The multifaceted roles of PARP1 in DNA repair and chromatin remodelling

Abstract

Cells are exposed to various endogenous and exogenous insults that induce DNA damage, which, if unrepaired, impairs genome integrity and leads to the development of various diseases, including cancer. Recent evidence has implicated poly(ADP-ribose) polymerase 1 (PARP1) in various DNA repair pathways and in the maintenance of genomic stability. The inhibition of PARP1 is therefore being exploited clinically for the treatment of various cancers, which include DNA repair-deficient ovarian, breast and prostate cancers. Understanding the role of PARP1 in maintaining genome integrity is not only important for the design of novel chemotherapeutic agents, but is also crucial for gaining insights into the mechanisms of chemoresistance in cancer cells. In this Review, we discuss the roles of PARP1 in mediating various aspects of DNA metabolism, such as single-strand break repair, nucleotide excision repair, double-strand break repair and the stabilization of replication forks, and in modulating chromatin structure.

Figure 1 |. The biochemical functions of poly(ADP-ribose) polymerase 1 in DNA damage repair.

a | The domains of poly(ADP-ribose) polymerase 1 (PARP1) are shown. PARP1 has a DNA-binding domain (DBD), which consists of three zinc finger motifs (ZF1–3) and also contains a nuclear localization signal (NLS); a central automodification domain, which contains an interaction motif termed the BRCA1 C terminus (BRCT) domain; and a carboxy-terminal catalytic domain that contains a signature of PARP proteins, the conserved domain (CD). The CD contains the active site and binds to NAD⁺ and also to the Trp-Gly-Arg (WGR) domain. b | PARP1 detects DNA damage through its DBD, and it is activated by synthesizing poly(ADP-ribose) (PAR) chains mainly on itself but also on some of its target proteins. NAD⁺ is used as substrate for PAR formation, and is replenished in the cells from nicotinamide, using ATP. PAR chains are rapidly catabolized by PAR glycohydrolase (PARG), ADP-ribosylhydrolase 3 (ARH3) and O-acyl-ADP-ribose deacylase 1 (OARD1). PARG cleaves the 2′,1″-O-glycosidic ribose–ribose bonds of PAR. However, cleavage of the terminal ADP-ribose moiety requires OARD1 and results in the release of mono(ADP-ribose). c | Poly(ADP)ribosylation (PARylation) of PARP1 and other target proteins, both covalently and non-covalently, results in the recruitment of multiple proteins that have roles in different aspects of DNA damage repair. Ade, adenosine; P, phosphate residue; Rib, ribose moiety; ssDNA, single-stranded DNA.

Figure 2 |. The roles of poly(ADP-ribose) polymerase 1 in excision repair.

a | Poly(ADP-ribose) polymerase 1 (PARP1) activity is required in different steps of single-strand break repair (SSBR). It is essential for the detection of the SSBs and is then required for the recruitment of X-ray repair cross-complementing protein 1 (XRCC1), which acts as a scaffold for the recruitment of polynucleotide kinase 3′- phosphatase (PNKP), aprataxin (APTX) and DNA ligase 3 (LIG3) to process the SSB. This is followed by the gap filling step, which is carried out by DNA polymerase δ (Pol δ), Pol ε and Pol β, and also requires PARP1 for stimulating the 5′ flap endonuclease activity of flap endonuclease 1 (FEN1). Finally, the DNA is ligated by LIG1. b | PARP1 is also required for the processing of SSBs at abortive DNA topoisomerase 1 (TOP1) cleavage complexes (TOP1cc). PARP1 recruits and activates tyrosyl-DNA phosphodiesterase 1 (TDP1), which cleaves the TOP1cc from the DNA. The SSB is then repaired by SSBR. c | PARP1 is important for the repair of bulky adducts by global genome nucleotide excision repair (GG-NER). In the initial step, lesion detection, the DNA damage-binding protein 1 (DDB1)–DDB2 complex is recruited to autopoly(ADP) ribosylated (autoPARylated) PARP1. This is followed by the recruitment of amplified in liver cancer protein 1 (ALC1), a step that is also mediated by PARP1. This results in chromatin decondensation, the recruitment of xeroderma pigmentosum group C-complementing protein (XPC) and RAD23B, and lesion verification, which involves recruiting XPB and XPD through the interaction of their binding partner XPA with PARP1. Following lesion verification, the bulky adduct is excised by the concerted action of two nucleases, excision repair cross-complementing group 1 protein (ERCC1) and XPG, and the resulting gap is filled by Pol δ, Pol ε and Pol κ, and ligated by LIG1 or LIG3. PCNA, proliferating cell nuclear antigen; RPA, replication protein A.

