Chromatin Remodeling at DNA Double-Strand Breaks

DNA double-strand breaks (DSBs) can arise from multiple sources, including exposure to ionizing radiation. The repair of DSBs involves both posttranslational modification of nucleosomes and concentration of DNA-repair proteins at the site of damage. Consequently, nucleosome packing and chromatin architecture surrounding the DSB may limit the ability of the DNA-damage response to access and repair the break. Here, we review early chromatin-based events that promote the formation of open, relaxed chromatin structures at DSBs and that allow the DNA-repair machinery to access the spatially confined region surrounding the DSB, thereby facilitating mammalian DSB repair. DNA double-strand breaks (DSBs) can arise from multiple sources, including exposure to ionizing radiation. The repair of DSBs involves both posttranslational modification of nucleosomes and concentration of DNA-repair proteins at the site of damage. Consequently, nucleosome packing and chromatin architecture surrounding the DSB may limit the ability of the DNA-damage response to access and repair the break. Here, we review early chromatin-based events that promote the formation of open, relaxed chromatin structures at DSBs and that allow the DNA-repair machinery to access the spatially confined region surrounding the DSB, thereby facilitating mammalian DSB repair. Maintaining the integrity of genetic information is critical both for normal cellular functions and for suppressing mutagenic events that can lead to cancer. Damage to DNA can arise from external sources, such as exposure to ionizing radiation (IR), ultraviolet radiation (UV), or environmental toxins, or from endogenous sources, such as reactive oxygen species or errors during DNA replication. These events can generate a wide range of DNA lesions, including modified bases or sugar residues, the formation of DNA adducts, crosslinking of the DNA strands, and production of single- and double-strand breaks (DSBs). Consequently, cells have evolved at least six different DNA-repair pathways to deal with these distinct types of DNA damage (Kennedy and D'Andrea, 2006Kennedy R.D. D'Andrea A.D. DNA repair pathways in clinical practice: lessons from pediatric cancer susceptibility syndromes.J. Clin. Oncol. 2006; 24: 3799-3808Crossref PubMed Scopus (111) Google Scholar). Among these lesions, DNA DSBs are particularly lethal because they result in physical cleavage of the DNA backbone. DSBs can occur through replication-fork collapse, during the processing of interstrand crosslinks, or following exposure to IR (Ciccia and Elledge, 2010Ciccia A. Elledge S.J. The DNA damage response: making it safe to play with knives.Mol. Cell. 2010; 40: 179-204Abstract Full Text Full Text PDF PubMed Scopus (491) Google Scholar; Jackson and Bartek, 2009Jackson S.P. Bartek J. The DNA-damage response in human biology and disease.Nature. 2009; 461: 1071-1078Crossref PubMed Scopus (682) Google Scholar; Kennedy and D'Andrea, 2006Kennedy R.D. D'Andrea A.D. DNA repair pathways in clinical practice: lessons from pediatric cancer susceptibility syndromes.J. Clin. Oncol. 2006; 24: 3799-3808Crossref PubMed Scopus (111) Google Scholar). Because IR (radiation therapy) is widely used to treat cancer, understanding how cells repair DSBs created by IR, and how this process is altered in tumors, is of high significance. DSB repair takes place within the complex organization of the chromatin, and it is clear from work in many model systems that chromatin structure and nucleosome organization represent a significant barrier to the efficient detection and repair of DSBs. Mammalian cells contain a diverse array of specialized chromatin structures, such as active genes, telomeres, replication forks, intergenic regions, and compact heterochromatin. These structures are distinguished by specific patterns of histone modifications, unique histone variants, arrays of chromatin-binding proteins, and the density of nucleosome packing (de Wit and van Steensel, 2009de Wit E. van Steensel B. Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies.Chromosoma. 2009; 118: 25-36Crossref PubMed Scopus (32) Google Scholar; Grewal and Jia, 2007Grewal S.I. Jia S. Heterochromatin revisited.Nat. Rev. Genet. 2007; 8: 35-46Crossref PubMed Scopus (480) Google Scholar; Peng and Karpen, 2008Peng J.C. Karpen G.H. Epigenetic regulation of heterochromatic DNA stability.Curr. Opin. Genet. Dev. 2008; 18: 204-211Crossref PubMed Scopus (66) Google Scholar). This complexity and diversity in chromatin organization present a series of challenges to the DSB-repair machinery. The impact of chromatin on DNA repair was first described in the "access-repair-restore" model (Smerdon, 1991Smerdon M.J. DNA repair and the role of chromatin structure.Curr. Opin. Cell Biol. 1991; 3: 422-428Crossref PubMed Google Scholar; reviewed in Soria et al., 2012Soria G. Polo S.E. Almouzni G. Prime, repair, restore: the active role of chromatin in the DNA damage response.Mol. Cell. 2012; 46: 722-734Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar). This model proposed the minimal steps needed to reorganize the chromatin and repair DNA damage. Broadly, the DSB-repair machinery must be able to (1) detect DNA damage in different chromatin structures; (2) remodel the local chromatin architecture to provide access to the site of damage; (3) reorganize the nucleosome-DNA template for processing and repair of the damage; and, importantly, (4) restore the local chromatin organization after repair has been completed. Since this model was first put forward in 1991, we now know many of the remodeling factors and histone-modifying enzymes that act to create open chromatin structures and promote DNA repair, as well as factors such as histone chaperones, deacetylases, and phosphatases that reassemble the chromatin after repair is complete. Here, we will focus on the "access" component of the "access-repair-restore" model, reviewing some of the early (seconds–minutes) remodeling events that occur after DNA damage and that are required to create open chromatin structures. Although the "access-repair-restore" model is likely applicable to the repair of all types of DNA damage, we will focus our discussion specifically on the repair of DNA DSBs. In particular, we will examine three broad chromatin-based events that occur during the first seconds-to-minutes after production of DSBs: (1) the formation of open chromatin structures at DSBs through acetylation of histone H4; (2) the importance of kap-1 in promoting chromatin relaxation in heterochromatin; and (3) the rapid polyADP-ribosylation (PARylation) of the chromatin by the polyADP-ribose polymerase (Parp) family, which promotes the transient recruitment of chromatin-remodeling enzymes and heterochromatin factors to the DSB. The mammalian DSB-repair pathway is a complex signaling mechanism that regulates the two key responses to DSBs—the rapid activation of cell-cycle checkpoints and the recruitment of DNA-repair proteins onto the chromatin at the DSB (Figure 1). The MRN complex, consisting of the mre11, rad50, and nbs1 proteins, is first recruited to DSBs, where it functions to recruit and activate the ATM protein kinase (Lavin, 2008Lavin M.F. Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer.Nat. Rev. Mol. Cell Biol. 2008; 9: 759-769Crossref PubMed Scopus (372) Google Scholar; Sun et al., 2010Sun Y. Jiang X. Price B.D. Tip60: connecting chromatin to DNA damage signaling.Cell Cycle. 2010; 9: 930-936Crossref PubMed Google Scholar). Activated ATM has been shown to phosphorylate hundreds of proteins (Matsuoka et al., 2007Matsuoka S. Ballif B.A. Smogorzewska A. McDonald 3rd, E.R. Hurov K.E. Luo J. Bakalarski C.E. Zhao Z. Solimini N. Lerenthal Y. et al.ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.Science. 2007; 316: 1160-1166Crossref PubMed Scopus (1037) Google Scholar), including proteins involved in checkpoint activation (e.g., p53 and chk2) and DNA-repair proteins such as brca1 and 53BP1 (Ciccia and Elledge, 2010Ciccia A. Elledge S.J. The DNA damage response: making it safe to play with knives.Mol. Cell. 2010; 40: 179-204Abstract Full Text Full Text PDF PubMed Scopus (491) Google Scholar; Jackson and Bartek, 2009Jackson S.P. Bartek J. The DNA-damage response in human biology and disease.Nature. 2009; 461: 1071-1078Crossref PubMed Scopus (682) Google Scholar; Kennedy and D'Andrea, 2006Kennedy R.D. D'Andrea A.D. DNA repair pathways in clinical practice: lessons from pediatric cancer susceptibility syndromes.J. Clin. Oncol. 2006; 24: 3799-3808Crossref PubMed Scopus (111) Google Scholar). A critical target for ATM is phosphorylation of the C terminus of the histone variant H2AX. Phosphorylated H2AX (referred to as γH2AX) creates a binding site for the BRCT domains of the mdc1 protein (Lou et al., 2006Lou Z. Minter-Dykhouse K. Franco S. Gostissa M. Rivera M.A. Celeste A. Manis J.P. van Deursen J. Nussenzweig A. Paull T.T. et al.MDC1 maintains genomic stability by participating in the amplification of ATM-dependent DNA damage signals.Mol. Cell. 2006; 21: 187-200Abstract Full Text Full Text PDF PubMed Scopus (272) Google Scholar; Stucki et al., 2005Stucki M. Clapperton J.A. Mohammad D. Yaffe M.B. Smerdon S.J. Jackson S.P. MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks.Cell. 2005; 123: 1213-1226Abstract Full Text Full Text PDF PubMed Scopus (431) Google Scholar) (Figure 1). Positioning of mdc1 at the DSB creates a docking site for additional DSB-repair proteins, including the MRN-ATM complex (Chapman and Jackson, 2008Chapman J.R. Jackson S.P. Phospho-dependent interactions between NBS1 and MDC1 mediate chromatin retention of the MRN complex at sites of DNA damage.EMBO Rep. 2008; 9: 795-801Crossref PubMed Scopus (105) Google Scholar; Melander et al., 2008Melander F. Bekker-Jensen S. Falck J. Bartek J. Mailand N. Lukas J. Phosphorylation of SDT repeats in the MDC1 N terminus triggers retention of NBS1 at the DNA damage-modified chromatin.J. Cell Biol. 2008; 181: 213-226Crossref PubMed Scopus (103) Google Scholar). Consequently, phosphorylation of H2AX by ATM spreads away from the DSB, creating γH2AX domains that extend for hundreds of kilobases along the chromatin from the DSB (Bonner et al., 2008Bonner W.M. Redon C.E. Dickey J.S. Nakamura A.J. Sedelnikova O.A. Solier S. Pommier Y. GammaH2AX and cancer.Nat. Rev. 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Thomson T.M. et al.Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase.Science. 2007; 318: 1637-1640Crossref PubMed Scopus (361) Google Scholar). Similar to γH2AX spreading, chromatin ubiquitination can also spread for tens of kilobases from the DSB (Xu et al., 2010Xu Y. Sun Y. Jiang X. Ayrapetov M.K. Moskwa P. Yang S. Weinstock D.M. Price B.D. The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair.J. Cell Biol. 2010; 191: 31-43Crossref PubMed Scopus (53) Google Scholar). This extension of chromatin ubiquitination is opposed by the activity of the two E3 ligases, TRIP12 and UBR5, which promote the ubiquitin-dependent degradation of RNF168 (Gudjonsson et al., 2012Gudjonsson T. Altmeyer M. Savic V. Toledo L. Dinant C. Grofte M. Bartkova J. Poulsen M. Oka Y. Bekker-Jensen S. et al.TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes.Cell. 2012; 150: 697-709Abstract Full Text Full Text PDF PubMed Scopus (27) Google Scholar). DSB repair therefore involves the sequential recruitment and concentration of thousands of copies of individual DSB-repair proteins onto the chromatin, as well as extensive posttranslational modification of the nucleosomes. The actual repair of DSBs can proceed through two distinct mechanisms: the error-prone nonhomologous end-joining (NHEJ) pathway and the error-free homologous recombination (HR) pathway (Huertas, 2010Huertas P. DNA resection in eukaryotes: deciding how to fix the break.Nat. Struct. Mol. Biol. 2010; 17: 11-16Crossref PubMed Scopus (84) Google Scholar; Jackson and Bartek, 2009Jackson S.P. Bartek J. The DNA-damage response in human biology and disease.Nature. 