Regulation of DNA‐damage responses and cell‐cycle progression by the chromatin remodelling factor CHD4

“In response to DNA damage, cells initiate a coordinated programme of events, termed the DNA-damage response (DDR), which is critical for maintenance of genome integrity and the prevention of ageing and tumourigenesis (Harper and Elledge, 2007; Jackson and Bartek, 2009).”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“Interestingly, proteomic screens in human cells have identified CHD4 as a target for DDR kinases (Matsuoka et al, 2007; Mu et al, 2007; Stokes et al, 2007).”

“It is, therefore, possible that such factors will display synergistic and/or antagonistic functions in the regulation of chromatin compaction at DNA-damage sites, as happens in the context of transcription (Ramirez-Carrozzi et al, 2006; Clapier and Cairns, 2009).”

“In response to DNA damage, cells initiate a coordinated programme of events, termed the DNA-damage response (DDR), which is critical for maintenance of genome integrity and the prevention of ageing and tumourigenesis (Harper and Elledge, 2007; Jackson and Bartek, 2009).”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“…DNA nicks also activate poly(ADP-ribose) poly- merase (PARP) enzymes that modify target proteins with poly(ADP-ribose) chains (PAR chains) at DNA-damage sites, thereby stimulating the recruitment and/or activity of repair factors (Malanga and Althaus, 2005; Hakme et al, 2008; Rouleau et al, 2010).”

“Furthermore, we found that this CHD4 phosphorylation was prevented when cells were incubated with Wortmannin (Sarkaria et al, 1998) or the ATM inhibitor KU-55933 (Hickson et al, 2004), but not the DNA-PK inhibitor NU-7441 (Leahy et al, 2004) (see Figure 3B; Supplementary Figure S4B).”

“These findings thereby help explain recent observa- tions linking NuRD to cellular ageing (Pegoraro et al, 2009) and might shed light on why patients expressing auto- antibodies against CHD4 display higher cancer incidence (Hill et al, 2001).”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“To address the biological significance of CHD4 to the DDR, we analysed the effects of its depletion, focusing initially on PARP-mediated repair of DNA breaks (Caldecott, 2008) and ATM-dependent signalling.”

“…complex (nucleosome remodelling deacetylase) that is unique in combining chromatin remodelling activity with histone deacetylase and demethylase functions involved in transcriptional repression (Wade et al, 1998; Xue et al, 1998; Zhang et al, 1998; Denslow and Wade, 2007; Ramirez and Hagman, 2009).”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“…complex (nucleosome remodelling deacetylase) that is unique in combining chromatin remodelling activity with histone deacetylase and demethylase functions involved in transcriptional repression (Wade et al, 1998; Xue et al, 1998; Zhang et al, 1998; Denslow and Wade, 2007; Ramirez and Hagman, 2009).”

“Cells were analysed 48–72 h after transfection.”

“Interestingly, CHD4 appears to be one of the several, and possibly many, chromatin remodelling factors recruited to DNA breaks in mammalian cells (Murr et al, 2006; Ahel et al, 2009; Gottschalk et al, 2009; Peng et al, 2009; Timinszky et al, 2009).”

“…it is tempting to speculate that this could be through local remo- delling of chromatin to facilitate DNA repair, perhaps in ways similar to those proposed for yeast and other mammalian chromatin remodelling complexes (Park et al, 2006; Ahel et al, 2009; Peng et al, 2009; Sinha et al, 2009).”

“…does not display canonical PAR-binding domains (Karras et al, 2005; Ahel et al, 2008), sequence analyses revealed the presence of putative PAR-binding motifs in the CHD4 amino- and carboxyl-terminal regions that loosely matched a characterized consensus (Pleschke et al, 2000; Gagne et al, 2008).”

“…to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and Cairns, 2009; van Attikum and Gasser, 2009).”

“…functions for CHD4 and other chromatin remodelling components is also relevant for cancer research in general, given that drugs targeting chromatin-modifying enzymes are being explored as anti- cancer therapies, both for use alone and in combination with DNA-damaging treatments (Ellis et al, 2009).”

