John M. Pascal

Poly(ADP-ribose) polymerase 1 (PARP1) is a central regulator of genome integrity and a major therapeutic target in cancer. It is a versatile reader of DNA and chromatin architecture, engaging canonical DNA strand breaks as well as replication-associated and non-canonical DNA structures, including unligated Okazaki fragments, stalled or reversed replication forks, G-quadruplexes, and R-loops. However, how PARP1 recognizes these diverse substrates, and whether they elicit distinct ADP-ribosylation outputs, remains unclear. In this Review, we propose that PARP1 does not respond to DNA damage as a uniform sensor but instead interprets lesion geometry, DNA topology and chromatin context, resulting in dynamic control of chromatin accessibility, repair-factor recruitment, replication fork remodelling, transcription-replication conflicts and PARP1 turnover at DNA lesions. This evolving understanding has important therapeutic implications. PARP inhibitor efficacy, toxicity and resistance are not determined solely by catalytic inhibition or by BRCA1 and BRCA2 status but reflect the combined effects of PARP1 retention, replication stress, repair-pathway choice, chromatin remodelling and tumour context.

RNA editing in mitochondria is vital for many eukaryotes. In plants, mitochondrial C-to-U deamination editing is catalyzed by tens to hundreds of PPR-DYW proteins, each typically dedicated to a specific site. Where retained, PPR-DYW family expanded independently in all eukaryotic groups examined here -- except in marine microeukaryotes diplonemids, which encode a single homolog despite deaminating their mitochondrial RNA at more than 100 sites. Here we characterize this unconventional deaminase, PPRD1, from Diplonema papillatum. Native affinity pulldown of the protein identified 20 predominantly sub-stoichiometric partners, including potential RNA-binding helical-repeat proteins. Among them, the divergent PolX-like protein DAPX1 consistently and reciprocally co-purified with PPRD1 in near-equal proportions. Structural modelling suggests that DAPX1 may stabilize the deaminase catalytic domain and expand its interaction interface. Silencing either PPRD1 or DAPX1 inhibited cell growth and reduced in vivo not only C-to-U, but also A-to-I deamination across five mitochondrial RNA-editing clusters encompassing 110 sites. Together, these results support a model of PPRD1 and DAPX1 forming the core of the Diplonema deamination-editing machinery, with sub-stoichiometric partners acting as specificity factors that guide accurate RNA editing with minimal off-target effects.

Adenosine diphosphate (ADP) ribosylation (ADPr) regulates multiple stress responses, yet substrates in the apoptotic machinery remain elusive. We show that a single, DNA damage–induced ADPr event controls proapoptotic PIDDosome (PIDD1/RAIDD/caspase-2) formation in response to unresolved interstrand DNA cross-links (ICL). ADPr targets conserved E783 in the PIDD1 death domain (DD); is catalyzed by poly(ADP-ribose) polymerase 4 (PARP4), a phylogenetically orphan PARP of previously unknown function; is reversed by the ribosylhydrolase activity of PARP14; and is triggered by Ataxia Telangiectasia and RAD3-related (ATR) phosphorylation–induced, PIAS1-mediated SUMOylation of the PIDD1 DD, which enables PARP4 docking. PIDD1 ADPr is dispensable for the recruitments of RAIDD and caspase-2 but essential for the dimerization of the caspase. Hence, denying E783 ADPr spares the onset of PIDDosome assembly but blocks its completion, thus eliminating caspase-2 activation and ensuing apoptosis. Conversely, removal of PARP14 forces apoptosis, even in cells with tolerable damage. The data identify PARP4 as an ICL response effector and illuminate a three-step modification sequence of the PIDD1 DD that conducts PIDDosome assembly from initiation to completion.

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

Transcription-coupled nucleotide excision repair (TC-NER or TCR) is initiated when the ATPase Cockayne syndrome protein B (CSB) recognizes a DNA lesion stalled RNA polymerase II (RNAPII) and forms a stable complex. Here, we report that poly(ADP-ribose) polymerase-1 (PARP1), that plays a key role in the lesion recognition step of global genomic NER, also facilitates the earliest step of TCR. PARP1, which is associated with RNAPII during normal transcription, interacts with and stabilizes CSB on the lesion-stalled RNAPII. CSB stimulates PARP1’s activity to form PAR, and in turn CSB is PARylated mainly at its N-terminal PAR-binding motif (PBM) to promote its stabilization with RNAPII, whereas its minor PARylation at the C-terminal domain suppresses its ATPase function, thus limiting the window of time for ATP-dependent lesion recognition by CSB. The loss of PARP1, treatment with inhibitors of PARP or poly(ADP-ribose) glycohydrolase (PARG) to prevent PAR synthesis or its catabolism to generate free PAR or engineering N-terminal PARylation-resistant CSB decrease the efficiency of cells for TCR. PARP1 mutant Caenorhabditis elegans larvae exhibit a pronounced TCR-deficient phenotype. Our findings uncover an evolutionarily conserved role of PARP1 and PAR metabolism in the initiation of TCR.

Non-covalent interactions of poly(ADP-ribose) (PAR) facilitate condensate formation, yet the impact of these interactions on condensate properties remains unclear. Here, we demonstrate that PAR-mediated interactions through PARP13, specifically the PARP13.2 isoform, are essential for modulating the dynamics of stress granules—a class of cytoplasmic condensates that form upon stress, including types frequently observed in cancers. Single amino acid mutations in PARP13, which reduce its PAR-binding activity, lead to the formation of smaller yet more numerous stress granules than observed in the wild-type. This fragmented stress granule phenotype is also apparent in PARP13 variants with cancer-associated single-nucleotide polymorphisms (SNPs) that disrupt PAR binding. Notably, this fragmented phenotype is conserved across a variety of stresses that trigger stress granule formation via diverse pathways. Furthermore, this PAR-binding mutant diminishes condensate dynamics and impedes fusion. Overall, our study uncovers the important role of PAR-protein interactions in stress granule dynamics and maturation, mediated through PARP13.

Cellular target engagement technologies enable quantification of intracellular drug binding; however, simultaneous assessment of drug-associated phenotypes has proven challenging. Here, we present cellular target engagement by accumulation of mutant as a platform that can concomitantly evaluate drug-target interactions and phenotypic responses using conditionally stabilized drug biosensors. We observe that drug-responsive proteotypes are prevalent among reported mutants of known drug targets. Compatible mutants appear to follow structural and biophysical logic that permits intra-protein and paralogous expansion of the biosensor pool. We then apply our method to uncouple target engagement from divergent cellular activities of MutT homolog 1 (MTH1) inhibitors, dissect Nudix hydrolase 15 (NUDT15)-associated thiopurine metabolism with the R139C pharmacogenetic variant, and profile the dynamics of poly(ADP-ribose) polymerase 1/2 (PARP1/2) binding and DNA trapping by PARP inhibitors (PARPi). Further, PARP1-derived biosensors facilitated high-throughput screening for PARP1 binders, as well as multimodal ex vivo analysis and non-invasive tracking of PARPi binding in live animals. This approach can facilitate holistic assessment of drug-target engagement by bridging drug binding events and their biological consequences.