{"gene":"PAXX","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2015,"finding":"PAXX (C9orf142) is a structural paralog of XRCC4, as determined by crystal structure, and directly interacts with Ku to promote DNA double-strand break repair by NHEJ. PAXX promotes Ku-dependent DNA ligation in vitro and facilitates assembly of core NHEJ factors on damaged chromatin in cells.","method":"Crystal structure determination, direct binding assay, in vitro ligation assay, RNAi/CRISPR-Cas9 KO with DSB sensitivity phenotype, chromatin fractionation","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure, in vitro reconstitution assay, mutagenesis, and cellular KO phenotype in a single rigorous study","pmids":["25574025"],"is_preprint":false},{"year":2015,"finding":"XLS/PAXX (c9orf142) co-purifies with DNA-PKcs and other core NHEJ factors (identified by affinity purification-mass spectrometry) and interacts with core NHEJ factors; its depletion impairs DSB repair consistent with an NHEJ defect.","method":"Affinity purification–mass spectrometry, co-immunoprecipitation, computational structural modeling, siRNA knockdown with DSB repair assay","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal AP-MS plus KD phenotype, single lab, two orthogonal methods","pmids":["25941166"],"is_preprint":false},{"year":2016,"finding":"PAXX forms a stable ternary complex with Ku bound to DNA through a direct interaction specifically with Ku70 (not Ku80), and this complex requires a bare DNA extension for stability. PAXX provides only weak stimulation of LIG4/XRCC4 ligation activity, which is unmasked when XLF is absent.","method":"Biochemical complex reconstitution, co-immunoprecipitation, in vitro ligation assay, PAXX-deficient cell lines","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of ternary complex plus ligation assay, single lab with multiple orthogonal methods","pmids":["27705800"],"is_preprint":false},{"year":2016,"finding":"PAXX function in V(D)J recombination depends on its interaction with Ku; PAXX and XLF have redundant functions in NHEJ such that combined deficiency abrogates DSB joining, whereas PAXX deficiency alone does not phenocopy loss of core NHEJ factors. Unlike XLF, PAXX's role does not overlap with ATM or the RAG complex.","method":"CRISPR/genetic KO mouse models, V(D)J recombination assays, epistasis analysis with ATM/RAG, Ku-binding mutants","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with multiple defined KO combinations replicated across labs, Ku-binding domain mutants tested functionally","pmids":["27601299"],"is_preprint":false},{"year":2016,"finding":"PAXX and XLF are functionally redundant for joining DSBs in G1-arrested pro-B cells during V(D)J recombination; combined PAXX/XLF deficiency abrogates DSB joining and sensitizes cells to ionizing radiation, but PAXX deficiency alone has no impact even in ATM-deficient pro-B lines.","method":"CRISPR/genetic KO in G1-arrested mouse pro-B cell lines, V(D)J recombination assay, IR sensitivity assay, class switch recombination assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic KO with defined cellular phenotype, replicated by multiple labs","pmids":["27601633"],"is_preprint":false},{"year":2017,"finding":"PAXX promotes accumulation of KU at DSBs in vivo, while XLF enhances LIG4 recruitment without affecting KU dynamics; these represent distinct but critically complementary molecular functions within NHEJ. Paxx/Xlf double-KO mice show severe genomic instability, neuronal apoptosis, and embryonic lethality.","method":"Mouse genetic KO models, live-cell imaging/ChIP for KU and LIG4 dynamics at DSBs, epistasis with ATM/DNA-PK inhibitors","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct measurement of KU accumulation at DSBs in vivo combined with genetic epistasis across multiple KO combinations, replicated across labs","pmids":["28051062"],"is_preprint":false},{"year":2016,"finding":"Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency in mice, but Paxx/Xlf double-knockout is synthetic-lethal in mammals, with embryonic lethality, genomic instability, CNS cell death, and near-complete block in lymphogenesis phenocopying Xrcc4-/- or Lig4-/- mice.","method":"Mouse genetic KO models, epistasis analysis across multiple NHEJ-deficient backgrounds","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genetic epistasis with multiple