“…complex (nucleosome remodelling deacetylase) that is unique in combining chromatin remodelling activity with histone deacetylase and demethylase functions involved in transcriptional repression (Wade et al, 1998; Xue et al, 1998; Zhang et al, 1998; Denslow and Wade, 2007; Ramirez and Hagman, 2009).”

“Localized DNA damage was generated by exposure of cells to a UV-A laser (Limoli and Ward, 1993; Lukas et al, 2003).”

“The work must be attributed back to the original author and commercial use is not permitted without specific permission.”

“CHD4 is well characterized as a catalytic subunit of the NuRD transcriptional repressor complex (Wade et al, 1998; Xue et al, 1998; Zhang et al, 1998; Denslow and Wade, 2007; Ramirez and Hagman, 2009).”

“…to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and Cairns, 2009; van Attikum and Gasser, 2009).”

“Furthermore, we found that this CHD4 phosphorylation was prevented when cells were incubated with Wortmannin (Sarkaria et al, 1998) or the ATM inhibitor KU-55933 (Hickson et al, 2004), but not the DNA-PK inhibitor NU-7441 (Leahy et al, 2004) (see Figure 3B; Supplementary Figure S4B).”

“Interestingly, CHD4 appears to be one of the several, and possibly many, chromatin remodelling factors recruited to DNA breaks in mammalian cells (Murr et al, 2006; Ahel et al, 2009; Gottschalk et al, 2009; Peng et al, 2009; Timinszky et al, 2009).”

“…does not display canonical PAR-binding domains (Karras et al, 2005; Ahel et al, 2008), sequence analyses revealed the presence of putative PAR-binding motifs in the CHD4 amino- and carboxyl-terminal regions that loosely matched a characterized consensus (Pleschke et al, 2000; Gagne et al, 2008).”

“Interestingly, CHD4 appears to be one of the several, and possibly many, chromatin remodelling factors recruited to DNA breaks in mammalian cells (Murr et al, 2006; Ahel et al, 2009; Gottschalk et al, 2009; Peng et al, 2009; Timinszky et al, 2009).”

“Notably, CHD4 is a likely target for DDR kinases (Matsuoka et al, 2007; Mu et al, 2007; Stokes et al, 2007), and loss of function of CHD4 or other NuRD components causes accumulation of DNA damage and features of accelerated ageing (Pegoraro et al, 2009).”

“…to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and Cairns, 2009; van Attikum and Gasser, 2009).”

“…it is tempting to speculate that this could be through local remo- delling of chromatin to facilitate DNA repair, perhaps in ways similar to those proposed for yeast and other mammalian chromatin remodelling complexes (Park et al, 2006; Ahel et al, 2009; Peng et al, 2009; Sinha et al, 2009).”

“…DNA nicks also activate poly(ADP-ribose) poly- merase (PARP) enzymes that modify target proteins with poly(ADP-ribose) chains (PAR chains) at DNA-damage sites, thereby stimulating the recruitment and/or activity of repair factors (Malanga and Althaus, 2005; Hakme et al, 2008; Rouleau et al, 2010).”

“Indeed, compacted chromatin can be refractory to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and…”

“This then brings about further chromatin alterations that permit recruitment of additional DDR mediators such as p53-binding protein 1 (53BP1) and breast cancer 1 (BRCA1; Panier and Durocher, 2009).”

“…it is tempting to speculate that this could be through local remo- delling of chromatin to facilitate DNA repair, perhaps in ways similar to those proposed for yeast and other mammalian chromatin remodelling complexes (Park et al, 2006; Ahel et al, 2009; Peng et al, 2009; Sinha et al, 2009).”

“Notably, CHD4 is a likely target for DDR kinases (Matsuoka et al, 2007; Mu et al, 2007; Stokes et al, 2007), and loss of function of CHD4 or other NuRD components causes accumulation of DNA damage and features of accelerated ageing (Pegoraro et al, 2009).”

“…DNA nicks also activate poly(ADP-ribose) poly- merase (PARP) enzymes that modify target proteins with poly(ADP-ribose) chains (PAR chains) at DNA-damage sites, thereby stimulating the recruitment and/or activity of repair factors (Malanga and Althaus, 2005; Hakme et al, 2008; Rouleau et al, 2010).”