2009; 461: 1071-1078Crossref PubMed Scopus (682) Google Scholar). NHEJ involves minimal processing of the damaged DNA by nucleases, followed by direct re-ligation of the DNA ends. NHEJ requires the Ku70/80 DNA-binding complex and the DNA-PKcs kinase. In contrast, HR requires the generation of single-stranded DNA (ssDNA) intermediates, which are used for homology searching within adjacent sister chromatids. The production of ssDNA requires the initial nuclease activity of the CtIP-MRN complex (Sartori et al., 2007Sartori A.A. Lukas C. Coates J. Mistrik M. Fu S. Bartek J. Baer R. Lukas J. Jackson S.P. Human CtIP promotes DNA end resection.Nature. 2007; 450: 509-514Crossref PubMed Scopus (402) Google Scholar), followed by further end processing by additional nucleases to produce ssDNA intermediates (Symington and Gautier, 2011Symington L.S. Gautier J. Double-strand break end resection and repair pathway choice.Annu. Rev. Genet. 2011; 45: 247-271Crossref PubMed Scopus (137) Google Scholar). This ssDNA is then used for homology searching in sister chromatids, which then provide the template for accurate repair of DSBs by HR. Importantly, because sister chromatids are only present during the S and G2 phases of the cell cycle, HR repair is restricted to this part of the cell cycle. Consequently, NHEJ predominates in G1 and HR in S and G2 phases. However, how cells regulate the choice between HR and NHEJ repair pathways is not well understood, although both the 53BP1 and brca1 proteins can play a key role in this choice (Bothmer et al., 2010Bothmer A. Robbiani D.F. Feldhahn N. Gazumyan A. Nussenzweig A. Nussenzweig M.C. 53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination.J. Exp. Med. 2010; 207: 855-865Crossref PubMed Scopus (76) Google Scholar; Bunting et al., 2010Bunting S.F. Callén E. Wong N. Chen H.T. Polato F. Gunn A. Bothmer A. Feldhahn N. Fernandez-Capetillo O. Cao L. et al.53BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks.Cell. 2010; 141: 243-254Abstract Full Text Full Text PDF PubMed Scopus (256) Google Scholar). The nucleosome is the basic functional unit of chromatin and consists of 147 bp of DNA wrapped around a histone octamer (Campos and Reinberg, 2009Campos E.I. Reinberg D. Histones: annotating chromatin.Annu. Rev. Genet. 2009; 43: 559-599Crossref PubMed Scopus (284) Google Scholar). Nucleosomes form linear 10 nm beads-on-a-string structures that pack together to form 30 nm arrays and other higher-order structures. The core of each nucleosome contains two H3-H4 dimers and two H2A-H2B dimers. The N-terminal tails of histones extend out from the nucleosome and contain conserved lysine residues that can be modified by acetylation, methylation, or ubiquitination. These modifications can function to attract specific chromatin complexes that can then alter nucleosome function. In addition to histone posttranslational modifications, chromatin organization is also regulated by multisubunit remodeling complexes built around a large motor ATPase. Four major ATPase families, including the SWI/SNF, CHD, INO80, and ISWI families, have been identified in eukaryotes (Clapier and Cairns, 2009Clapier C.R. Cairns B.R. The biology of chromatin remodeling complexes.Annu. Rev. Biochem. 