combinations, replicated across independent labs","pmids":["27798842"],"is_preprint":false},{"year":2018,"finding":"PAXX, XLF, and XRCC4 share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity, and are required for recruitment of Pol λ to laser-induced DNA damage sites. This stimulation requires a direct interaction between the SP/8 kDa domain of Pol λ and the N-terminal head domains of XRCC4 paralogs, facilitating recognition of the 5' end of substrate gaps. PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends.","method":"Co-immunoprecipitation/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment assay, incompatible end-joining assay in cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay plus direct protein interaction plus domain mapping plus cellular recruitment assay in a single study","pmids":["30250067"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM and X-ray crystallography structures of PAXX C-terminal Ku-binding motif bound to Ku70/80 identify residues critical for the Ku70/PAXX interaction in vitro and in cells. PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK end-bridging dimers (mediated by either Ku80 or XLF), providing complementary advantage for DNA end synapsis and end joining.","method":"Cryo-EM, X-ray crystallography, mutagenesis of Ku70/PAXX interface residues, in vitro end-joining assay, cellular end-joining assay","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution structure plus interface mutagenesis plus functional end-joining assays in vitro and in cells","pmids":["37256950"],"is_preprint":false},{"year":2018,"finding":"PAXX deficiency causes modest sensitivity to DNA damage in human HAP1 cells (unlike XRCC4 or XLF deficiency) and PAXX-deficient murine CH12F3 B cells perform class switch recombination at near-wild-type levels, indicating that PAXX is largely dispensable for CSR and basal NHEJ in these cell systems.","method":"Genetic KO (CRISPR, mouse Paxx-/- CH12F3 cells), DSB-inducing agent sensitivity assay, CSR assay, chromosomal break analysis","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic KO with multiple cellular phenotype readouts, single lab","pmids":["29511621"],"is_preprint":false},{"year":2019,"finding":"Chemoresistance to doxorubicin or cisplatin in osteosarcoma cells results in enhanced PAXX–Ku70 interaction and elevated NHEJ efficiency; disruption of the PAXX–Ku70 interaction with small molecule M11 re-sensitizes resistant cells to these drugs.","method":"Co-immunoprecipitation of PAXX-Ku70 in resistant cells, NHEJ efficiency assay, small-molecule inhibitor (M11) treatment with drug sensitivity assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP plus functional rescue with small molecule, single lab, single study","pmids":["31640855"],"is_preprint":false},{"year":2018,"finding":"PAXX interacts with DNA polymerase β (Pol β) and contributes to base excision repair (BER); PAXX-deficient cells show increased sensitivity to the BER-substrate drug temozolomide in glioma cells.","method":"Co-immunoprecipitation of PAXX with Pol β, PAXX-deficient cell lines, TMZ sensitivity assay","journal":"Journal of molecular neuroscience","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP plus KD phenotype, single lab, no in vitro reconstitution or domain mapping","pmids":["30238427"],"is_preprint":false},{"year":2017,"finding":"PAXX is excluded from the nucleus during HSV-1 infection, and PAXX-/- cells show a defect in viral genome replication efficiency but produce greater numbers of infectious virions, indicating PAXX restricts HSV-1 infection in a manner distinct from other c-NHEJ factors.","method":"PAXX-/- cell lines, immunofluorescence localization during HSV-1 infection, viral replication and infectious virion production assays","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiment plus functional KO phenotype in viral context, single lab","pmids":["29144403"],"is_preprint":false},{"year":2019,"finding":"In human HAP1 cells, XLF but not PAXX genetically interacts with DNA-PKcs (i.e., XLF/DNA-PKcs double KO is more severe than either single KO, whereas PAXX/DNA-PKcs double KO phenocopies DNA-PKcs single KO). ATM has overlapping functions with DNA-PKcs, XLF, and XRCC4, but not with PAXX, in response to DSBs.","method":"CRISPR-generated human HAP1 single and double KO cell lines, DSB-inducing agent sensitivity assay, chromosomal