The poly(ADP-ribose) polymerase superfamily (PARP superfamily) comprises a group of enzymes with ADP-ribosyltransferase (ART) activity. They catalyze the transfer of ADP-ribose (ADPr) units from the coenzyme nicotinamide adenine dinucleotide (NAD+) to specific amino acid residues on target proteins, modifying proteins through a post-translational modification (PTM) known as ADP-ribosylation (ADPRylation) [1], [2]. The PARP superfamily comprises 17 members that catalyze either poly-ADP-ribosylation (PARylation) or mono-ADP-ribosylation (MARylation) [1], [2], [3]. Among them, PARP1, the founding member of the family, can synthesize long and branched chains of poly-ADP-ribose (PAR), typically functioning in the DNA damage response, and is responsible for over 90 % of the total activity in the cell [4]. PARP2 is functionally like PARP1 and can synthesize PAR chains. TNKS1 and TNKS2 (also known as PARP5a and PARP5b) are primarily involved in telomere maintenance and regulation of the Wnt signaling pathway and can synthesize PAR chains. PARP3, PARP4, PARP6–12, and PARP14–16 mainly perform MARylation, modifying specific substrates with a single ADPr (or MAR). Among these, PARP9 may not have considerable enzymatic activity on its own, but it can perform MARylation modifications when interacting with other protein complexes [5]. PARP13, although harboring a putative ART domain, lacks catalytic activity and is considered as a pseudoenzyme [1], [2], [3], [6] (Table 1).

In the homeostasis of PARylation, the degradation of PAR and MAR is mainly conducted by a group of specific hydrolases known as ADP-ribose hydrolases, which are responsible for removing ADPr moieties from proteins, nucleic acids, and metabolites. Two types of enzymes primarily erase ADP-ribosylation modifications: macrodomains and ADP-ribose hydrolases (ARHs) [22], [23], [24]. The macrodomain family includes MacroD1, MacroD2, terminal ADP-ribose glycohydrolase (TARG1), and poly(ADP-ribose) glycohydrolase (PARG), where MacroD1, MacroD2, and TARG1 can hydrolyze MAR, especially targeting ADP-ribosylated aspartate/glutamate residues. The ARH family comprises three members: ARH1, ARH2, and ARH3, with ARH2 lacking prominent enzymatic activity. PARG primarily hydrolyzes PAR chains, whereas ARH3 acts as an auxiliary enzyme for PARG. Yet, ARH3 is able to remove specifically serine-linked MAR, independent of PARG [25], [26], [27]. TARG1 also participates in the hydrolysis of PAR chains. ARH1 hydrolyzes only MAR, mediating the release of ADPr from arginine residues of target proteins [22], [23], [24]. Of note, a recent study showed that macrodomain-containing PARP9 and PARP14 exhibit glycohydrolase activity [28].

The multifaceted PARylation system including PAR synthesizers (mainly PARP1) and erasers as well as PAR binding proteins (readers), regulates many cellular processes, such as DNA damage signaling and repair, replication stress response, chromatin remodeling, transcription, inflammation, differentiation, cell death, ribosomal function, RNA processing, and modulation of tumor suppressor [1], [2], [22], [29], [30], [31], [32]

PARP1 is the most extensively studied member of the PARP family [32], [33]. The PARP1 protein comprises three parts: the DNA-binding domain (DBD) at the N-terminus, the auto-modification domain in the middle, and the catalytic domain (C-terminal catalytic domain, CAT) at the C-terminus [32] (Fig. 1).

The DBD contains three zinc-finger structures (ZFI, ZFII, and ZFIII). ZFI and ZFII recognize and bind to DNA lesions, with ZFII having a high affinity for DNA ends [34], [35], [36]. The DBD also contains a nuclear localization signal (NLS) and a caspase cleavage site (DEVD, amino acids 214–217) that generates 24 kDa and 89 kDa fragments during apoptosis [32] (Fig. 1).

The automodification domain contains a breast cancer susceptibility gene 1 (BRCA1) C-terminal (BRCT) domain that facilitates auto-PARylation and protein interactions [37], and a tryptophan-glycine-arginine (WGR) rich domain that cooperates with ZFI/ZFIII to recognize DNA ends contributing to the overall DNA-binding capability of PARP1, and relay DNA damage signals to the CAT [36] (Fig. 1).

CAT contains an autoinhibitory domain (HD) and an (ADP-ribosyl) transferase (ART) motif (also known as the PARP signature sequence) (Fig. 1).

When PARP1 binds to damaged (base, or single strand) DNA, the HD conformational changes, enabling NAD+ access to the ART catalytic pocket [36], [38], [39]. It contains a highly conserved catalytic triad comprising H862, Y896, and E988, which also serves as the binding site for most clinical PARP inhibitors [29], [40]. WGR and CAT structural domains are also involved in transcription and chromatin remodeling by binding to nucleosome histone H4 for chromatin relaxation [41], [42], whereas BRCT collaborates with WGR to reorganize nucleosome packing, supporting PARP1's dual roles in transcription and chromatin-associated repair [42], [43], [44] (Fig. 1).

