{"gene":"PARP4","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":1999,"finding":"PARP4 (p193/VPARP) was identified as a poly(ADP-ribose) polymerase: its catalytic domain, expressed and purified from bacteria, catalyzes a poly(ADP-ribosylation) reaction in vitro. Purified vault particles retain this enzymatic activity, and MVP is a substrate for vault-associated PARP activity. A portion of p193 localizes to the nucleus and to the mitotic spindle.","method":"Yeast two-hybrid screen (identification of MVP interaction), peptide sequence analysis, in vitro poly(ADP-ribosylation) assay with purified recombinant catalytic domain, immunofluorescence and biochemical fractionation","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic reconstitution with purified protein, substrate identification (MVP), localization by immunofluorescence; foundational study replicated by subsequent work","pmids":["10477748"],"is_preprint":false},{"year":2004,"finding":"CryoEM difference mapping localized VPARP (PARP4) to three density bands lining the inner surface of the vault particle, establishing its structural position within the assembled vault ribonucleoprotein complex.","method":"Cryoelectron microscopy and single-particle image reconstruction with difference mapping of recombinant vaults co-expressing MVP and VPARP","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct structural localization by cryoEM with difference mapping, single lab but rigorous structural method","pmids":["15504404"],"is_preprint":false},{"year":2005,"finding":"Newly synthesized VPARP is completely incorporated into vault particles within 1.5 hours and is stable once incorporated. The C-terminal region of VPARP lacking poly(ADP-ribose)polymerase activity is sufficient for co-sedimentation with MVP-assembled vault-like particles, indicating that PARP4 enzymatic activity is not required for its interaction with MVP.","method":"Immunoprecipitation pulse-chase assay, co-sedimentation of C-terminal VPARP truncation mutant with MVP particles in E. coli expression system","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and co-sedimentation with defined truncation mutant, single lab, two orthogonal approaches","pmids":["15567158"],"is_preprint":false},{"year":2001,"finding":"p193 (PARP4) encodes a proapoptotic activity in cardiomyocytes: a C-terminal truncation mutant of p193 confers prosurvival activity, and combined expression of this mutant with a dominant-interfering p53 mutant blocks E1A-induced apoptosis in embryonic stem cell-derived cardiomyocytes, demonstrating that p193 and p53 define two distinct proapoptotic pathways that restrict cardiomyocyte cell cycle activity.","method":"Transgene expression of p193 truncation mutant in differentiating embryonic stem cell-derived cardiomyocytes; apoptosis assays combined with cell cycle analysis; structure-function analysis","journal":"Circulation research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via dominant-interfering mutants and apoptosis readout, single lab with multiple constructs","pmids":["11375269"],"is_preprint":false},{"year":2004,"finding":"Expression of a dominant-interfering p193 (PARP4) mutant in transgenic cardiomyocytes induces cardiomyocyte cell cycle reentry at the infarct border zone after myocardial infarction and reduces hypertrophic growth in interventricular septa, indicating p193 normally restricts cardiomyocyte cell cycle activity in the injured adult heart.","method":"Transgenic mouse model expressing dominant-interfering p193 mutant under cardiac-specific promoter; BrdU incorporation assay; histological analysis post-coronary artery occlusion","journal":"Circulation research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo loss-of-function with specific cell cycle and hypertrophy phenotypic readouts, single lab","pmids":["15142950"],"is_preprint":false},{"year":2006,"finding":"Endogenous p193/CUL7 (PARP4) forms a complex with Parc (a parkin-like ubiquitin ligase) and p53, as detected by immunoprecipitation/Western analysis. Expression of a dominant-interfering p193 truncation (1152stop) confers resistance to MG132- and etoposide-induced apoptosis, but this resistance is independent of disruption of the endogenous p193/CUL7–Parc–p53 complex.","method":"Immune precipitation/Western blot analysis; apoptosis assays in U2OS cells expressing dominant-interfering p193 mutant","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying a three-protein complex, functional apoptosis assay, single lab","pmids":["17229476"],"is_preprint":false},{"year":2015,"finding":"siRNA knockdown of PARP4 in HCC1143 breast cancer cells significantly enhanced cell proliferation, suggesting PARP4 functions as a tumor suppressor in breast cancer cells.","method":"siRNA knockdown; cell proliferation assay","journal":"Endocrine-related cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single method (proliferation assay after siRNA), single lab, no pathway placement","pmids":["26699384"],"is_preprint":false},{"year":2023,"finding":"X-ray crystal structures of the PARP4 catalytic domain reveal an active site open to NAD+ interaction (in contrast to the closed conformation of PARP1), and structures of the minimal ADP-ribosyltransferase fold show active site alterations that restrict PARP4 to mono(ADP-ribose) rather than poly(ADP-ribose) modifications. The BRCT-WGR-CAT construct has lower activity than the CAT domain alone, indicating the BRCT and WGR domains regulate catalytic output. PARP4 was also shown to interact with vault RNA, with the BRCT domain primarily responsible for this interaction, though vault RNA binding does not stimulate mono(ADP-ribosylation) activity.","method":"X-ray crystallography; in vitro ADP-ribosylation activity assays; RNA-binding assays with vault RNA","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures combined with biochemical activity assays and RNA-binding assays; multiple orthogonal methods in one study","pmids":["37971310"],"is_preprint":false},{"year":2025,"finding":"X-ray structure of the isolated PARP4 BRCT domain was determined, and structure-based mutagenesis identified four BRCT mutants that disrupt vault RNA interaction to varying degrees. An