break analysis, genetic epistasis","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic epistasis in human cells with multiple KO combinations, single lab","pmids":["31141305"],"is_preprint":false},{"year":2025,"finding":"A single conserved amino acid substitution in PAXX at the Ku70/80 contact interface dramatically stabilizes the PAXX–Ku repair complex, causes co-dependent mislocalization of PAXX and Ku to the nucleoli, and accelerates NHEJ repair specifically of DSBs requiring end processing (radiation-induced DSBs), revealing that repair complex stability at the Ku70/PAXX interface is rate-limiting for NHEJ of complex DSBs.","method":"Structure-guided mutagenesis of PAXX Ku70/80 interface, live-cell imaging of PAXX and Ku localization, NHEJ repair kinetics assay with radiation-induced vs. restriction enzyme DSBs","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structure-guided mutagenesis with functional repair assay, single lab, single study","pmids":["40659092"],"is_preprint":false},{"year":2025,"finding":"PAXX promotes DSB end synapsis during NHEJ in a manner partially redundant with DNA-PKcs and XLF; PAXX becomes important for blunt DSB end joining when DNA-PKcs or XLF is disrupted, but PAXX loss does not magnify the DNA-PKcs-mediated suppression of microhomology-mediated deletions, distinguishing its function from DNA-PKcs in end-use fidelity.","method":"Cas9-reporter end-joining assay in PAXX-/-, DNA-PKcs-inhibited, and XLF-/- single and combined-deficient human cell lines; indel profiling","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic KO/inhibitor epistasis with defined molecular readout, single lab, multiple combined deficiency conditions","pmids":["40546969"],"is_preprint":false},{"year":2021,"finding":"An XRCC4 separation-of-function mutation (M61R) that abolishes XRCC4–XLF filament formation while preserving LIG4 stabilization reveals that PAXX is functionally redundant with XRCC4-XLF filaments during V(D)J recombination; crossing Xrcc4-M61R mice onto Paxx-/- background causes severe immunodeficiency and embryonic lethality, identifying a direct functional interplay between XRCC4 and PAXX in NHEJ.","method":"Xrcc4 separation-of-function knock-in mouse crossed onto Paxx-/- background; V(D)J recombination assay; CNS apoptosis analysis; genetic epistasis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Moderate — defined separation-of-function allele combined with Paxx-/- in vivo genetic epistasis, single lab with multiple phenotypic readouts","pmids":["34519267"],"is_preprint":false}],"current_model":"PAXX is an accessory NHEJ factor and structural paralog of XRCC4 and XLF that directly binds Ku70 via its C-terminal motif (structurally defined by cryo-EM/crystallography), recruits and stabilizes KU at DSBs, promotes DNA end synapsis in alternate DNA-PK end-bridging dimers together with XLF, stimulates DNA polymerase λ activity through its N-terminal head domain to facilitate gap-filling, and is functionally redundant with XLF (and partially with DNA-PKcs) such that combined loss causes synthetic lethality in mice due to catastrophic failure of NHEJ-dependent neurogenesis and lymphocyte development."},"narrative":{"mechanistic_narrative":"PAXX (C9orf142) is an accessory factor of the classical non-homologous end-joining (NHEJ) pathway and a structural paralog of XRCC4 that promotes repair of DNA double-strand breaks (DSBs) [PMID:25574025]. Its principal molecular role is to engage the DSB-recognition machinery directly: PAXX binds Ku through a C-terminal motif that contacts Ku70 specifically, forming a stable PAXX–Ku–DNA ternary complex that requires a bare DNA extension and that drives accumulation of Ku at breaks in cells [PMID:27705800, PMID:28051062, PMID:37256950]. High-resolution cryo-EM and crystallographic analysis define the Ku70/PAXX interface and show that PAXX and XLF can bind the Ku heterodimer simultaneously, acting as alternative structural bridges in DNA-PK end-bridging dimers to promote DNA end synapsis [PMID:37256950, PMID:40546969]. Through its N-terminal head domain, PAXX—like its paralogs XRCC4 and XLF—interacts with and stimulates DNA polymerase λ and is required for its recruitment to damage sites, facilitating gap-filling and joining of incompatible ends [PMID:30250067]. Functionally, PAXX is largely redundant with XLF and partially with DNA-PKcs: loss