2009; 78: 273-304Crossref PubMed Scopus (455) Google Scholar). These remodeling complexes utilize the energy from ATP hydrolysis to (1) remove nucleosomes from the chromatin and create open DNA sequences; (2) shift the position of the nucleosome relative to the DNA by exposing (or burying) a DNA sequence (nucleosome sliding); or (3) exchange pre-existing histones for specialized histone variants. Chromatin-remodeling complexes and histone modifications can alter the interaction within or between adjacent nucleosomes and recruit chromatin-binding proteins to specific regions (Cairns, 2005Cairns B.R. Chromatin remodeling complexes: strength in diversity, precision through specialization.Curr. Opin. Genet. Dev. 2005; 15: 185-190Crossref PubMed Scopus (106) Google Scholar; Campos and Reinberg, 2009Campos E.I. Reinberg D. Histones: annotating chromatin.Annu. Rev. Genet. 2009; 43: 559-599Crossref PubMed Scopus (284) Google Scholar). Nucleosomes can therefore be envisaged as dynamic hubs to which chromatin-modifying proteins and specific modifications attach and that regulate the function and packing of the DNA in the chromatin. The importance of chromatin organization in maintaining genomic stability is underscored by studies demonstrating that mutation rates are not even across the human genome. Sequencing of multiple cancer genomes has revealed that mutations accumulate at much higher levels in compact, H3K9me3-rich heterochromatin domains (Schuster-Böckler and Lehner, 2012Schuster-Böckler B. Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells.Nature. 2012; 488: 504-507Crossref PubMed Scopus (46) Google Scholar), consistent with the slower rates of DNA repair reported in heterochromatin (Goodarzi et al., 2008Goodarzi A.A. Noon A.T. Deckbar D. Ziv Y. Shiloh Y. Löbrich M. Jeggo P.A. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin.Mol. Cell. 2008; 31: 167-177Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar; Noon et al., 2010Noon A.T. Shibata A. Rief N. Löbrich M. Stewart G.S. Jeggo P.A. Goodarzi A.A. 53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair.Nat. Cell Biol. 2010; 12: 177-184Crossref PubMed Scopus (110) Google Scholar). Further, inserts and deletions are depleted around nucleosomes, whereas mutations tend to cluster on the nucleosomal DNA (Chen et al., 2012Chen X. Chen Z. Chen H. Su Z. Yang J. Lin F. Shi S. He X. Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes.Science. 2012; 335: 1235-1238Crossref PubMed Scopus (8) Google Scholar; Sasaki et al., 2009Sasaki S. Mello C.C. Shimada A. Nakatani Y. Hashimoto S. Ogawa M. Matsushima K. Gu S.G. Kasahara M. Ahsan B. et al.Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.Science. 2009; 323: 401-404Crossref PubMed Scopus (60) Google Scholar; Tolstorukov et al., 2011Tolstorukov M.Y. Volfovsky N. Stephens R.M. Park P.J. Impact of chromatin structure on sequence variability in the human genome.Nat. Struct. Mol. Biol. 2011; 18: 510-515Crossref PubMed Scopus (15) Google Scholar), and both can be influenced by the presence of specific epigenetic modifications on the nucleosome (Schuster-Böckler and Lehner, 2012Schuster-Böckler B. Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells.Nature. 2012; 488: 504-507Crossref PubMed Scopus (46) Google Scholar; Tolstorukov et al., 2011Tolstorukov M.Y. Volfovsky N. Stephens R.M. Park P.J. Impact of chromatin structure on sequence variability in the human genome.Nat. Struct. Mol. Biol. 2011; 18: 510-515Crossref PubMed Scopus (15) Google Scholar). Some of these differences in mutation rates may accrue by negative selection (for example, selection against mutations in coding regions) or through protection of the DNA from mutagens by association with nucleosomes. However, the elevated mutation rates in compact, transcriptionally silent heterochromatin domains (Schuster-Böckler and Lehner, 2012Schuster-Böckler B. Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells.Nature. 