“…to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and Cairns, 2009; van Attikum and Gasser, 2009).”

“Localized DNA damage was generated by exposure of cells to a UV-A laser (Limoli and Ward, 1993; Lukas et al, 2003).”

“…to full DDR activation (Murga et al, 2007), and accumulating evidence suggests pivotal and direct functions for chromatin remodelling factors in relieving such inhibitory effects (Bao and Shen, 2007; Downs et al, 2007; Osley et al, 2007; Clapier and Cairns, 2009; van Attikum and Gasser, 2009).”

“…complex (nucleosome remodelling deacetylase) that is unique in combining chromatin remodelling activity with histone deacetylase and demethylase functions involved in transcriptional repression (Wade et al, 1998; Xue et al, 1998; Zhang et al, 1998; Denslow and Wade, 2007; Ramirez and Hagman, 2009).”

“…it is tempting to speculate that this could be through local remo- delling of chromatin to facilitate DNA repair, perhaps in ways similar to those proposed for yeast and other mammalian chromatin remodelling complexes (Park et al, 2006; Ahel et al, 2009; Peng et al, 2009; Sinha et al, 2009).”

“Consistent with this, we found that depletion of the p300 acetyltransferase, which is responsible for p53 Lys-382 acetylation (Carter and Vousden, 2009; Kruse and Gu, 2009), reduced both p53 acetylation and p21 levels, and moreover, rescued cell-cycle progression in CHD4-depleted cells (Figure 6F and G), supporting th…”

“…22, 2010 ª2010 Elsevier Inc. 181 182 Molecular Cell 40, October 22, 2010 ª2010 Elsevier Inc. recruitment of DNA repair and chromatin modifying complexes, such as polycomb and histone deacetylase (HDAC) complexes, at DNA damage sites (Polo et al., 2010; Schreiber et al., 2006; Chou et al., 2010).”

“PARylation at DNA breaks is also required for accrual of the chromatin remodeling factors ALC1 and CHD4 (Ahel et al. 2009; Gottschalk et al. 2009; Chou et al. 2010; Polo et al. 2010), the Polycomb histone-modifying complex (Chou et al. 2010), and the histone variant macroH2A (Timinszky et al. 2009).”

“Although binding to PAR chains seems to recruit these complexes to DNA break”

“The recruitment of NuRD complexes to DSBs requires PARylation of the chromatin by PARP1 (Chou et al., 2010; Polo et al., 2010).”

“Other NuRD complex subunits have also been shown to have post-translational modifications, such as phosphorylation and acetylatio”

“PARP1 mediates recruitment of repair proteins to DNA damage via the transient polymerization of branched poly(ADP-ribose) (PAR) structures; and it is likely that RBMX localization is similarly facilitated 1, 22, 23 .”

“Various chromatin remodelers, including INO80 (Gospodinov et al., 2011; Kashiwaba et al., 2010; Neumann et al., 2012; Papamichos-Chronakis et al., 2011), SMARCAD1 (Fun 30 in yeast) (Chen et al., 2012; Costelloe et al., 2012; Lee et al., 2010), p400 (Xu et al., 2010, 2012), chromodomain helicase DNA-binding protein 4 (…”

“KU-55933 (118500) and NADþ (20-221) were from Millipore.”

“ATM-mediated pathways have also been shown to be involved in chromatin relaxation (Goodarzi et al., 2008; Moyal et al., 2011; Polo et al., 2010; Ziv et al., 2006), nucleosome remodeling (Goodarzi et al.”

“Both the SSB repair protein XRCC1 and chromatin remodeling factor CHD4 are recruited to DNA damage in a PARP-dependent manner (21, 68); however, depletion of FUS did not disrupt targeting of either XRCC1 or CHD4 (data not shown).”

“Interestingly, PARP plays an important role in damage-induced transcriptional repression, including by promoting the recruitment of the ZMYND8-NuRD chromatin remodeling complex to damage chromatin where it participates in repressing transcription in the vicinity of DSBs [80, 95, 99, 100], Given these results for other…”

“The DNA damage recruitment dynamics of ZMYND8 are similar to those reported for the NuRD complex (i.e., CHD4) (Polo et al. 2010).”