electropositive surface region of the BRCT domain mediates nucleic acid binding. The isolated BRCT domain is sufficient to mediate interaction with vault RNA.","method":"X-ray crystallography; structure-based mutagenesis; in vitro vault RNA-binding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis with functional validation, multiple orthogonal methods in one study","pmids":["40412520"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structure of the human vault cage in complex with PARP4 and NAD+ revealed atomic-level details of the PARP4-MVP binding interface and unexpected NAD+-binding sites within the interior of the vault cage. Proteomics of vaults from wild-type vs. PARP4-depleted cells showed PARP4 incorporation regulates the subset of cargo proteins associated with the vault and its subcellular localization.","method":"Cryo-EM structure determination; proteomics of immunopurified vault particles from wild-type and PARP4-depleted cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with functional proteomics validation, multiple orthogonal methods","pmids":["40691181"],"is_preprint":false},{"year":2024,"finding":"PARP4 depletion or the I1039T mutation promotes tumorigenicity of KRAS- or EGFR-driven lung cancer cells independently of the vault complex. Quantitative mass spectrometry interactomics identified hnRNPM as a novel PARP4 interaction partner. Loss of hnRNPM similarly promotes tumor formation and results in dysregulated intronic splicing patterns that are also observed in PARP4 knockdown cells.","method":"In vitro and in vivo tumorigenicity assays; quantitative mass spectrometry interactomics; transcriptomic splicing analysis in cell lines and patient tumors","journal":"Genome medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based interactomics identifying novel binding partner, functional tumorigenicity assays in vitro and in vivo, splicing analysis; single lab","pmids":["39034402"],"is_preprint":false},{"year":2025,"finding":"PARP4 catalyzes mono-ADP-ribosylation of Ku80 and thereby participates in non-homologous end joining (NHEJ) DNA double-strand break repair. PARP4 deficiency impairs DSB repair and sensitizes melanoma cells to ATM inhibitor in a synthetic lethal manner.","method":"PARP4 knockdown/knockout; DSB repair assays (NHEJ pathway markers); Ku80 mono-ADP-ribosylation assay; cell viability assays with ATM inhibitor","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — identification of substrate (Ku80) via ADP-ribosylation assay with loss-of-function and pathway (NHEJ) placement; single lab","pmids":["39885134"],"is_preprint":false},{"year":2026,"finding":"PARP4 ADP-ribosylates PIDD1 at conserved E783 in the PIDD1 death domain (DD) in response to DNA interstrand cross-links (ICL). This modification is triggered downstream of ATR phosphorylation-induced, PIAS1-mediated SUMOylation of the PIDD1 DD, which enables PARP4 docking. E783 ADP-ribosylation is required for caspase-2 dimerization and PIDDosome completion, but not for RAIDD and caspase-2 recruitment. PARP14 (a ribosylhydrolase) reverses this modification. Loss of PARP4 eliminates caspase-2 activation and apoptosis in response to ICL.","method":"ADP-ribosylation assays with PIDD1 substrate; mutagenesis of E783; PARP4 and PARP14 knockdown/knockout; caspase-2 dimerization and PIDDosome assembly assays; genetic epistasis with ATR and PIAS1","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — substrate identified (PIDD1 E783), writer (PARP4) and eraser (PARP14) defined, site-specific mutagenesis, mechanistic epistasis (ATR→SUMOylation→PARP4 docking→ADPr), multiple orthogonal functional readouts","pmids":["42054439"],"is_preprint":false},{"year":2023,"finding":"PARP4 expression is epigenetically regulated by promoter CpG methylation: hypomethylation of specific CpG sites (cg18582260 and cg17117459) in the PARP4 promoter correlates with upregulated PARP4 mRNA in cisplatin-resistant ovarian cancer cell lines. Treating cisplatin-sensitive cell lines with a demethylation agent restores PARP4 expression. Depletion of PARP4 in cisplatin-resistant cell lines reduced cisplatin chemoresistance and promoted cisplatin-induced DNA fragmentation.","method":"Bisulfite methylation analysis; demethylating agent treatment; siRNA knockdown; cell viability and DNA fragmentation assays","journal":"BMB reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epigenetic regulation demonstrated by methylation profiling plus functional rescue experiment; knockdown with defined cellular phenotype; single lab","pmids":["37013346"],"is_preprint":false}],"current_model":"PARP4 (VPARP) is a mono(ADP-ribose) polymerase that resides within the cytoplasmic vault ribonucleoprotein organelle, where its BRCT domain binds vault RNA and its C-terminus docks onto MVP at atomic-level contacts revealed by cryo-EM; within the vault it ADP-ribosylates MVP and regulates vault cargo selection and subcellular localization. Outside the vault complex, PARP4 ADP-ribosylates PIDD1 at E783 downstream of an ATR→SUMOylation cascade to complete PIDDosome assembly and activate caspase-2 in response to DNA interstrand cross-links, while PARP14 reverses this mark; PARP4 also ADP-ribosylates Ku80 to support non-homologous end joining, interacts with hnRNPM to regulate pre-mRNA splicing, and in cardiomyocytes acts as a proapoptotic regulator whose antagonism permits cell cycle reentry."