Upon binding to damaged DNA, PARP1 is activated and consumes NAD+ to synthesize negatively charged long and branched PAR chains [35], which serve as scaffolds for DNA repair factors while facilitating PARP1 dissociation from DNA through charge repulsion [4], [31], [32]. These PAR chains are rapidly degraded by dePARylating enzymes (including PARG, ARH3, MacroD1, MacroD2, and TARG1) into recyclable metabolic units [24]. It is also known that excessive PARP1 activation depletes intracellular NAD+ (50 %-80 %), disrupting NAD+-dependent processes like glycolysis and the tricarboxylic acid cycle, ultimately triggering an energy crisis [45], [46], [47], [48]. This depletion leads to TNF-α-mediated necrotic cell death [49], [50], [51] and ATP-exhaustion-associated Parthanatos, a caspase-independent cell death linked to neurodegenerative, cardiovascular, and oncological pathologies [52], [53].

PARP inhibitors or deletion counteract NAD+ depletion [48], [54], [55] and elevate nicotinamide (NAM) levels [56], [57] demonstrating protective effects across disease models. They preserve pancreatic β-cell function in diabetes, mitigate kidney injury, and reduce obesity in high-fat diet models [54], [58], [59], [60], [61], [62]. In myocardial ischemia-reperfusion injury, PARP inhibition attenuates ROS-induced apoptosis [63]. In Alzheimer’s disease, PARP inhibitors (e.g., NAM and 3-ABA) prevent neuronal PAR accumulation [64] and lymphocyte vulnerability [65], with efficacy correlating with dementia severity [64], [65], [66].

PARP1 hyperactivation can also suppresse the NAD+-dependent deacetylase sirtuin 1 (SIRT1) activity via NAD+ depletion, inducing transcriptional coactivator PGC-1α hyperacetylation and mitochondrial dysfunction [66], [67]. Concurrently, it activates neurotoxic microglial responses through matrix metalloproteinase-9 (MMP-9) and proinflammatory signaling [66], [68], [69]. Genetic or pharmacological PARP1 inhibition restores NAD+ levels, rescues mitochondrial respiration, and blocks neuroinflammation [66], [67], [68], [69]. Thus, the dynamics of PARylation are regarded as a critical homeostatic regulator in cells that respond to genotoxic stimuli.

Chromatin provides the physical and chemical environment for DNA damage repair through its dynamic structural changes and histone modifications, while regulating the selection and efficiency of repair pathways to maintain genomic integrity [32], [70]. PARP1 and PARylation regulate chromatin remodeling through various mechanisms, affecting key cellular processes such as DNA repair and gene expression [71]. PARP1 can PARylate histone tails, causing chromatin relaxation and eviction of nucleosomes from DNA, allowing the recruitment of chromatin remodeling factors, for example, through their binding to PAR, further relaxing chromatin to facilitate DNA repair [72] and access of transcription factors to chromatin [32]. PARP1 involvement in chromatin remodeling manifests this process. For example, nucleosome PARylation enhances H3 tail dynamics without affecting its core structure. PARylation inhibits nucleosome stacking and self-association, reorganizing biomolecular condensates containing nucleosomes and DNA repair factors [73]. As a part of DNA damage response, PARP1 recruits chromatin remodeling enzymes, such as HPF1 or ALC1, and other enzymes containing PAR binding domains to DNA damage sites [35], [74]. The combined action of PARP1 and HPF1 triggers rapid chromatin disassembly by PARylating histones near DNA damage sites, facilitating the recruitment of DNA damage repair factors [75]. ALC1 interacts with PAR through its macrodomain and is recruited to the damage site, further promoting chromatin remodeling near the damage site and providing a more favorable chromatin environment for the assembly and repair of the nucleotide excision repair (NER) complex [74], [76].

In addition, numerous studies have demonstrated that PARP1 and PARylation regulate gene transcription via chromatin remodeling in addition to their direct role through interaction with transcription factors [32]. PARP1 can directly bind to nucleosomes and PARylate all four core histones H2A, H2B, H3, and H4, influencing transcription [77], [78]. PARP1 PARylates and competes with histone linker H1 for DNA binding, affecting the activity of gene promoters and expression of immediate early genes [79], [80]. Moreover, PARP1 is functionally associated with histone variants such as H2Av, H2AZ, and MacroH2A1.1, which affects chromatin structure and gene expression [77], [81].

PARP1 can PARylate lysine demethylase 5B (KDM5B) by affecting its binding to chromatin and demethylation activity, affecting gene transcriptional activation and silencing [82]. Chemical inhibition or genetic ablation of PARP1 increases the expression of the polycomb repressive complex 2 (PRC2) member EZH2, leading to increased levels of inhibiting H3K27 trimethylation [83]. PARP1 modifies the lysine demethylase KDM4D by PARylation, which removes trimethylated and dimethylated residues at H3K9, to regulate the methylation status of H3K9 and transcriptional activation and silencing of genes [84]. In addition, in response to DNA damage, PARP1 PARylates the CycT1 subunit of the P-TEFb complex, which disrupts CycT1 phase separation and inhibits the hyperphosphorylation of RNA polymerase II, inhibiting transcription elongation and global transcription [85].