Detecting ATM-Dependent Chromatin Modification in DNA Damage and Heat Shock Response

  • Sandeep Misri
  • Shruti Pandita
  • Tej K. Pandita
Part of the Methods in Molecular Biology book series (MIMB, volume 523)


The ataxia telangiectasia-mutated gene product (ATM), whose loss of function is responsible for ataxia telangiectasia (A-T), is a protein kinase that interacts with several substrates and is implicated in mitogenic signal transduction, chromosome condensation, meiotic recombination, cell-cycle control and telomere maintenance (Pandita, Expert Reviews in Molecular Medicine 5:1–21, 2003; Pandita, Oncogene 21:611–618, 2002; Matsuoka et al., Science 316:1160–1166, 2007). The ATM protein kinase is primarily activated in response to DNA double-strand breaks (DSBs) caused by ionizing radiation (IR) or radiomimetic drugs (Pandita et al., Oncogene 19:1386–1391, 2000). ATM is also activated by heat shock, which occurs independent of DNA damage (Hunt et al., Can Res 69:3010–3017, 2007). ATM is observed at the sites of DNA damage, where it is autophosphorylated and is dissociated from its non-active dimeric form to the active monomeric form (Bakkenist and Kastan, Nature 421:499–506, 2003). The ATM protein appears to be a part of the sensory machinery that detects DSBs during meiosis or mitosis, or breaks consequent to the damage by free radicals. Recent studies support the argument that ATM activation is regulated by chromatin modifications (Gupta, Mol Cell Biol 25:5292–5305, 2005). This review summarizes the multiple approaches used to discern the role of ATM in chromatin modification in response to DNA damage as well as heat shock.

Key words

Ataxia telangiectasia telomerase DNA double-stranded breaks chromatin modification heat shock 



The authors thank the former and current members of the laboratory, who have carried the work presented in this manuscript. This work was supported by funds from NIH (CA10445, CA123232)