},"narrative":{"mechanistic_narrative":"PARP4 (VPARP/p193) is a mono(ADP-ribose) transferase that functions both as a structural and enzymatic component of the cytoplasmic vault ribonucleoprotein and as a free regulator of DNA-damage signaling and apoptosis [PMID:10477748, PMID:42054439]. Within the vault, PARP4 docks onto MVP through its C-terminal region in an activity-independent manner, lines the inner surface of the assembled particle, and ADP-ribosylates MVP [PMID:10477748, PMID:15504404, PMID:15567158, PMID:40691181]; its BRCT domain binds vault RNA through an electropositive surface, and PARP4 incorporation governs vault cargo selection and subcellular localization [PMID:37971310, PMID:40412520, PMID:40691181]. Crystallographic analysis shows the catalytic active site is open to NAD+ but configured to deposit mono- rather than poly(ADP-ribose), with the BRCT and WGR domains tuning catalytic output [PMID:37971310]. Outside the vault, PARP4 ADP-ribosylates PIDD1 at E783 downstream of an ATR-phosphorylation/PIAS1-SUMOylation cascade that licenses PARP4 docking, a mark required for caspase-2 dimerization and PIDDosome completion in response to DNA interstrand cross-links and reversed by the hydrolase PARP14 [PMID:42054439]. PARP4 also mono-ADP-ribosylates Ku80 to support non-homologous end joining, such that its loss impairs double-strand break repair and confers synthetic lethality with ATM inhibition [PMID:39885134], and it interacts with hnRNPM to regulate intronic pre-mRNA splicing and restrain tumorigenicity independently of the vault [PMID:39034402]. Consistent with a tumor-restraining and proapoptotic role, PARP4 normally limits cardiomyocyte cell cycle reentry [PMID:11375269, PMID:15142950] and its depletion enhances cancer cell proliferation and chemoresistance [PMID:26699384, PMID:37013346].","teleology":[{"year":1999,"claim":"Established PARP4 as a bona fide ADP-ribosylating enzyme and a resident component of the vault particle, defining MVP as a substrate.","evidence":"Yeast two-hybrid, in vitro ADP-ribosylation with purified recombinant catalytic domain, and immunofluorescence","pmids":["10477748"],"confidence":"High","gaps":["Did not resolve whether enzymatic activity is required for vault association","Functional consequence of MVP ADP-ribosylation unknown"]},{"year":2001,"claim":"Defined a proapoptotic, cell-cycle-restricting role for PARP4 in cardiomyocytes distinct from p53.","evidence":"Dominant-interfering p193 truncation mutants in ES-cell-derived cardiomyocytes with apoptosis and cell cycle readouts","pmids":["11375269"],"confidence":"Medium","gaps":["Molecular mechanism of the proapoptotic activity not defined","Relies on truncation/dominant-interfering constructs rather than endogenous loss"]},{"year":2004,"claim":"Localized PARP4 structurally to the vault interior and showed it restricts cardiomyocyte cell cycle reentry in vivo after injury.","evidence":"CryoEM difference mapping of recombinant vaults; transgenic dominant-interfering p193 mouse with BrdU and histology post-infarction","pmids":["15504404","15142950"],"confidence":"Medium","gaps":["CryoEM resolution did not give atomic contacts","In vivo phenotype based on dominant-interfering allele, not knockout"]},{"year":2005,"claim":"Showed PARP4 incorporation into vaults is rapid and stable and that its C-terminus, not its catalytic activity, mediates MVP binding.","evidence":"Pulse-chase immunoprecipitation and co-sedimentation of a C-terminal truncation with MVP particles in E. coli","pmids":["15567158"],"confidence":"Medium","gaps":["Atomic-level interface not mapped","Single-lab biochemical reconstitution"]},{"year":2006,"claim":"Placed PARP4 in a complex with CUL7/Parc and p53, linking it to apoptotic regulation though distinct from its proapoptotic activity.","evidence":"Reciprocal Co-IP/Western and apoptosis assays in U2OS cells with dominant-interfering mutant","pmids":["17229476"],"confidence":"Medium","gaps":["Apoptosis resistance shown to be independent of complex disruption, leaving mechanism unresolved","No reciprocal validation of direct PARP4-p53 contact"]},{"year":2015,"claim":"Provided initial functional evidence for PARP4 as a tumor suppressor in breast cancer.","evidence":"siRNA knockdown and proliferation assay in HCC1143 cells","pmids":["26699384"],"confidence":"Low","gaps":["Single proliferation assay, single cell line, no pathway placement","No mechanism linking PARP4 enzymatic activity to growth restraint"]},{"year":2023,"claim":"Resolved the catalytic and BRCT architecture explaining why PARP4 is a mono-ART and how its domains regulate activity and bind vault RNA.","evidence":"X-ray crystallography of catalytic and BRCT-WGR-CAT constructs with in vitro activity and vault RNA-binding assays; bisulfite methylation profiling and rescue for promoter regulation","pmids":["37971310","37013346"],"confidence":"Medium","gaps":["Vault RNA binding does not stimulate activity, so its functional role remains undefined","Physiological substrates beyond MVP not addressed structurally"]},{"year":2024,"claim":"Identified hnRNPM as a PARP4 partner and a vault-independent role in pre-mRNA splicing and tumor restraint.","evidence":"Quantitative MS interactomics, in vitro/in vivo tumorigenicity assays, and transcriptomic splicing analysis in cells and patient tumors","pmids":["39034402"],"confidence":"Medium","gaps":["Whether ADP-ribosylation of hnRNPM mediates the splicing effect not shown","Single-lab interactomics"]},{"year":2025,"claim":"Delivered atomic-resolution definition of the PARP4-MVP/NAD+ vault interface, the BRCT-vault RNA contact, and a Ku80-dependent role in NHEJ.","evidence":"Cryo-EM of the vault cage with PARP4/NAD+ plus vault proteomics; BRCT crystal structure with mutagenesis; Ku80 ADP-ribosylation and DSB repair assays with ATM-inhibitor synthetic lethality","pmids":["40691181","40412520","39885134"],"confidence":"High","gaps":["Function of interior vault NAD+-binding sites unresolved","Mechanism by which PARP4 selects vault cargo not defined"]},{"year":2026,"claim":"Defined a complete writer-eraser ADP-ribosylation switch controlling PIDDosome assembly and caspase-2 activation after interstrand cross-links.","evidence":"PIDD1 E783 ADP-ribosylation and site-specific mutagenesis, PARP4/PARP14 loss-of-function, caspase-2 dimerization and PIDDosome assays, epistasis with ATR and PIAS1","pmids":["42054439"],"confidence":"High","gaps":["Whether vault-resident or free PARP4 performs this modification unclear","Generality beyond ICL-induced stress not tested"]},{"year":null,"claim":"How PARP4's vault-resident enzymatic activity, splicing role, and DNA-damage signaling functions are coordinated within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No model integrating vault localization with substrate access to PIDD1/Ku80","Physiological role of vault RNA binding to the BRCT domain unknown","Catalytic versus scaffolding contributions to tumor suppression not