2012; 488: 504-507Crossref PubMed Scopus (46) Google Scholar) imply that chromatin packing may impact the detection or repair of damage by the DNA-repair machinery. That is, the ability of the DNA-repair machinery to access the DNA can have a significant impact on genomic stability within specific regions. One of the best of the best characterized changes in chromatin organization is the rapid formation of open chromatin structures at DSBs. Several groups have demonstrated that this process is associated with increased acetylation of histones H2A and H4 on nucleosomes at DSBs (Downs et al., 2004Downs J.A. Allard S. Jobin-Robitaille O. Javaheri A. Auger A. Bouchard N. Kron S.J. Jackson S.P. Côté J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.Mol. Cell. 2004; 16: 979-990Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar; Jha et al., 2008Jha S. Shibata E. Dutta A. 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; 28: 2690-2700Crossref PubMed Scopus (71) Google Scholar; Kusch et al., 2004Kusch T. Florens L. Macdonald W.H. Swanson S.K. Glaser R.L. Yates 3rd, J.R. Abmayr S.M. Washburn M.P. Workman J.L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions.Science. 2004; 306: 2084-2087Crossref PubMed Scopus (364) Google Scholar; Murr et al., 2006Murr R. Loizou J.I. Yang Y.G. Cuenin C. Li H. Wang Z.Q. Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks.Nat. Cell Biol. 2006; 8: 91-99Crossref PubMed Scopus (261) Google Scholar). This acetylation extends for hundreds of kilobases away from the break (Downs et al., 2004Downs J.A. Allard S. Jobin-Robitaille O. Javaheri A. Auger A. Bouchard N. Kron S.J. Jackson S.P. Côté J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.Mol. Cell. 2004; 16: 979-990Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar; Murr et al., 2006Murr R. Loizou J.I. Yang Y.G. Cuenin C. Li H. Wang Z.Q. Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks.Nat. Cell Biol. 2006; 8: 91-99Crossref PubMed Scopus (261) Google Scholar; Xu et al., 2010Xu Y. Sun Y. Jiang X. Ayrapetov M.K. Moskwa P. Yang S. Weinstock D.M. Price B.D. The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair.J. Cell Biol. 2010; 191: 31-43Crossref PubMed Scopus (53) Google Scholar), similar to the spreading of γH2AX (Figure 1). The acetylation of histone H4 at DSBs is dependent on the Tip60 acetyltransferase, a haploinsufficient tumor-suppressor protein that is required for the repair of DSBs (Doyon and Côté, 2004Doyon Y. Côté J. The highly conserved and multifunctional NuA4 HAT complex.Curr. Opin. Genet. Dev. 2004; 14: 147-154Crossref PubMed Scopus (157) Google Scholar; Gorrini et al., 2007Gorrini C. Squatrito M. Luise C. Syed N. Perna D. Wark L. Martinato F. Sardella D. Verrecchia A. Bennett S. et al.Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage response.Nature. 2007; 448: 1063-1067Crossref PubMed Scopus (116) Google Scholar; Sun et al., 2010Sun Y. Jiang X. Price B.D. Tip60: connecting chromatin to DNA damage signaling.Cell Cycle. 2010; 9: 930-936Crossref PubMed Google Scholar). Tip60 is rapidly recruited to DSBs, where it can acetylate multiple DDR proteins, including histones H2A and H4, the ATM kinase, p53, and other repair proteins (Bird et al., 2002Bird A.W. Yu D.Y. Pray-Grant M.G. Qiu Q. Harmon K.E. Megee P.C. Grant P.A. Smith M.M. Christman M.F. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair.Nature. 2002; 419: 411-415Crossref PubMed Scopus (324) Google Scholar; Ikura et al., 2007Ikura T. Tashiro S. Kakino A. Shima H. Jacob N. Amunugama R. Yoder K. Izumi S. Kuraoka I. Tanaka K. et al.DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics.Mol. Cell. Biol. 2007; 27: 7028-7040Crossref PubMed Scopus (165) Google Scholar; Jha et al., 2008Jha S. Shibata E. Dutta A. 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; 28: 2690-2700Crossref PubMed Scopus (71) Google Scholar; Sun et al., 2005Sun Y. Jiang X. Chen S. Fernandes N. Price B.D. A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM.Proc. Natl. Acad. Sci. USA. 2005; 102: 13182-13187Crossref PubMed Scopus (249) Google Scholar, Sun et al., 2010Sun Y. Jiang X. Price B.D. Tip60: connecting chromatin to DNA damage signaling.Cell Cycle. 