS  PubMed  Google Scholar 

  35. Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847

    Article  CAS  PubMed  Google Scholar 

  36. Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, Horikoshi M, Scully R, Qin J, Nakatani Y (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102:463–473

    Article  CAS  PubMed  Google Scholar 

  37. Sun Y, Jiang X, Chen S, Fernandes N, Price BD (2005) A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proc Natl Acad Sci U S A 102:13182–13187

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR III, Abmayr SM, Washburn MP, Workman JL (2004) Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084–2087

    Article  CAS  PubMed  Google Scholar 

  39. Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, Grant PA, Smith MM, Christman MF (2002) Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419:411–415

    Article  CAS  PubMed  Google Scholar 

  40. Tanaka A, Tanizawa H, Sriswasdi S, Iwasaki O, Chatterjee AG, Speicher DW, Levin HL, Noguchi E, Noma K (2012) Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation. Mol Cell 48:532–546

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Chen CC, Carson JJ, Feser J, Tamburini B, Zabaronick S, Linger J, Tyler JK (2008) Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell 134:231–243

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Gupta A, Hunt CR, Chakraborty S, Pandita RK, Yordy J, Ramnarain DB, Horikoshi N, Pandita TK (2014) Role of 53BP1 in the regulation of DNA double-strand break repair pathway choice. Radiat Res 181:1–8

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Gupta A, Hunt CR, Hedge ML, Chakraborty S, Udayakumar D, Horikoshi N, Singh M, Ramnarain DB, Hittelman WN, Namjoshi S et al (2014) MOF phosphorylation by ATM regulates 53BP1-mediated double-strand break repair pathway choice. Cell Rep 8(1):177–189

    Article  CAS  PubMed  Google Scholar 

  44. Horikoshi N, Kumar P, Sharma GG, Chen M, Hunt CR, Westover K, Chowdhury S, Pandita TK (2013) Genome-wide distribution of histone H4 Lysine 16 acetylation sites and their relationship to gene expression. Genome Integr 4:3

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. Kuninger D, Lundblad J, Semirale A, Rotwein P (2007) A non-isotopic in vitro assay for histone acetylation. J Biotechnol 131:253–260

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Errico A, Costanzo V (2010) Differences in the DNA replication of unicellular eukaryotes and metazoans: known unknowns. EMBO Rep 11(4):270–278

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Koren A, Soifer I, Barkai N (2010) MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Res 20(6):781–790

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  49. Burrell RA, McClelland SE, Endesfelder D, Groth P, Weller MC, Shaikh N, Domingo E, Kanu N, Dewhurst SM, Gronroos E et al (2013) Replication stress links structural and numerical cancer chromosomal instability. Nature 494:492–496

    Article  CAS  PubMed  Google Scholar 

  50. Wilsker D, Petermann E, Helleday T, Bunz F (2008) Essential function of Chk1 can be uncoupled from DNA damage checkpoint and replication control. Proc Natl Acad Sci U S A 105:20752–20757

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  51. Saleh-Gohari N, Bryant HE, Schultz N, Parker KM, Cassel TN, Helleday T (2005) Spontaneous homologous recombination is induced by collapsed replication forks that are caused by endogenous DNA single-strand breaks. Mol Cell Biol 25:7158–7169

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Arnaudeau C, Lundin C, Helleday T (2001) DNA double-strand breaks associated with replication forks are predominantly repaired by homologous recombination involving an exchange mechanism in mammalian cells. J Mol Biol 307:1235–1245

    Google Scholar 

  53. Singh M, Hunt CR, Pandita RK, Kumar R, Yang CR, Horikoshi N, Bachoo R, Serag S, Story MD, Shay JW et al (2013) Lamin A/C depletion enhances DNA damage-induced stalled replication fork arrest. Mol Cell Biol 33:1210–1222