separated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,11,12]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,7,11,12]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[7,8]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,9]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[11,12]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3,12]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[10]}],"complexes":["vault ribonucleoprotein particle"],"partners":["MVP","HNRNPM","PIDD1","KU80","PARP14","CUL7","P53"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UKK3","full_name":"Protein mono-ADP-ribosyltransferase PARP4","aliases":["193 kDa vault protein","ADP-ribosyltransferase diphtheria toxin-like 4","ARTD4","PARP-related/IalphaI-related H5/proline-rich","PH5P","Poly [ADP-ribose] polymerase 4","PARP-4","Vault poly(ADP-ribose) polymerase","VPARP"],"length_aa":1724,"mass_kda":192.6,"function":"Mono-ADP-ribosyltransferase that mediates mono-ADP-ribosylation of target proteins","subcellular_location":"Cytoplasm; Nucleus; Cytoplasm, cytoskeleton, spindle","url":"https://www.uniprot.org/uniprotkb/Q9UKK3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PARP4","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PARP4","total_profiled":1310},"omim":[{"mim_id":"612695","title":"VAULT RNA 1-1; VTRNA1-1","url":"https://www.omim.org/entry/612695"},{"mim_id":"607519","title":"POLY(ADP-RIBOSE) POLYMERASE FAMILY, MEMBER 4; PARP4","url":"https://www.omim.org/entry/607519"},{"mim_id":"605088","title":"MAJOR VAULT PROTEIN; MVP","url":"https://www.omim.org/entry/605088"},{"mim_id":"601686","title":"TELOMERASE-ASSOCIATED PROTEIN 1; TEP1","url":"https://www.omim.org/entry/601686"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Microtubules","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Mitotic spindle","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PARP4"},"hgnc":{"alias_symbol":["VAULT3","p193","VPARP","VWA5C","ARTD4"],"prev_symbol":["ADPRTL1"]},"alphafold":{"accession":"Q9UKK3","domains":[{"cath_id":"3.40.50.10190","chopping":"11-92","consensus_level":"high","plddt":88.9632,"start":11,"end":92},{"cath_id":"-","chopping":"135-255","consensus_level":"high","plddt":76.6986,"start":135,"end":255},{"cath_id":"1.20.142.10","chopping":"261-378","consensus_level":"medium","plddt":82.8618,"start":261,"end":378},{"cath_id":"3.90.228.10","chopping":"380-576","consensus_level":"medium","plddt":84.7201,"start":380,"end":576},{"cath_id":"2.60.40.1730","chopping":"624-842_1171-1182_1190-1201","consensus_level":"high","plddt":78.481,"start":624,"end":1201},{"cath_id":"3.40.50.410","chopping":"868-1040","consensus_level":"medium","plddt":86.3239,"start":868,"end":1040},{"cath_id":"-","chopping":"1574-1721","consensus_level":"high","plddt":83.9974,"start":1574,"end":1721}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKK3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKK3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKK3-F1-predicted_aligned_error_v6.png","plddt_mean":69.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PARP4","jax_strain_url":"https://www.jax.org/strain/search?query=PARP4"},"sequence":{"accession":"Q9UKK3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UKK3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UKK3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKK3"}},"corpus_meta":[{"pmid":"10477748","id":"PMC_10477748","title":"The 193-kD vault protein, VPARP, is a novel poly(ADP-ribose) polymerase.","date":"1999","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/10477748","citation_count":340,"is_preprint":false},{"pmid":"15504404","id":"PMC_15504404","title":"Cryoelectron microscopy imaging of recombinant and tissue derived vaults: localization of the MVP N termini and VPARP.","date":"2004","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15504404","citation_count":75,"is_preprint":false},{"pmid":"14990695","id":"PMC_14990695","title":"Cul7/p185/p193 binding to simian virus 40 large T antigen has a role in cellular transformation.","date":"2004","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/14990695","citation_count":63,"is_preprint":false},{"pmid":"15142950","id":"PMC_15142950","title":"Expression of mutant p193 and p53 permits cardiomyocyte cell cycle reentry after myocardial infarction in transgenic mice.","date":"2004","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/15142950","citation_count":51,"is_preprint":false},{"pmid":"26699384","id":"PMC_26699384","title":"Germline PARP4 mutations in patients with primary thyroid and breast cancers.","date":"2015","source":"Endocrine-related cancer","url":"https://pubmed.ncbi.nlm.nih.gov/26699384","citation_count":50,"is_preprint":false},{"pmid":"11375269","id":"PMC_11375269","title":"Coexpression of mutant p53 and p193 renders embryonic stem cell-derived cardiomyocytes responsive to the growth-promoting activities of adenoviral E1A.","date":"2001","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/11375269","citation_count":27,"is_preprint":false},{"pmid":"15567158","id":"PMC_15567158","title":"Characterization of MVP and VPARP assembly into vault ribonucleoprotein complexes.","date":"2005","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/15567158","citation_count":24,"is_preprint":false},{"pmid":"39034402","id":"PMC_39034402","title":"PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression.","date":"2024","source":"Genome medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39034402","citation_count":14,"is_preprint":false},{"pmid":"31119570","id":"PMC_31119570","title":"Assessment of PARP4 as a candidate breast cancer susceptibility gene.","date":"2019","source":"Breast cancer research and treatment","url":"https://pubmed.ncbi.nlm.nih.gov/31119570","citation_count":13,"is_preprint":false},{"pmid":"37013346","id":"PMC_37013346","title":"Identification of a novel PARP4 gene promoter CpG locus associated with cisplatin chemoresistance.","date":"2023","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/37013346","citation_count":12,"is_preprint":false},{"pmid":"17229476","id":"PMC_17229476","title":"Expression of a mutant p193/CUL7 molecule confers resistance to MG132- and etoposide-induced apoptosis independent of p53 or Parc