of PAXX alone produces only modest DSB-repair defects, but combined PAXX/XLF deficiency abolishes end joining and is synthetic-lethal in mice, causing embryonic lethality, genomic instability, CNS apoptosis, and a near-complete block in lymphocyte development that phenocopies Xrcc4 or Lig4 loss [PMID:27601299, PMID:27601633, PMID:27798842]. Genetic interplay extends to XRCC4 itself, as PAXX is redundant with XRCC4–XLF filaments during V(D)J recombination [PMID:34519267]. The stability of the PAXX–Ku interface is rate-limiting for NHEJ of complex, end-processing-requiring DSBs, with interface-stabilizing mutations accelerating repair of radiation-induced breaks [PMID:40659092].","teleology":[{"year":2015,"claim":"Established PAXX as a previously unrecognized NHEJ factor by showing it is a structural paralog of XRCC4 that binds Ku and promotes Ku-dependent end ligation, defining its place in the core repair machinery.","evidence":"Crystal structure, direct binding and in vitro ligation assays, and CRISPR/RNAi KO with DSB-sensitivity and chromatin-assembly readouts","pmids":["25574025","25941166"],"confidence":"High","gaps":["Did not resolve which Ku subunit PAXX contacts","Magnitude of contribution relative to XLF/XRCC4 not established"]},{"year":2016,"claim":"Defined the molecular basis of PAXX's Ku engagement, showing a Ku70-specific, DNA-dependent ternary complex and that its ligation-stimulating role is weak and unmasked only when XLF is absent.","evidence":"Biochemical reconstitution of PAXX–Ku–DNA complex, co-IP, in vitro ligation assays in PAXX-deficient cells","pmids":["27705800"],"confidence":"High","gaps":["Atomic-resolution interface not yet defined","Quantitative redundancy with XLF not mapped genetically"]},{"year":2016,"claim":"Resolved why PAXX single loss is mild by demonstrating functional redundancy with XLF—combined deficiency abolishes DSB joining and V(D)J recombination, while PAXX alone does not phenocopy core factor loss and acts independently of ATM/RAG.","evidence":"CRISPR/genetic KO mouse models and G1-arrested pro-B cell lines, V(D)J and class-switch assays, IR sensitivity, epistasis with ATM/RAG, Ku-binding mutants","pmids":["27601299","27601633","27798842"],"confidence":"High","gaps":["Mechanistic distinction between PAXX and XLF activities not yet defined","Basis for synthetic lethality at the molecular level unresolved"]},{"year":2017,"claim":"Assigned PAXX and XLF distinct, complementary molecular tasks—PAXX promotes Ku accumulation at DSBs whereas XLF enhances LIG4 recruitment—and confirmed the developmental consequences of combined loss in vivo.","evidence":"Mouse KO models with live-cell imaging/ChIP of Ku and LIG4 dynamics, epistasis with ATM/DNA-PK inhibitors","pmids":["28051062"],"confidence":"High","gaps":["How PAXX stabilizes Ku mechanistically not structurally explained","Whether the two functions are strictly separable or overlap partially"]},{"year":2018,"claim":"Extended PAXX function beyond Ku tethering to gap-filling, showing PAXX (with XRCC4 and XLF) binds and stimulates DNA polymerase λ via its N-terminal head domain and is required for Pol λ recruitment to damage.","evidence":"Co-IP/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment, incompatible end-joining assay","pmids":["30250067"],"confidence":"High","gaps":["Relative contribution of each paralog to Pol λ stimulation in vivo not quantified","Structural basis of the head domain–Pol λ contact not defined"]},{"year":2018,"claim":"Probed cell-context dependence of PAXX, finding it largely dispensable for CSR and basal NHEJ in some human and mouse systems, and reported lower-confidence links to base excision repair via Pol β and a viral restriction role against HSV-1.","evidence":"Genetic KO with DSB/CSR and chromosomal-break readouts; Co-IP with Pol β and TMZ sensitivity; HSV-1 infection localization and replication assays","pmids":["29511621","30238427","29144403"],"confidence":"Medium","gaps":["Pol β/BER link rests on a single Co-IP without reconstitution or domain mapping","HSV-1 restriction mechanism distinct from NHEJ not defined","Cell-type basis for variable PAXX dependence unexplained"]},{"year":2019,"claim":"Refined the epistatic map in human cells, showing PAXX—unlike XLF—does not genetically interact with DNA-PKcs or overlap with ATM, distinguishing its functional niche from other accessory