Figure 3 |. The roles of poly(ADP-ribose) polymerase 1 in detection and repair of DNA double-strand breaks.

a | Poly(ADP-ribose) polymerase 1 (PARP1) is required for the robust detection of DNA double-strand breaks (DSBs) and for the initial DNA damage response through its interaction with meiotic recombination 11 (MRE11) and the apical checkpoint kinase ataxia telangiectasia mutated (ATM). b | PARP1 has a role in DNA end resection during the homologous recombination (HR) process through the recruitment of MRE11 to DSBs, which is followed by binding of the single strand by replication protein A (RPA). This reaction also requires breast cancer type 1 susceptibility protein (BRCA1), and PARP1 may stimulate it by indirectly recruiting BRCA1 through its interaction with BRCA1-associated RING domain protein 1 (BARD1). PARP1 is also required at later steps to suppress HR, probably by limiting the extent of DNA end resection. Resection is limited by the stabilization of poly(ADP)ribosylated (PARylated) BRCA1, which is then bound by receptor-associated protein 80 (RAP80). The interaction with RAP80 stabilizes BRCA1 and suppresses HR, which results in limited strand invasion and in the subsequent repair of the DSB. c | PARP1 is also involved in DSB repair by stimulating classical non-homologous end joining (cNHEJ). When DSBs are channelled for repair by cNHEJ, they are bound by KU70–KU80 dimers, which activate DNA-dependent protein kinase catalytic subunit (DNA-PKcs). PARP1 interacts with DNA-PKcs and probably stimulates its activity without the requirement of KU proteins. PARP1 is also involved in chromatin remodelling during cNHEJ by facilitating the recruitment of chromodomain helicase DNA-binding protein 2 (CHD2), which then facilitates the recruitment of X-ray repair cross-complementing protein 4 (XRCC4) and DNA ligase 4 (LIG4) for DNA ligation. d | PARP1 has a role in alternative NHEJ (aNHEJ), which is active in the absence of cNHEJ. aNHEJ requires processing of the DNA ends by MRE11, which is recruited by PARP1. The resected ends are then joined though sequence microhomology and the gap is filled by DNA polymerase θ (Pol θ) and ligated by LIG3. Whether PARP1 is required for the recruitment of Pol θ is unknown (question mark).

Figure 4 |. Poly(ADP-ribose) polymerase 1 helps maintain the stability of replication forks.

a | Replication fork reversal and restart. Various types of replication stress-inducing agents cause replication fork reversal to stabilize stalled replication forks. Poly(ADP-ribose) polymerase 1 (PARP1) is recruited to stalled replication forks for lesion detection and repair, in coordination with the replication machinery (not shown). PARP1 stabilizes reversed forks by inhibiting the activity of ATP-dependent DNA helicase Q1 (RECQ1), which can otherwise restart the fork. Following the repair of the lesion (not shown), RECQ1 can be activated, which allows branch migration of the reversed fork (dashed arrow), thereby mediating replication restart. b | Synthetic lethality. Stalled replications forks are detected by PARP1, which recruits the nuclease meiotic recombination 11 (MRE11) to mediate fork restart through limited processing of DNA at the forks. Disengagement of MRE11 from replication forks is required for their protection, which might be mediated by breast cancer type 2 susceptibility protein (BRCA2). In the absence of BRCA2, MRE11 has unlimited access to stalled forks. In combination with PARP inhibition, which limits PARP1 control of MRE11, this results in excessive DNA degradation, which might result in fork collapse and DSB formation. As cells lacking BRCA2 are deficient in DSB repair by homologous recombination (HR), PARP1 inhibition-mediated fork collapse and DSB formation results in cellular lethality. c | Synthetic viability. Loss of PARP1 activity results in defective MRE11 recruitment. If BRCA2 activity is lost after the loss of PARP1, MRE11 accessibility is diminished at stalled replication forks and they are therefore protected from degradation. Such cells are defective in DSB repair by HR, but they are viable owing to replication fork protection.

Figure 5 |. Chromatin changes induced by poly(ADP-ribose) polymerase 1 — integrating DNA repair.

DNA damage in the context of chromatin results in poly(ADP-ribose) polymerase 1 (PARP1) activation and autopoly(ADP)ribosylation (autoPARylation). PARP1 also PARylates histone tails, which results in chromatin relaxation and in nucleosome eviction from the DNA. This also allows the recruitment of several chromatin remodellers through their binding to PAR, which further relax chromatin to facilitate DNA repair. These chromatin remodellers include amplified in liver cancer protein 1 (ALC1), SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5), chromodomain helicase DNA-binding protein 2 (CHD2), which also incorporates the histone variant H3.3 into nucleosomes, and the transcription factor NR4A (a member of the nuclear orphan receptors). Conversely, repressive chromatin modifiers, such as CHD4 and Polycomb repressive complex 1 (PRC1), are also recruited to sites of DNA damage by binding to PAR. They might be recruited to inhibit transcription at flanking regions to facilitate DNA repair. RNF168, RING finger protein 168.