binding.","date":"2006","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/17229476","citation_count":12,"is_preprint":false},{"pmid":"37971310","id":"PMC_37971310","title":"Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP.","date":"2023","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/37971310","citation_count":11,"is_preprint":false},{"pmid":"28551640","id":"PMC_28551640","title":"vPARP Adjusts MVP Expression in Drug-resistant Cell Lines in Conjunction with MDR Proteins.","date":"2017","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/28551640","citation_count":11,"is_preprint":false},{"pmid":"31203137","id":"PMC_31203137","title":"Genetic variants of PARP4 gene and PARP4P2 pseudogene in patients with multiple primary tumors including thyroid cancer.","date":"2019","source":"Mutation research","url":"https://pubmed.ncbi.nlm.nih.gov/31203137","citation_count":10,"is_preprint":false},{"pmid":"15093136","id":"PMC_15093136","title":"Analysis of MVP and VPARP promoters indicates a role for chromatin remodeling in the regulation of MVP.","date":"2004","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/15093136","citation_count":9,"is_preprint":false},{"pmid":"19435717","id":"PMC_19435717","title":"Expression of a transgene encoding mutant p193/CUL7 preserves cardiac function and limits infarct expansion after myocardial infarction.","date":"2009","source":"Heart (British Cardiac Society)","url":"https://pubmed.ncbi.nlm.nih.gov/19435717","citation_count":7,"is_preprint":false},{"pmid":"32316696","id":"PMC_32316696","title":"Modification of PARP4, XRCC3, and RAD51 Gene Polymorphisms on the Relation between Bisphenol A Exposure and Liver Abnormality.","date":"2020","source":"International journal of environmental research and public health","url":"https://pubmed.ncbi.nlm.nih.gov/32316696","citation_count":6,"is_preprint":false},{"pmid":"40691181","id":"PMC_40691181","title":"Structural insights into the roles of PARP4 and NAD+ binding in the human vault cage.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40691181","citation_count":4,"is_preprint":false},{"pmid":"39885134","id":"PMC_39885134","title":"PARP4 deficiency enhances sensitivity to ATM inhibitor by impairing DNA damage repair in melanoma.","date":"2025","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/39885134","citation_count":3,"is_preprint":false},{"pmid":"35627777","id":"PMC_35627777","title":"Modification Effect of PARP4 and ERCC1 Gene Polymorphisms on the Relationship between Particulate Matter Exposure and Fasting Glucose Level.","date":"2022","source":"International journal of environmental research and public health","url":"https://pubmed.ncbi.nlm.nih.gov/35627777","citation_count":2,"is_preprint":false},{"pmid":"40412520","id":"PMC_40412520","title":"Crystal structure and mutagenesis of a nucleic acid-binding BRCT domain in human PARP4.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40412520","citation_count":1,"is_preprint":false},{"pmid":"38979142","id":"PMC_38979142","title":"Structural Insights into the Roles of PARP4 and NAD + in the Human Vault Cage.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38979142","citation_count":1,"is_preprint":false},{"pmid":"41999525","id":"PMC_41999525","title":"PARP4 drives tumor progression by promoting glioma cell proliferation and invasion as a potential therapeutic target.","date":"2026","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41999525","citation_count":0,"is_preprint":false},{"pmid":"42054439","id":"PMC_42054439","title":"PARP4 ADP-ribosylates PIDD1 to complete a phospho/SUMO/PAR-ylation cascade that orchestrates PIDDosome assembly.","date":"2026","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/42054439","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.06.25337172","title":"Somatic Mosaicism Patterns Define Clinical-Surgical Subtypes of Focal Cortical Dysplasia Through Cell-Type-Specific Expression","date":"2025-10-07","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.06.25337172","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.27.601040","title":"Structural Insights into the Roles of PARP4 and NAD  <sup>+</sup>  in the Human Vault Cage","date":"2024-06-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.27.601040","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.20.649719","title":"Greater Expression of DNA Repair Pathways in Sharks vs. Rays/Skates Based on Transcriptomic Analyses","date":"2025-04-21","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.20.649719","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15377,"output_tokens":3857,"usd":0.051993,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11628,"output_tokens":3545,"usd":0.073383,"stage2_stop_reason":"end_turn"},"total_usd":0.125376,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"PARP4 (p193/VPARP) was identified as a poly(ADP-ribose) polymerase: its catalytic domain, expressed and purified from bacteria, catalyzes a poly(ADP-ribosylation) reaction in vitro. Purified vault particles retain this enzymatic activity, and MVP is a substrate for vault-associated PARP activity. A portion of p193 localizes to the nucleus and to the mitotic spindle.\",\n      \"method\": \"Yeast two-hybrid screen (identification of MVP interaction), peptide sequence analysis, in vitro poly(ADP-ribosylation) assay with purified recombinant catalytic domain, immunofluorescence and biochemical fractionation\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic reconstitution with purified protein, substrate identification (MVP), localization by immunofluorescence; foundational study replicated by subsequent work\",\n      \"pmids\": [\"10477748\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CryoEM difference mapping localized VPARP (PARP4) to three density bands lining the inner surface of the vault particle, establishing its structural position within the assembled vault ribonucleoprotein complex.