PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis

Langelier, Marie-France; Pascal, John M.

doi:10.1016/j.sbi.2013.01.003

Cited by 185 publications

(160 citation statements)

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“…5b). This footprint is compatible with either one or two PARP-1 molecules enveloping around the UV-lesion, similar to the reported binding of either one 31 or two 21 PARP-1 molecules at the site of DNA strand breaks. The N-terminal DNA binding domain of PARP-1 that is known to be recruited to DNA strand breaks 20 was also recruited to UV-lesions without strand breaks, indicating more general property of this domain of PARP-1 to bind to different types of DNA damages.…”

Section: No Effect Of Parp-1 and Ddb2 Binding On Cpd-photolyase Mediasupporting

confidence: 87%

Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro

Purohit

Robu

Shah

et al. 2016

Sci Rep

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The existing methodologies for studying robust responses of poly (ADP-ribose) polymerase-1 (PARP-1) to DNA damage with strand breaks are often not suitable for examining its subtle responses to altered DNA without strand breaks, such as UV-damaged DNA. Here we describe two novel assays with which we characterized the interaction of PARP-1 with UV-damaged DNA in vivo and in vitro. Using an in situ fractionation technique to selectively remove free PARP-1 while retaining the DNA-bound PARP-1, we demonstrate a direct recruitment of the endogenous or exogenous PARP-1 to the UV-lesion site in vivo after local irradiation. In addition, using the model oligonucleotides with single UV lesion surrounded by multiple restriction enzyme sites, we demonstrate in vitro that DDB2 and PARP-1 can simultaneously bind to UV-damaged DNA and that PARP-1 casts a bilateral asymmetric footprint from −12 to +9 nucleotides on either side of the UV-lesion. These techniques will permit characterization of different roles of PARP-1 in the repair of UV-damaged DNA and also allow the study of normal housekeeping roles of PARP-1 with undamaged DNA.The abundance of poly (ADP-ribose) polymerase-1 (PARP-1) in mammalian cells and its rapid catalytic activation to form polymers of ADP-ribose (PAR) in the presence of various types of DNA damages with or without strand breaks has made it an ideal first responder at the lesion site to influence downstream events 1,2 . Apart from DNA damages, PARP-1 is also recruited to DNA during normal physiological processes such as transcription and chromatin remodeling 3 , which do not involve overt DNA damage but just altered DNA structures. While we know much more about how PARP-1 rapidly recognizes and binds to single or double strand breaks in DNA, we know very little about how PARP-1 interacts with DNA damages or altered DNA structures without strand breaks. The key reason is that the existing methodologies that readily identify interactions of PARP-1 with DNA strand breaks are not sufficiently sensitive to study the relatively weaker responses of PARP-1 to DNA damage without strand breaks. The response of PARP-1 to UVC-induced direct photolesions, such as cyclobutane pyrimidine dimers (CPD) that are formed without any DNA strand breaks exemplifies this problem.Recent studies from others and our team have shown the involvement of PARP-1 in the host cell reactivation 4 and specifically in the nucleotide excision repair (NER) of UV-damaged DNA through its interaction with early NER protein DDB2 [5][6][7] . Additional studies have shown that downstream NER proteins XPA 8,9 and XPC 10 are PARylated. Thus, PARP-1 possibly has multiple roles in NER, but we do not yet fully understand its interactions with UV-damaged DNA or other NER proteins due to two major challenges. The first challenge is that unlike for many NER proteins, the abundance of endogenous PARP-1 in the nucleus makes it nearly impossible to visualize its dynamics of recruitment to UV-damaged DNA in situ using conventional immunocytological methods. T...

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Section: No Effect Of Parp-1 and Ddb2 Binding On Cpd-photolyase Mediasupporting

confidence: 87%

Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro

Purohit

Robu

Shah

et al. 2016

Sci Rep

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“…An improved understanding of the structural basis for DNA-dependent PARP1 activation Langelier and Pascal, 2013) has led to a new hypothesis that inhibitor-induced reverse-allosteric signaling may drive PARP-trapping activity (Murai et al, 2012). Using a fluorescence anisotropy-based DNA-binding assay, 10-to 40-fold differences in the biochemical trapping potency have been reported among the PARP inhibitors with comparable potencies in inhibiting catalysis, further suggesting possible inhibitor-specific allosteric effects (Murai et al, 2012(Murai et al, , 2014a.…”

Section: Structural Basis For Parp-dna Trappingmentioning

confidence: 99%

Trapping Poly(ADP-Ribose) Polymerase

Shen

Aoyagi-Scharber

Wang

2015

J Pharmacol Exp Ther

201

188

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Recent findings indicate that a major mechanism by which poly (ADP-ribose) polymerase (PARP) inhibitors kill cancer cells is by trapping PARP1 and PARP2 to the sites of DNA damage. The PARP enzyme-inhibitor complex "locks" onto damaged DNA and prevents DNA repair, replication, and transcription, leading to cell death. Several clinical-stage PARP inhibitors, including veliparib, rucaparib, olaparib, niraparib, and talazoparib, have been evaluated for their PARP-trapping activity. Although they display similar capacity to inhibit PARP catalytic activity, their relative abilities to trap PARP differ by several orders of magnitude, with the ability to trap PARP closely correlating with each drug's ability to kill cancer cells. In this article, we review the available data on molecular interactions between these clinical-stage PARP inhibitors and PARP proteins, and discuss how their biologic differences might be explained by the trapping mechanism. We also discuss how to use the PARP-trapping mechanism to guide the development of PARP inhibitors as a new class of cancer therapy, both for singleagent and combination treatments.