2010; 9: 930-936Crossref PubMed Google Scholar; Sykes et al., 2006Sykes S.M. Mellert H.S. Holbert M.A. Li K. Marmorstein R. Lane W.S. McMahon S.B. Acetylation of the p53 DNA-binding domain regulates apoptosis induction.Mol. Cell. 2006; 24: 841-851Abstract Full Text Full Text PDF PubMed Scopus (269) Google Scholar). Tip60 functions in DSB repair as a subunit of the human NuA4 (hNuA4) remodeling complex. hNuA4 contains at least 16 subunits (Doyon and Côté, 2004Doyon Y. Côté J. The highly conserved and multifunctional NuA4 HAT complex.Curr. Opin. Genet. Dev. 2004; 14: 147-154Crossref PubMed Scopus (157) Google Scholar), of which 4 posses catalytic activity—the Tip60 acetyltransferase, the p400 motor ATPase, and the Ruvbl1 and Ruvbl2 helicase-like proteins. Multiple subunits of hNuA4, including Tip60 (Sun et al., 2009Sun Y. Jiang X. Xu Y. Ayrapetov M.K. Moreau L.A. Whetstine J.R. Price B.D. Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60.Nat. Cell Biol. 2009; 11: 1376-1382Crossref PubMed Scopus (99) Google Scholar), Trrap (Downs et al., 2004Downs J.A. Allard S. Jobin-Robitaille O. Javaheri A. Auger A. Bouchard N. Kron S.J. Jackson S.P. Côté J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.Mol. Cell. 2004; 16: 979-990Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar; Kusch et al., 2004Kusch T. Florens L. Macdonald W.H. Swanson S.K. Glaser R.L. Yates 3rd, J.R. Abmayr S.M. Washburn M.P. Workman J.L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions.Science. 2004; 306: 2084-2087Crossref PubMed Scopus (364) Google Scholar; Murr et al., 2006Murr R. Loizou J.I. Yang Y.G. Cuenin C. Li H. Wang Z.Q. Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks.Nat. Cell Biol. 2006; 8: 91-99Crossref PubMed Scopus (261) Google Scholar), p400 (Xu et al., 2010Xu Y. Sun Y. Jiang X. Ayrapetov M.K. Moskwa P. Yang S. Weinstock D.M. Price B.D. The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair.J. Cell Biol. 2010; 191: 31-43Crossref PubMed Scopus (53) Google Scholar), and ruvbl1 and ruvbl2 (Jha et al., 2008Jha S. Shibata E. Dutta A. 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; 28: 2690-2700Crossref PubMed Scopus (71) Google Scholar) are corecruited to DSBs, suggesting that these proteins are recruited together as components of hNuA4. Interestingly, hNuA4 is a fusion of two separate yeast complexes—the smaller yeast NuA4 (yNuA4) complex, which contains the Tip60 homolog esa1, and the ySWR1 complex, which contains the Swr1 ATPase and the yeast Ruvbl1 and Ruvbl2 homologs (Clapier and Cairns, 2009Clapier C.R. Cairns B.R. The biology of chromatin remodeling complexes.Annu. Rev. Biochem. 2009; 78: 273-304Crossref PubMed Scopus (455) Google Scholar; Doyon and Côté, 2004Doyon Y. Côté J. The highly conserved and multifunctional NuA4 HAT complex.Curr. Opin. Genet. Dev. 2004; 14: 147-154Crossref PubMed Scopus (157) Google Scholar). Both yNuA4 (Downs et al., 2004Downs J.A. Allard S. Jobin-Robitaille O. Javaheri A. Auger A. Bouchard N. Kron S.J. Jackson S.P. Côté J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.Mol. Cell. 2004; 16: 979-990Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar) and ySWR1 complexes (Papamichos-Chronakis et al., 2006Papamichos-Chronakis M. Krebs J.E. Peterson C.L. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage.Genes Dev. 2006; 20: 2437-2449Crossref PubMed Scopus (104) Google Scholar; van Attikum et al., 2007van Attikum H. Fritsch O. Gasser S.M. Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks.EMBO J. 2007; 26: 4113-4125Crossref PubMed Scopus (111) Google Scholar) are recruited to enzymatically generated DSBs in yeast. However, whereas yNuA4 and SWR1 are recruited to DSBs through direct interaction with γH2AX (Downs et al., 2004Downs J.A. Allard S. Jobin-Robitaille O. Java