\",\n      \"method\": \"Cryoelectron microscopy and single-particle image reconstruction with difference mapping of recombinant vaults co-expressing MVP and VPARP\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct structural localization by cryoEM with difference mapping, single lab but rigorous structural method\",\n      \"pmids\": [\"15504404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Newly synthesized VPARP is completely incorporated into vault particles within 1.5 hours and is stable once incorporated. The C-terminal region of VPARP lacking poly(ADP-ribose)polymerase activity is sufficient for co-sedimentation with MVP-assembled vault-like particles, indicating that PARP4 enzymatic activity is not required for its interaction with MVP.\",\n      \"method\": \"Immunoprecipitation pulse-chase assay, co-sedimentation of C-terminal VPARP truncation mutant with MVP particles in E. coli expression system\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and co-sedimentation with defined truncation mutant, single lab, two orthogonal approaches\",\n      \"pmids\": [\"15567158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"p193 (PARP4) encodes a proapoptotic activity in cardiomyocytes: a C-terminal truncation mutant of p193 confers prosurvival activity, and combined expression of this mutant with a dominant-interfering p53 mutant blocks E1A-induced apoptosis in embryonic stem cell-derived cardiomyocytes, demonstrating that p193 and p53 define two distinct proapoptotic pathways that restrict cardiomyocyte cell cycle activity.\",\n      \"method\": \"Transgene expression of p193 truncation mutant in differentiating embryonic stem cell-derived cardiomyocytes; apoptosis assays combined with cell cycle analysis; structure-function analysis\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via dominant-interfering mutants and apoptosis readout, single lab with multiple constructs\",\n      \"pmids\": [\"11375269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Expression of a dominant-interfering p193 (PARP4) mutant in transgenic cardiomyocytes induces cardiomyocyte cell cycle reentry at the infarct border zone after myocardial infarction and reduces hypertrophic growth in interventricular septa, indicating p193 normally restricts cardiomyocyte cell cycle activity in the injured adult heart.\",\n      \"method\": \"Transgenic mouse model expressing dominant-interfering p193 mutant under cardiac-specific promoter; BrdU incorporation assay; histological analysis post-coronary artery occlusion\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo loss-of-function with specific cell cycle and hypertrophy phenotypic readouts, single lab\",\n      \"pmids\": [\"15142950\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Endogenous p193/CUL7 (PARP4) forms a complex with Parc (a parkin-like ubiquitin ligase) and p53, as detected by immunoprecipitation/Western analysis. Expression of a dominant-interfering p193 truncation (1152stop) confers resistance to MG132- and etoposide-induced apoptosis, but this resistance is independent of disruption of the endogenous p193/CUL7–Parc–p53 complex.\",\n      \"method\": \"Immune precipitation/Western blot analysis; apoptosis assays in U2OS cells expressing dominant-interfering p193 mutant\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying a three-protein complex, functional apoptosis assay, single lab\",\n      \"pmids\": [\"17229476\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"siRNA knockdown of PARP4 in HCC1143 breast cancer cells significantly enhanced cell proliferation, suggesting PARP4 functions as a tumor suppressor in breast cancer cells.\",\n      \"method\": \"siRNA knockdown; cell proliferation assay\",\n      \"journal\": \"Endocrine-related cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single method (proliferation assay after siRNA), single lab, no pathway placement\",\n      \"pmids\": [\"26699384\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"X-ray crystal structures of the PARP4 catalytic domain reveal an active site open to NAD+ interaction (in contrast to the closed conformation of PARP1), and structures of the minimal ADP-ribosyltransferase fold show active site alterations that restrict PARP4 to mono(ADP-ribose) rather than poly(ADP-ribose) modifications. The BRCT-WGR-CAT construct has lower activity than the CAT domain alone, indicating the BRCT and WGR domains regulate catalytic output. PARP4 was also shown to interact with vault RNA, with the BRCT domain primarily responsible for this interaction, though vault RNA binding does not stimulate mono(ADP-ribosylation) activity.\",\n      \"method\": \"X-ray crystallography; in vitro ADP-ribosylation activity assays; RNA-binding assays with vault RNA\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures combined with biochemical activity assays and RNA-binding assays; multiple orthogonal methods in one study\",\n      \"pmids\": [\"37971310\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"X-ray structure of the isolated PARP4 BRCT domain was determined, and structure-based mutagenesis identified four BRCT mutants that disrupt vault RNA interaction to varying degrees. An electropositive surface region of the BRCT domain mediates nucleic acid binding. The isolated BRCT domain is sufficient to mediate interaction with vault RNA.\",\n      \"method\": \"X-ray crystallography; structure-based mutagenesis; in vitro vault RNA-binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis with functional validation, multiple orthogonal methods in one study\",\n      \"pmids\": [\"40412520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the human vault cage in complex with PARP4 and NAD+ revealed atomic-level details of the PARP4-MVP binding interface and unexpected NAD+-binding sites within the interior of the vault cage. Proteomics of vaults from wild-type vs. PARP4-depleted cells showed PARP4 incorporation regulates the subset of cargo proteins associated with the vault and its subcellular localization.\",\n      \"method\": \"Cryo-EM structure determination; proteomics of immunopurified vault particles from wild-type and PARP4-depleted cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with functional proteomics validation, multiple orthogonal methods\",\n      \"pmids\": [\"40691181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PARP4 depletion or the I1039T mutation promotes tumorigenicity of KRAS- or EGFR-driven lung cancer cells independently of the vault complex. Quantitative mass spectrometry interactomics identified hnRNPM as a novel PARP4 interaction partner. Loss of hnRNPM similarly promotes tumor formation and results in dysregulated intronic splicing patterns that are also observed in PARP4 knockdown cells.