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“…PARP-1 is believed to play important roles in DNA damage recognition, chromatin modulation, and DNA damage signaling. Although PARP-1 is recognized as a crucial target molecule for anticancer therapy, its underlying mechanism in vivo has remained undefined (19,25,32). In this study, we found a mutual relationship between PARP-1 activation and K5 acetylation by TIP60 that is dependent on the dynamic exchange of H2AX at DNA damage sites, which might be a crucial link coupling the DNA damage response and chromatin modulation (Fig.…”

Section: Discussionmentioning

confidence: 63%

“…PARP-1 itself is also the primary protein target for PARP-1-mediated (ADP-ribosyl)ation in vivo. The activity of PARP-1 is rapidly stimulated upon binding to DNA breaks; however, auto(ADP-ribosyl)ation facilitates PARP-1 dis-sociation from DNA, possibly by charge repulsion (23)(24)(25)(26). Thus, the binding of PARP-1 to DNA breaks is transient, and this allows the assembly of other repair proteins at the sites of DNA damage.…”

mentioning

confidence: 99%

Coordinated Regulation of TIP60 and Poly(ADP-Ribose) Polymerase 1 in Damaged-Chromatin Dynamics

Ikura

Furuya

Fukuto

et al. 2016

Molecular and Cellular Biology

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fThe dynamic exchange of histones alleviates the nucleosome barrier and simultaneously facilitates various aspects of cellular DNA metabolism, such as DNA repair and transcription. In response to DNA damage, the acetylation of Lys5 in the histone variant H2AX, catalyzed by TIP60, plays a key role in promoting histone exchange; however, the detailed molecular mechanism still is unclear. Here, we show that the TIP60 complex includes poly(ADP-ribose) polymerase 1 (PARP-1). PARP-1 is required for the rapid exchange of H2AX on chromatin at DNA damage sites. It is known that PARP-1 binds dynamically to damaged chromatin and is crucial for the subsequent recruitment of other repair factors, and its auto-poly(ADP-ribosyl)ation is required for the dynamics. We also show that the acetylation of histone H2AX at Lys5 by TIP60, but not the phosphorylation of H2AX, is required for the ADP-ribosylation activity of PARP-1 and its dynamic binding to damaged chromatin. Our results indicate the reciprocal regulation of K5 acetylation of H2AX and PARP-1, which could modulate the chromatin structure to facilitate DNA metabolism at damage sites. This could explain the rather undefined roles of PARP-1 in various DNA damage responses. P osttranslational modifications of histones are a fundamental process for the chromatin remodeling machinery in DNA metabolism, including transcription, DNA replication, and DNA repair (1, 2). These histone modifications either serve as the binding interface for regulatory factors in chromatin reorganization or function as a platform in a signaling cascade, such as in the DNA damage checkpoint response (1, 3). In addition to histone modifications, the incorporation or eviction of histone variants regulates chromatin dynamics and could directly promote DNA metabolism in the context of chromatin (4-9). Thus, it is important to clarify how the histone variants' dynamics at DNA damage sites and their modifications are coordinated upon commitment to each type of DNA metabolism. Such clarification would promote a better understanding of the significance of histone variants, which potentially play active roles, rather than simply functioning as barriers, during DNA metabolism (10).Upon DNA damage, Ser139 (S139) of H2AX, a histone H2A variant, is phosphorylated at DNA damage sites, and the phosphorylated H2AX functions as an anchor to retain DNA damage response (DDR) factors on the DNA damage sites (11-14). We previously reported that the acetylation of H2AX at lysine 5 (K5Ac) is required to facilitate histone H2AX exchange at DNA damage sites and also is necessary for the efficient assembly of NBS1 at these sites by promoting its turnover rate (9, 15). K5 acetylation of H2AX is catalyzed by the histone acetyltransferase TIP60 complex, which coordinates the signaling and repair of DNA damage via chromatin reorganization (9, 16-18). Importantly, the phosphorylation of H2AX on S139 is not required to facilitate H2AX exchange or to promote NBS1 turnover at DNA damage sites (9, 15). These findings indicated the dist...

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PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis

Cited by 185 publications

References 61 publications

Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro

Characterization of the interactions of PARP-1 with UV-damaged DNA in vivo and in vitro

Trapping Poly(ADP-Ribose) Polymerase

Coordinated Regulation of TIP60 and Poly(ADP-Ribose) Polymerase 1 in Damaged-Chromatin Dynamics

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