“Furthermore, many subunits of NuRD are recruited to DSBs in a, at least for CHD4 and MTA1, poly(ADP ribose) polymerase (PARP)-dependent manner, but surprisingly, do not require phosphorylation of H2AX [128-131].”

“Somewhat paradoxically, proteins that promote chromatin compaction, such as HP1, KAP-1, SPOC1, su(var)3-9 methyltransferase variant 1 (SUV3-9), PDRM2 methyltransferase, macro H2A, and histone deacetylases (HDACs), have also been shown to be recruited to the sites of DSBs (Ayoub et al., 2009; Ayrapetov et al., 2014; Ba…”

“NuRD complex rapidly accumulates in cells at sites of doublestrand breaks in a manner dependent on the activity of poly(ADP ribose) polymerase, PARP [95, 97].”

“…was therefore proposed that the PAR-recruited NuRD complex facilitates the latter process by imposing a transient repressive chromatin state at DNA lesions, although a causal CHD4 contribution to the removal of RNA polymerase II still needs to be established (Chou et al , 2010; Polo et al , 2010).”

“One defined role of CHD4 in DSB repair is to recruit repressive chromatin to open chromatin regions in active gene promoters (Chou et al., 2010; Larsen et al., 2010; Polo et al., 2010), serving to protect transcribed regions during repair (Chou et al.”

“p53 acetylation status, [2]), independent of regulating gene expression.”

“other syndromes and multi-system developmental disorders.(113) Studies have shown temporal and tissue specific function of chromatin remodelers during heart development and thereby any mutation leads to the advancement of many cardiovascular tissues.”

“…and PARP inhibitors in cancer settings deficient in the KDM5A-ZMY ND8–NuRD JCB • Volume 216 • NumBer 7 • 20171968 pathway, given the therapeutic benefit associated with these treatments in DDR-deficient cancers (Helleday et al., 2008; Chou et al., 2010; Polo et al., 2010; Spruijt et al., 2016).”

“…(PAR) structures and are responsible for the recruitment of a number of factors to sites of DNA damage, including ALC1, RBMX, and components of MRN and NuRD complexes, among others (Adamson et al., 2012; Ahel et al., 2009; Chou et al., 2010; Haince et al., 2008; Polo et al., 2010).”

“Among their interacting partners are proteins recently shown to be involved in cellular responses to DSBs, including SFPQ (15), CHD4 (16), and UBR5 (17) (Supplementary Fig.”

“To date, many proteins have been shown to be recruited in a PAR-dependent manner by cell imaging techniques: MRE11 (6), NBS1 (6), APLF (46), XRCC1 (57), CHD4 (58), NuRD (59) and ALC1 (47).”

“The recent identification of chromatinassociated proteins whose recruitment to DNA damage sites is pADPr-dependent [e.g.: CHD4 (38,73), MTA1(73), MRE11(74), NBS1(74), ALC1(39,40), APLF (75,76), XRCC1 (68), BMI-1 (77), MEL-18 (73)] also points towards this model.”

“Additionally, the DNA damage– induced reduction in histone density also required the activity of PARP1, which has recently been linked to chromatin remodeling in response to double-strand DNA breaks (Ahel et al., 2009; Gottschalk et al., 2009; Chou et al., 2010; Polo et al., 2010).”

“Similarly, it was recently shown that PARP1 and Really Interesting New Gene finger protein (RNF)8 ubiquitin ligase regulate the recruitment of the catalytic subunit of the NuRD repressor complex, CHD4, to DNA-breakage sites (49, 61).”

“itself and acceptor proteins, directs the recruitment of the chromatin remodeling enzymes ALC1 and CHD4 to DSBs (Ahel et al., 2009; Chou et al., 2010; Gottschalk et al., 2009; Luijsterburg et al., 2012a; Polo et al., 2010).”

“Kinetic analysis of Alc1 retention at laserinduced damage sites suggest Alc1 acts at an early stage in the DDR. 48.”

“For DSBs, PARP1 and the PAR chains cause the recruitment of the nucleosome remodelling deacetylase (NuRD) complex (100,101) and the polycomb group (PcG) proteins (101–103), all of which are essential for the effective repair of DSBs (100,102–104) (Figure 1C).”