\",\n      \"method\": \"In vitro and in vivo tumorigenicity assays; quantitative mass spectrometry interactomics; transcriptomic splicing analysis in cell lines and patient tumors\",\n      \"journal\": \"Genome medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based interactomics identifying novel binding partner, functional tumorigenicity assays in vitro and in vivo, splicing analysis; single lab\",\n      \"pmids\": [\"39034402\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PARP4 catalyzes mono-ADP-ribosylation of Ku80 and thereby participates in non-homologous end joining (NHEJ) DNA double-strand break repair. PARP4 deficiency impairs DSB repair and sensitizes melanoma cells to ATM inhibitor in a synthetic lethal manner.\",\n      \"method\": \"PARP4 knockdown/knockout; DSB repair assays (NHEJ pathway markers); Ku80 mono-ADP-ribosylation assay; cell viability assays with ATM inhibitor\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — identification of substrate (Ku80) via ADP-ribosylation assay with loss-of-function and pathway (NHEJ) placement; single lab\",\n      \"pmids\": [\"39885134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PARP4 ADP-ribosylates PIDD1 at conserved E783 in the PIDD1 death domain (DD) in response to DNA interstrand cross-links (ICL). This modification is triggered downstream of ATR phosphorylation-induced, PIAS1-mediated SUMOylation of the PIDD1 DD, which enables PARP4 docking. E783 ADP-ribosylation is required for caspase-2 dimerization and PIDDosome completion, but not for RAIDD and caspase-2 recruitment. PARP14 (a ribosylhydrolase) reverses this modification. Loss of PARP4 eliminates caspase-2 activation and apoptosis in response to ICL.\",\n      \"method\": \"ADP-ribosylation assays with PIDD1 substrate; mutagenesis of E783; PARP4 and PARP14 knockdown/knockout; caspase-2 dimerization and PIDDosome assembly assays; genetic epistasis with ATR and PIAS1\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — substrate identified (PIDD1 E783), writer (PARP4) and eraser (PARP14) defined, site-specific mutagenesis, mechanistic epistasis (ATR→SUMOylation→PARP4 docking→ADPr), multiple orthogonal functional readouts\",\n      \"pmids\": [\"42054439\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PARP4 expression is epigenetically regulated by promoter CpG methylation: hypomethylation of specific CpG sites (cg18582260 and cg17117459) in the PARP4 promoter correlates with upregulated PARP4 mRNA in cisplatin-resistant ovarian cancer cell lines. Treating cisplatin-sensitive cell lines with a demethylation agent restores PARP4 expression. Depletion of PARP4 in cisplatin-resistant cell lines reduced cisplatin chemoresistance and promoted cisplatin-induced DNA fragmentation.\",\n      \"method\": \"Bisulfite methylation analysis; demethylating agent treatment; siRNA knockdown; cell viability and DNA fragmentation assays\",\n      \"journal\": \"BMB reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epigenetic regulation demonstrated by methylation profiling plus functional rescue experiment; knockdown with defined cellular phenotype; single lab\",\n      \"pmids\": [\"37013346\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PARP4 (VPARP) is a mono(ADP-ribose) polymerase that resides within the cytoplasmic vault ribonucleoprotein organelle, where its BRCT domain binds vault RNA and its C-terminus docks onto MVP at atomic-level contacts revealed by cryo-EM; within the vault it ADP-ribosylates MVP and regulates vault cargo selection and subcellular localization. Outside the vault complex, PARP4 ADP-ribosylates PIDD1 at E783 downstream of an ATR→SUMOylation cascade to complete PIDDosome assembly and activate caspase-2 in response to DNA interstrand cross-links, while PARP14 reverses this mark; PARP4 also ADP-ribosylates Ku80 to support non-homologous end joining, interacts with hnRNPM to regulate pre-mRNA splicing, and in cardiomyocytes acts as a proapoptotic regulator whose antagonism permits cell cycle reentry.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PARP4 (VPARP/p193) is a mono(ADP-ribose) transferase that functions both as a structural and enzymatic component of the cytoplasmic vault ribonucleoprotein and as a free regulator of DNA-damage signaling and apoptosis [#0, #12]. Within the vault, PARP4 docks onto MVP through its C-terminal region in an activity-independent manner, lines the inner surface of the assembled particle, and ADP-ribosylates MVP [#0, #1, #2, #9]; its BRCT domain binds vault RNA through an electropositive surface, and PARP4 incorporation governs vault cargo selection and subcellular localization [#7, #8, #9]. Crystallographic analysis shows the catalytic active site is open to NAD+ but configured to deposit mono- rather than poly(ADP-ribose), with the BRCT and WGR domains tuning catalytic output [#7]. Outside the vault, PARP4 ADP-ribosylates PIDD1 at E783 downstream of an ATR-phosphorylation/PIAS1-SUMOylation cascade that licenses PARP4 docking, a mark required for caspase-2 dimerization and PIDDosome completion in response to DNA interstrand cross-links and reversed by the hydrolase PARP14 [#12]. PARP4 also mono-ADP-ribosylates Ku80 to support non-homologous end joining, such that its loss impairs double-strand break repair and confers synthetic lethality with ATM inhibition [#11], and it interacts with hnRNPM to regulate intronic pre-mRNA splicing and restrain tumorigenicity independently of the vault [#10]. Consistent with a tumor-restraining and proapoptotic role, PARP4 normally limits cardiomyocyte cell cycle reentry [#3, #4] and its depletion enhances cancer cell proliferation and chemoresistance [#6, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established PARP4 as a bona fide ADP-ribosylating enzyme and a resident component of the vault particle, defining MVP as a substrate.