Dependence of radiation-induced H2AX phosphorylation on histone methylation: Evidence from the chromatin immunoprecipitation assay

References

• Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.
   PubMed Web of Science ®Google Scholar
• Bekker-Jensen S, Lukas C, Kitagawa R, Melander F, Kastan MB, Bartek J, Lukas J. 2006. Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks. J Cell Biol 173:195–206.
   PubMed Web of Science ®Google Scholar
• Bewersdorf J, Bennett BT, Knight KL. 2006. H2AX chromatin structures and their response to DNA damage revealed by 4Pi microscopy. Proc Natl Acad Sci USA 103:18137–18142.
   PubMed Web of Science ®Google Scholar
• Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH. 2011. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144:732–744.
   PubMed Web of Science ®Google Scholar
• Costes SV, Chiolo I, Pluth JM, Barcellos-Hoff MH, Jakob B. 2010. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization. Mutat Res 704:78–87.
   PubMed Web of Science ®Google Scholar
• Cowell IG, Sunter NJ, Singh PB, Austin CA, Durkacz BW, Tilby MJ. 2007. gammaH2AX foci form preferentially in euchromatin after ionising-radiation. PLoS One 2:e1057.
   PubMed Web of Science ®Google Scholar
• Davídková M, Stísová V, Goffinont S, Gillard N, Castaing B, Spotheim-Maurizot M. 2006. Modification of DNA radiolysis by DNA-binding proteins: Structural aspects. Radiat Prot Dosimetry 122:100–105.
   PubMedGoogle Scholar
• Dietzel S, Zolghadr K, Hepperger C, Belmont AS. 2004. Differential large-scale chromatin compaction and intranuclear positioning of transcribed versus non-transcribed transgene arrays containing beta-globin regulatory sequences. J Cell Sci 117:4603–4614.
   PubMedGoogle Scholar
• Dixon WJ, Mood AM. 1946. The statistical sign test. J Am Stat Assoc 41:557–566.
   PubMed Web of Science ®Google Scholar
• Eissenberg JC, Reuter G. 2009. Cellular mechanism for targeting heterochromatin formation in Drosophila. Int Rev Cell Mol Biol 273:1–47.
   PubMedGoogle Scholar
• Elia MC, Bradley MO. 1992. Influence of chromatin structure on the induction of DNA double strand breaks by ionizing radiation. Cancer Res 52:1580–1586.
   PubMed Web of Science ®Google Scholar
• Falk M, Lukasova E, Gabrielova B, Ondrej V, Kozubek S. 2007. Chromatin dynamics during DSB repair. Biochim Biophys Acta 1773:1534–1545.
   PubMed Web of Science ®Google Scholar
• Falk M, Lukásová E, Kozubek S. 2008. Chromatin structure influences the sensitivity of DNA to gamma-radiation. Biochim Biophys Acta 1783:2398–2414.
   PubMed Web of Science ®Google Scholar
• Gontijo AM, Green CM, Almouzni G. 2003. Repairing DNA damage in chromatin. Biochimie 85:1133–1147.
   PubMedGoogle Scholar
• Goodarzi AA, Noon AT, Deckbar D, Ziv Y, Shiloh Y, Löbrich M, Jeggo PA. 2008. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 31:167–177.
   PubMed Web of Science ®Google Scholar
• Hublitz P, Albert M, Peters AH. 2009. Mechanisms of transcriptional repression by histone methylation. Int J Dev Biol 53:335–354.
   PubMed Web of Science ®Google Scholar
• Iacovoni JS, Caron P, Lassadi I, Nicolas E, Massip L, Trouche D, Legube G. 2010. High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome. EMBO J 29:1446–1457.
   PubMed Web of Science ®Google Scholar
• Jakob B, Splinter J, Conrad S, Voss KO, Zink D, Durante M, Löbrich M, Taucher-Scholz G. 2011. DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin. Nucleic Acids Res 39:6489–6499.
   PubMed Web of Science ®Google Scholar
• Karagiannis TC, Harikrishnan KN, El-Osta A. 2007. Disparity of histone deacetylase inhibition on repair of radiation-induced DNA damage on euchromatin and constitutive heterochromatin compartments. Oncogene 26:3963–3971.