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  54. Trenz K, Smith E, Smith S, Costanzo V (2006) ATM and ATR promote Mre11 dependent restart of collapsed replication forks and prevent accumulation of DNA breaks. EMBO J 25:1764–1774

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. Bolderson E, Scorah J, Helleday T, Smythe C, Meuth M (2004) ATM is required for the cellular response to thymidine induced replication fork stress. Hum Mol Genet 13:2937–2945

    Article  CAS  PubMed  Google Scholar 

  56. Pandita TK, Gregoire V, Dhingra K, Hittelman WN (1994) Effect of chromosome size on aberration levels caused by gamma radiation as detected by fluorescence in situ hybridization. Cytogenet Cell Genet 67:94–101

    Article  CAS  PubMed  Google Scholar 

  57. Dhar S, Squire JA, Hande MP, Wellinger RJ, Pandita TK (2000) Inactivation of 14-3-3sigma influences telomere behavior and ionizing radiation-induced chromosomal instability. Mol Cell Biol 20:7764–7772

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Pandita TK (1983) Effect of temperature variation on sister chromatid exchange frequency in cultured human lymphocytes. Hum Genet 63:189–190

    Article  CAS  PubMed  Google Scholar 

  59. Pandita TK (1988) Assessment of the mutagenic potential of a fungicide Bavistin using multiple assays. Mutat Res 204:627–643

    Article  CAS  PubMed  Google Scholar 

  60. Pandita RK, Sharma GG, Laszlo A, Hopkins KM, Davey S, Chakhparonian M, Gupta A, Wellinger RJ, Zhang J, Powell SN et al (2006) Mammalian rad9 plays a role in telomere stability, s- and g2-phase-specific cell survival, and homologous recombinational repair. Mol Cell Biol 26:1850–1864

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  61. Sharma GG, Hwang KK, Pandita RK, Gupta A, Dhar S, Parenteau J, Agarwal M, Worman HJ, Wellinger RJ, Pandita TK (2003) Human heterochromatin protein 1 isoforms HP1(Hsalpha) and HP1(Hsbeta) interfere with hTERT-telomere interactions and correlate with changes in cell growth and response to ionizing radiation. Mol Cell Biol 23:8363–8376

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  62. Bredemeyer AL, Sharma GG, Huang CY, Helmink BA, Walker LM, Khor KC, Nuskey B, Sullivan KE, Pandita TK, Bassing CH et al (2006) ATM stabilizes DNA double-strand-break complexes during V(D)J recombination. Nature 442:466–470

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank the former and current members of the laboratory, who have carried out the work presented in this manuscript. We thank all the colleagues around the world whose scientific contributions helped to write this article. This work was supported by funds from several NIH grants including CA129537 (TKP) and CA154320 (TKP).

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Authors and Affiliations

  1. Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA

    Durga Udayakumar, Nobuo Horikoshi & Clayton Hunt

  2. Department of Gastroenterology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA

    Lopa Mishra

  3. Department of Radiation Oncology, Houston Methodist Research Institute, 6550 Fannin St, Houston, TX, 77030, USA

    Tej K. Pandita Ph.D.

Authors
  1. Durga Udayakumar
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  2. Nobuo Horikoshi
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  3. Lopa Mishra
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  4. Clayton Hunt
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  5. Tej K. Pandita Ph.D.
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Corresponding author

Correspondence to Tej K. Pandita Ph.D. .

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Editors and Affiliations

  1. H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA

    Srikumar P. Chellappan

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Udayakumar, D., Horikoshi, N., Mishra, L., Hunt, C., Pandita, T.K. (2015). Detecting ATM-Dependent Chromatin Modification in DNA Damage Response. In: Chellappan, S. (eds) Chromatin Protocols. Methods in Molecular Biology, vol 1288. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2474-5_18

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  • DOI: https://doi.org/10.1007/978-1-4939-2474-5_18

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2473-8

  • Online ISBN: 978-1-4939-2474-5

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