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro ADP-ribosylation with purified recombinant catalytic domain, and immunofluorescence\",\n      \"pmids\": [\"10477748\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether enzymatic activity is required for vault association\", \"Functional consequence of MVP ADP-ribosylation unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined a proapoptotic, cell-cycle-restricting role for PARP4 in cardiomyocytes distinct from p53.\",\n      \"evidence\": \"Dominant-interfering p193 truncation mutants in ES-cell-derived cardiomyocytes with apoptosis and cell cycle readouts\",\n      \"pmids\": [\"11375269\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of the proapoptotic activity not defined\", \"Relies on truncation/dominant-interfering constructs rather than endogenous loss\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Localized PARP4 structurally to the vault interior and showed it restricts cardiomyocyte cell cycle reentry in vivo after injury.\",\n      \"evidence\": \"CryoEM difference mapping of recombinant vaults; transgenic dominant-interfering p193 mouse with BrdU and histology post-infarction\",\n      \"pmids\": [\"15504404\", \"15142950\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"CryoEM resolution did not give atomic contacts\", \"In vivo phenotype based on dominant-interfering allele, not knockout\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showed PARP4 incorporation into vaults is rapid and stable and that its C-terminus, not its catalytic activity, mediates MVP binding.\",\n      \"evidence\": \"Pulse-chase immunoprecipitation and co-sedimentation of a C-terminal truncation with MVP particles in E. coli\",\n      \"pmids\": [\"15567158\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Atomic-level interface not mapped\", \"Single-lab biochemical reconstitution\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Placed PARP4 in a complex with CUL7/Parc and p53, linking it to apoptotic regulation though distinct from its proapoptotic activity.\",\n      \"evidence\": \"Reciprocal Co-IP/Western and apoptosis assays in U2OS cells with dominant-interfering mutant\",\n      \"pmids\": [\"17229476\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Apoptosis resistance shown to be independent of complex disruption, leaving mechanism unresolved\", \"No reciprocal validation of direct PARP4-p53 contact\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided initial functional evidence for PARP4 as a tumor suppressor in breast cancer.\",\n      \"evidence\": \"siRNA knockdown and proliferation assay in HCC1143 cells\",\n      \"pmids\": [\"26699384\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single proliferation assay, single cell line, no pathway placement\", \"No mechanism linking PARP4 enzymatic activity to growth restraint\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved the catalytic and BRCT architecture explaining why PARP4 is a mono-ART and how its domains regulate activity and bind vault RNA.\",\n      \"evidence\": \"X-ray crystallography of catalytic and BRCT-WGR-CAT constructs with in vitro activity and vault RNA-binding assays; bisulfite methylation profiling and rescue for promoter regulation\",\n      \"pmids\": [\"37971310\", \"37013346\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Vault RNA binding does not stimulate activity, so its functional role remains undefined\", \"Physiological substrates beyond MVP not addressed structurally\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified hnRNPM as a PARP4 partner and a vault-independent role in pre-mRNA splicing and tumor restraint.\",\n      \"evidence\": \"Quantitative MS interactomics, in vitro/in vivo tumorigenicity assays, and transcriptomic splicing analysis in cells and patient tumors\",\n      \"pmids\": [\"39034402\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ADP-ribosylation of hnRNPM mediates the splicing effect not shown\", \"Single-lab interactomics\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Delivered atomic-resolution definition of the PARP4-MVP/NAD+ vault interface, the BRCT-vault RNA contact, and a Ku80-dependent role in NHEJ.\",\n      \"evidence\": \"Cryo-EM of the vault cage with PARP4/NAD+ plus vault proteomics; BRCT crystal structure with mutagenesis; Ku80 ADP-ribosylation and DSB repair assays with ATM-inhibitor synthetic lethality\",\n      \"pmids\": [\"40691181\", \"40412520\", \"39885134\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Function of interior vault NAD+-binding sites unresolved\", \"Mechanism by which PARP4 selects vault cargo not defined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined a complete writer-eraser ADP-ribosylation switch controlling PIDDosome assembly and caspase-2 activation after interstrand cross-links.\",\n      \"evidence\": \"PIDD1 E783 ADP-ribosylation and site-specific mutagenesis, PARP4/PARP14 loss-of-function, caspase-2 dimerization and PIDDosome assays, epistasis with ATR and PIAS1\",\n      \"pmids\": [\"42054439\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether vault-resident or free PARP4 performs this modification unclear\", \"Generality beyond ICL-induced stress not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PARP4's vault-resident enzymatic activity, splicing role, and DNA-damage signaling functions are coordinated within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No model integrating vault localization with substrate access to PIDD1/Ku80\", \"Physiological role of vault RNA binding to the BRCT domain unknown\", \"Catalytic versus scaffolding contributions to tumor suppression not separated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 11, 12]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 7, 11, 12]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005819\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [11, 12]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3, 12]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [\n      \"vault ribonucleoprotein particle\"\n    ],\n    \"partners\": [\n      \"MVP\",\n      \"hnRNPM\",\n      \"PIDD1\",\n      \"Ku80\",\n      \"PARP14\",\n      \"CUL7\",\n      \"p53\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}