   PubMed Web of Science ®Google Scholar
• Kim JA, Kruhlak M, Dotiwala F, Nussenzweig A, Haber JE. 2007. Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals. J Cell Biol 178:209–218.
   PubMed Web of Science ®Google Scholar
• Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Müller WG, McNally JG, Bazett-Jones DP, Nussenzweig A. 2006. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J Cell Biol 172:823–834.
   PubMed Web of Science ®Google Scholar
• Loizou JI, Murr R, Finkbeiner MG, Sawan C, Wang ZQ, Herceg Z. 2006. Epigenetic information in chromatin: The code of entry for DNA repair. Cell Cycle 5:696–701.
   PubMed Web of Science ®Google Scholar
• MacPhail SH, Banáth JP, Yu TY, Chu EH, Lambur H, Olive PL. 2003. Expression of phosphorylated histone H2AX in cultured cell lines following exposure to X-rays. Int J Radiat Biol 79:351–358.
   PubMed Web of Science ®Google Scholar
• Manders EMM, Verbeek FJ, Aten JA. 1993. Measurement of co-localization of object in dual-colour confocal images. J Microscopy 169: 375–382.
   PubMed Web of Science ®Google Scholar
• Meier A, Fiegler H, Muñoz P, Ellis P, Rigler D, Langford C, Blasco MA, Carter N, Jackson SP. 2007. Spreading of mammalian DNA-damage response factors studied by ChIP-chip at damaged telomeres. EMBO J 26:2707–2718.
   PubMed Web of Science ®Google Scholar
• Muñoz DP, Kawahara M, Yannone SM. 2013. An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells. Nucleic Acids Res 41:2894–2906.
   PubMedGoogle Scholar
• Noon AT, Shibata A, Rief N, Löbrich M, Stewart GS, Jeggo PA, Goodarzi AA. 2010. 53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair. Nat Cell Biol 12:177–184.
   PubMed Web of Science ®Google Scholar
• Paull TT, Rogakou EP, Yamazaki V, Kirchgessner CU, Gellert M, Bonner WM. 2000. A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr Biol 10: 886–895.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. 2009. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10:143.
   PubMed Web of Science ®Google Scholar
• Sak A, Stuschke M, Wurm R, Budach V. 2000. Protection of DNA from radiation-induced double-strand breaks: Influence of replication and nuclear proteins. Int J Radiat Biol 76:749–756.
   PubMed Web of Science ®Google Scholar
• SAS Institute Inc. 1989. SAS/STAT user's guide, version 6, 4th ed. Vol.. Cary, NC: SAS Institute Inc. ed. Vol.1/2.
   Google Scholar
• Savic V, Yin B, Maas NL, Bredemeyer AL, Carpenter AC, Helmink BA, Yang-Iott KS, Sleckman BP, Bassing CH. 2009. Formation of dynamic gamma-H2AX domains along broken DNA strands is distinctly regulated by ATM and MDC1 and dependent upon H2AX densities in chromatin. Mol Cell 34:298–310.
   PubMed Web of Science ®Google Scholar
• Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, Haber JE, Lichten M. 2004. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol 14:1703–1711.
   PubMed Web of Science ®Google Scholar
• Spotheim-Maurizot M, Davídková M. 2011. Radiation damage to DNA in DNA-protein complexes. Mutat Res 711:41–48.
   PubMed Web of Science ®Google Scholar
• Xu Y, Ayrapetov MK, Xu C, Gursoy-Yuzugullu O, Hu Y, Price BD. 2012. Histone H2A.Z controls a critical chromatin remodeling step required for DNA double-strand break repair. Mol Cell 48:723–733.
   PubMed Web of Science ®Google Scholar
• Yunis JJ, Yasmineh WG. 1970. Satellite DNA in constitutive heterochromatin of the guinea pig. Science 168:263–265.
   PubMedGoogle Scholar
• Ziv Y, Bielopolski D, Galanty Y, Lukas C, Taya Y, Schultz DC, Lukas J, Bekker-Jensen S, Bartek J, Shiloh Y. 2006. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat Cell Biol 8:870–876.
   PubMed Web of Science ®Google Scholar