  1. 1.
    Scott, S.P., and Pandita, T.K. 2006. The cellular control of DNA double-strand breaks. J Cell Biochem 99(6):1463–1475. Google Scholar
  2. 2.
    Richardson, C., Horikoshi, N., and Pandita, T.K. 2004. The role of the DNA double-strand break response network in meiosis. DNA Repair (Amst) 3:1149–1164.CrossRefGoogle Scholar
  3. 3.
    Pandita, T.K. 2003. A multifaceted role for ATM in genome maintenance. In Expert Reviews in Molecular Medicine 5:1–21.PubMedCrossRefGoogle Scholar
  4. 4.
    Pandita, T.K. 2002. ATM function and telomere stability. Oncogene 21:611–618.PubMedCrossRefGoogle Scholar
  5. 5.
    Pandita, T.K., Pathak, S., and Geard, C.R. 1995. Chromosome end associations, telomeres and telomerase activity in ataxia telangiectasia cells. Cytogenet Cell Genet 71:86–93.PubMedCrossRefGoogle Scholar
  6. 6.
    Wood, L.D., Halvorsen, T.L., Dhar, S., Baur, J.A., Pandita, R.K., Wright, W.E., Hande, M.P., Calaf, G., Hei, T.K., Levine, F., et al. 2001. Characterization of ataxia telangiectasia fibroblasts with extended life-span through telomerase expression. Oncogene 20:278–288.PubMedCrossRefGoogle Scholar
  7. 7.
    Pandita, T.K., and Hittelman, W.N. 1992. Initial chromosome damage but not DNA damage is greater in ataxia telangiectasia cells. Radiat Res 130:94–103.PubMedCrossRefGoogle Scholar
  8. 8.
    Pandita, T.K., and Hittelman, W.N. 1992. The contribution of DNA and chromosome repair deficiencies to the radiosensitivity of ataxia-telangiectasia. Radiat Res 131:214–223.PubMedCrossRefGoogle Scholar
  9. 9.
    Morgan, S.E., Lovly, C., Pandita, T.K., Shiloh, Y., and Kastan, M.B. 1997. Fragments of ATM which have dominant-negative or complementing activity. Mol Cell Biol 17:2020–2029.PubMedGoogle Scholar
  10. 10.
    Hunt, C.R., Pandita, R.K., 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.PubMedCrossRefGoogle Scholar
  11. 11.
    Pandita, T.K., Lieberman, H.B., Lim, D.S., Dhar, S., Zheng, W., Taya, Y., and Kastan, M.B. 2000. Ionizing radiation activates the ATM kinase throughout the cell cycle. Oncogene 19:1386–1391.PubMedCrossRefGoogle Scholar
  12. 12.
    Hari, K.L., Santerre, A., Sekelsky, J.J., McKim, K.S., Boyd, J.B., and Hawley, R.S. 1995. The mei-41 gene of D. melanogaster is a structural and functional homolog of the human ataxia telangiectasia gene. Cell 82:815–821.PubMedCrossRefGoogle Scholar
  13. 13.
    Kim, S.T., Xu, B., and Kastan, M.B. 2002. Involvement of the cohesin protein, Smc1, in Atm-dependent and independent responses to DNA damage. Genes Dev 16:560–570.PubMedCrossRefGoogle Scholar
  14. 14.
    Yazdi, P.T., Wang, Y., Zhao, S., Patel, N., Lee, E.Y., and Qin, J. 2002. SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint. Genes Dev 16:571–582.PubMedCrossRefGoogle Scholar
  15. 15.
    Carson, C.T., Schwartz, R.A., Stracker, T.H., Lilley, C.E., Lee, D.V., and Weitzman, M.D. 2003. The Mre11 complex is required for ATM activation and the G2/M checkpoint. Embo J 22:6610–6620.PubMedCrossRefGoogle Scholar
  16. 16.
    Karlseder, J., Hoke, K., Mirzoeva, O.K., Bakkenist, C., Kastan, M.B., Petrini, J.H., and Lange Td, T. 2004. The Telomeric Protein TRF2 Binds the ATM Kinase and Can Inhibit the ATM-Dependent DNA Damage Response. PLoS Biol 2:E240.PubMedCrossRefGoogle Scholar
  17. 17.
    Lee, J.H., and Paull, T.T. 2005. ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 308:551–554.PubMedCrossRefGoogle Scholar
  18. 18.
    Smilenov, L.B., Dhar, S., and Pandita, T.K. 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.PubMedGoogle Scholar
  19. 19.
    Bakkenist, C.J., and Kastan, M.B. 2003. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421:499–506.PubMedCrossRefGoogle Scholar
  20. 20.
    Gupta, A., Sharma, G.G., Young, C.S.H., Agarwal, M.,Smith, E.R., Paull, T.T., Lucchesi, J.C., Khanna, K.K., Ludwig, T., and Pandita, T.K.,. 2005. Involvement of human MOF in ATM function. Mol Cell Biol 25:5292–5305.PubMedCrossRefGoogle Scholar
  21. 21.