“…chromatin marks, such as methylation of H3K9, and recruitment of the NuRD–CHD4 complex are two other examples of a transient, repressive chromatin state that appear to be critical for the DDR (Chou et al., 2010; Larsen et al., 2010; Polo et al., 2010; Smeenk et al., 2010; Chiolo et al., 2011).”

“In contrast, both RNF8 and PARP activity appeared to contribute to CHD4 assembly at sites of DNA damage (132, 135).”

“Additionally, PARylation is also involved in the recruitment and the regulation of several chromatin-remodeling enzymes whose ATP-dependent activity could promote chromatin relaxation (Chou et al., 2010; Polo et al., 2010; Smeenk et al., 2013).”

“CHD4 is phosphorylated at multiple sites (Bouazoune and Brehm 2005; Polo et al. 2010; Urquhart et al. 2011).”

“CHD4 (Mi-2b) Refs (46,108-111) NuRD complex; checkpoint signaling and DNA damage repair; promotes CD4 gene expression during T cell development.”

“In fact, for other important DDR players, the information available indicates that p300/CBP may interact with them, while there is no evidence of their acetylation.”

“Endogenous CHD4 was recruited to laser-generated DSBs marked by phosphorylated histone H2AX ( g H2AX; Figure 6A), in line with several recent reports (Chou et al , 2010; Larsen et al , 2010; Polo et al , 2010; Smeenk et al , 2010).”

“The alternative pathway (A-EJ) is initiated by an Mre11-mediated end-resection activity in a manner similar to HR and involves additional proteins such as PARP1, XRCC1, DNA ligase III and histone H1 (14–20).”

“This could reconcile our results with previous studies and possibly explain how both PAR and ZMYND8 could stimulate the recruitment of CHD4 and MBD2 (Chou et al., 2010; Luijsterburg et al., 2012; Polo et al., 2010; Sun et al., 2016).”

“The chromatin surrounding DSBs is rapidly and transiently PARylated (Figure 2) causing the recruitment of the NuRD complex [72,73], which harbors both ATP-dependent chromatin remodeling and histone deacetylase activities.”

“We thus proposed that SIRT6 and CHD4 may coordinate their action in DDR.”

“GFP tagged full length, C-terminal, and N-terminal human CHD4 constructs were generously provided by Stephen Jackson (Cambridge) (Polo et al., 2010).”

“Recent studies have shown the importance of CHD4 in response to ionizing radiation and PARP inhibitors [29-32, 38].”

“It is essential for cell cycle progression (Polo et al., 2010), DNA damage response (Larsen et al.”

“PARP1 is involved in the early recruitment of theMRN complex to DSBs (Haince et al. 2008) and interacts with cNHEJ components such as WRN (Adelfalk et al. 2003), Ku (Li et al. 2004) and DNAPK (Spagnolo et al. 2012).”

“PARP also promotes the recruitment of the ZMYND8-NuRD chromatin remodeling complex to damaged chromatin where it participates in repressing transcription in the vicinity of DSBs (Chou et al. 2010; Polo et al. 2010; Gong et al. 2015; Spruijt et al. 2016).”

“3100 | J. K. Sims and P. A. Wade Molecular Biology of the Cell mal chromatin architecture, including the Mi-2/NuRD complex (Sillibourne et al., 2007; Pegoraro et al., 2009; Chou et al., 2010; Cohet et al., 2010; Larsen et al., 2010; Misteli, 2010; Polo et al., 2010; Smeenk et al., 2010).”

“Sites of high PARP1 activity in vivo recruit ATP-dependent remodelers, including ALC1 (Amplified in Liver Cancer 1; also known as CHD1L), CHD2, CHD4, SMARCA5/SNF2H and Drosophila Mi-2 (Chou et al., 2010; Murawska et al., 2011; Polo et al., 2010; Smeenk et al., 2013).”

“of the G1/S cell cycle transition and ATM-associated DNA damage responses [56].”

“Originally identified as a key component of a histone deacetylase complex that promotes transcriptional repression [58], CHD4/NuRD binds directly to poly-ADP-ribose and requires PARP activity for its recruitment to damage sites [55, 56].”