    Mahadevaiah, S.K., Turner, J.M., Baudat, F., Rogakou, E.P., de Boer, P., Blanco-Rodriguez, J., Jasin, M., Keeney, S., Bonner, W.M., and Burgoyne, P.S. 2001. Recombinational DNA double-strand breaks in mice precede synapsis. Nat Genet 27:271–276.PubMedCrossRefGoogle Scholar
  22. 22.
    Rogakou, E.P., Boon, C., Redon, C., and Bonner, W.M. 1999. Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146:905–916.PubMedCrossRefGoogle Scholar
  23. 23.
    Bassing, C.H., Chua, K.F., Sekiguchi, J., Suh, H., Whitlow, S.R., Fleming, J.C., Monroe, B.C., Ciccone, D.N., 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.Google Scholar
  24. 24.
    Smith, E.R., Pannuti, A., Gu, W., Steurnagel, A., Cook, R.G., Allis, C.D., and Lucchesi, J.C. 2000. The drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol Cell Biol 20:312–318.PubMedCrossRefGoogle Scholar
  25. 25.
    Akhtar, A., and Becker, P.B. 2000. Activation of transcription through histone H4 acetylation by MOF, an acetyltransferase essential for dosage compensation in Drosophila. Mol Cell 5:367–375.PubMedCrossRefGoogle Scholar
  26. 26.
    Tse, C., Sera, T., Wolffe, A.P., and Hansen, J.C. 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.PubMedGoogle Scholar
  27. 27.
    Turner, B.M., Birley, A.J., and 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.PubMedCrossRefGoogle Scholar
  28. 28.
    Shogren-Knaak, M., Ishii, H., Sun, J.M., Pazin, M.J., Davie, J.R., and Peterson, C.L. 2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847.PubMedCrossRefGoogle Scholar
  29. 29.
    Ikura, T., Ogryzko, V.V., Grigoriev, M., Groisman, R., Wang, J., Horikoshi, M., Scully, R., Qin, J., and Nakatani, Y. 2000. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102:463–473.PubMedCrossRefGoogle Scholar
  30. 30.
    Sun, Y., Jiang, X., Chen, S., Fernandes, N., and Price, B.D. 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.Google Scholar
  31. 31.
    Kusch, T., Florens, L., Macdonald, W.H., Swanson, S.K., Glaser, R.L., Yates, J.R., 3rd, Abmayr, S.M., Washburn, M.P., and Workman, J.L. 2004. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084–2087.PubMedCrossRefGoogle Scholar
  32. 32.
    Bird, A.W., Yu, D.Y., Pray-Grant, M.G., Qiu, Q., Harmon, K.E., Megee, P.C., Grant, P.A., Smith, M.M., and Christman, M.F. 2002. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419:411–415.PubMedCrossRefGoogle Scholar
  33. 33.
    Pandita, T.K., Gregoire, V., Dhingra, K., and Hittelman, W.N. 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.PubMedCrossRefGoogle Scholar
  34. 34.
    Dhar, S., Squire, J.A., Hande, M.P., Wellinger, R.J., and Pandita, T.K. 2000. Inactivation of 14-3-3 sigma influences telomere behavior and ionizing radiation-induced chromosomal instability. Mol Cell Biol 20:7764–7772.PubMedCrossRefGoogle Scholar
  35. 35.
    Pandita, T.K. 1983. Effect of temperature variation on sister chromatid exchange frequency in cultured human lymphocytes. Hum Genet 63:189–190.PubMedCrossRefGoogle Scholar
  36. 36.
    Pandita, T.K. 1988. Assessment of the mutagenic potential of a fungicide Bavistin using multiple assays. Mutat Res 204:627–643.PubMedCrossRefGoogle Scholar
  37. 37.
    Pandita, R.K., Sharma, G.G., Laszlo, A., Hopkins, K.M., Davey, S., Chakhparonian, M., Gupta, A., Wellinger, R.J., Zhang, J., Powell, S.N., 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.PubMedCrossRefGoogle Scholar
  38. 38.
    Sharma, G.G., Hwang, K.K., Pandita, R.K., Gupta, A., Dhar, S., Parenteau, J., Agarwal, M., Worman, H.J., Wellinger, R.J., and Pandita, T.K. 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.PubMedCrossRefGoogle Scholar
  39. 39.
    Bredemeyer, A.L., Sharma, G.G., Huang, C.Y., Helmink, B.A., Walker, L.M., Khor, K.C., Nuskey, B., Sullivan, K.E., Pandita, T.K., Bassing, C.H., et al. 2006. ATM stabilizes DNA double-strand-break complexes during V(D)J recombination. Nature 442:466–470.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Sandeep Misri
    • 1
  • Shruti Pandita
    • 1
  • Tej K. Pandita
    • 2
  1. 1.Washington University School of MedicineSt LouisUSA
  2. 2.Department of Radiation OncologyWashington University School of MedicineSt LouisUSA

Personalised recommendations