factors.","evidence":"CRISPR single/double KO HAP1 cells, DSB sensitivity, chromosomal break analysis, genetic epistasis; plus Co-IP/small-molecule (M11) chemoresistance study","pmids":["31141305","31640855"],"confidence":"Medium","gaps":["Mechanistic reason for lack of DNA-PKcs interaction not explained","M11/chemoresistance link is single-lab Co-IP plus inhibitor rescue"]},{"year":2023,"claim":"Delivered the atomic-resolution view of the Ku70/PAXX interface and showed PAXX and XLF can co-occupy Ku to form alternate DNA-PK end-bridging dimers, providing a structural model for redundant end-synapsis bridging.","evidence":"Cryo-EM, X-ray crystallography, interface mutagenesis, in vitro and cellular end-joining assays","pmids":["37256950"],"confidence":"High","gaps":["Dynamics of switching between PAXX- and XLF-bridged dimers in cells not resolved","Contribution of each bridging mode to repair fidelity not quantified"]},{"year":2025,"claim":"Connected PAXX–Ku complex stability to repair kinetics, showing an interface-stabilizing substitution accelerates NHEJ of end-processing-requiring DSBs and that PAXX promotes end synapsis partially redundantly with DNA-PKcs and XLF for blunt-end joining.","evidence":"Structure-guided interface mutagenesis with live-cell imaging and repair kinetics; Cas9-reporter end-joining with indel profiling across PAXX/DNA-PKcs/XLF-deficient cells","pmids":["40659092","40546969"],"confidence":"Medium","gaps":["Single-lab studies awaiting independent confirmation","Physiological significance of nucleolar mislocalization unclear","How interface stability tunes repair rate mechanistically not fully defined"]},{"year":2021,"claim":"Demonstrated direct functional interplay between PAXX and XRCC4, showing PAXX is redundant with XRCC4–XLF filaments in V(D)J recombination via a filament-deficient XRCC4 separation-of-function allele.","evidence":"Xrcc4-M61R knock-in mouse crossed onto Paxx-/- background, V(D)J and CNS apoptosis assays, genetic epistasis","pmids":["34519267"],"confidence":"High","gaps":["Whether PAXX substitutes structurally for XRCC4-XLF filaments not shown biochemically","Molecular basis of the rescue not defined"]},{"year":null,"claim":"How the alternate PAXX- and XLF-bridged DNA-PK synaptic complexes are dynamically selected and coordinated during repair of different break types, and whether PAXX's reported BER and viral-restriction roles reflect genuine NHEJ-independent functions, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No real-time structural data on bridging-mode selection in cells","BER/Pol β link unconfirmed by reconstitution","HSV-1 restriction mechanism undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[2,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,12]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[0,5]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[14]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,3,6,8]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,4,6,16]}],"complexes":["DNA-PK end-bridging dimer","PAXX-Ku-DNA ternary complex"],"partners":["XRCC6","XRCC5","DNA-PKCS","XLF","XRCC4","POLL","POLB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BUH6","full_name":"Protein PAXX","aliases":["Paralog of XRCC4 and XLF","XRCC4-like small protein"],"length_aa":204,"mass_kda":21.6,"function":"Non-essential DNA repair protein involved in DNA non-homologous end joining (NHEJ); participates in double-strand break (DSB) repair and V(D)J recombination (PubMed:25574025, PubMed:25670504, PubMed:25941166, PubMed:27705800). May act as a scaffold required for accumulation of the Ku heterodimer, composed of XRCC5/Ku80 and XRCC6/Ku70, at double-strand break sites and promote the assembly and/or stability of the NHEJ machinery (PubMed:25574025, PubMed:25670504, PubMed:25941166). Involved in NHEJ by promoting the ligation of blunt-ended DNA ends (PubMed:27703001). Together with NHEJ1/XLF, collaborates with DNA polymerase lambda (POLL) to promote joining of non-cohesive DNA ends (PubMed:25670504, PubMed:30250067). Constitutes a non-essential component of classical NHEJ: has a complementary but distinct function with NHEJ1/XLF in DNA repair (PubMed:27705800). Able to restrict infection by herpesvirus 1 (HSV-1) via an unknown mechanism (PubMed:29144403)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9BUH6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PAXX","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PAXX","total_profiled":1310},"omim":[{"mim_id":"620676","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 61; CCDC61","url":"https://www.omim.org/entry/620676"},{"mim_id":"616315","title":"PAXX NONHOMOLOGOUS END JOINING FACTOR; PAXX","url":"https://www.omim.org/entry/616315"},{"mim_id":"611290","title":"NONHOMOLOGOUS END-JOINING FACTOR 1; NHEJ1","url":"https://www.omim.org/entry/611290"},{"mim_id":"611003","title":"SMOKING AS A QUANTITATIVE TRAIT LOCUS 1; SQTL1","url":"https://www.omim.org/entry/611003"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PAXX"},"hgnc":{"alias_symbol":["XLS"],"prev_symbol":["C9orf142"]},"alphafold":{"accession":"Q9BUH6","domains":[{"cath_id":"2.170.210,2.170.210","chopping":"9-117","consensus_level":"high","plddt":92.0121,"start":9,"end":117}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BUH6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BUH6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BUH6-F1-predicted_aligned_error_v6.png","plddt_mean":82.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PAXX","jax_strain_url":"https://www.jax.org/strain/search?query=PAXX"},"sequence":{"accession":"Q9BUH6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BUH6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BUH6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BUH6"}},"corpus_meta":[{"pmid":"25574025","id":"PMC_25574025","title":"DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair.","date":"2015","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/25574025","citation_count":248,"is_preprint":false},{"pmid":"17659302","id":"PMC_17659302","title":"Molecular basis of Bcl-xL's target recognition versatility revealed by the structure of Bcl-xL in complex with the BH3 domain of Beclin-1.","date":"2007","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17659302","citation_count":159,"is_preprint":false},{"pmid":"27705800","id":"PMC_27705800","title":"PAXX Is an Accessory c-NHEJ Factor that Associates with Ku70 and Has Overlapping Functions with XLF.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27705800","citation_count":88,"is_preprint":false},{"pmid":"28051062","id":"PMC_28051062","title":"PAXX promotes KU accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28051062","citation_count":86,"is_preprint":false},{"pmid":"27601633","id":"PMC_27601633","title":"PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line.","date":"2016","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/27601633","citation_count":86,"is_preprint":false},{"pmid":"27601299","id":"PMC_27601299","title":"Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27601299","citation_count":73,"is_preprint":false},{"pmid":"27798842","id":"PMC_27798842","title":"Synthetic lethality between PAXX and XLF in mammalian development.","date":"2016","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/27798842","citation_count":66,"is_preprint":false},{"pmid":"25941166","id":"PMC_25941166","title":"XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair.","date":"2015","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/25941166","citation_count":58,"is_preprint":false},{"pmid":"27830975","id":"PMC_27830975","title":"Deficiency of XLF and PAXX prevents DNA double-strand break repair by non-homologous end joining in lymphocytes.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27830975","citation_count":40,"is_preprint":false},{"pmid":"37256950","id":"PMC_37256950","title":"PAXX binding to the NHEJ machinery explains functional redundancy with XLF.","date":"2023","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/37256950","citation_count":36,"is_preprint":false},{"pmid":"29077092","id":"PMC_29077092","title":"PAXX and Xlf interplay revealed by impaired CNS development and immunodeficiency of double KO mice.","date":"2017","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/29077092","citation_count":35,"is_preprint":false},{"pmid":"30250067","id":"PMC_30250067","title":"PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30250067","citation_count":26,"is_preprint":false},{"pmid":"31141305","id":"PMC_31141305","title":"Genetic interaction between DNA repair factors PAXX, XLF, XRCC4 and DNA-PKcs in human cells.","date":"2019","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/31141305","citation_count":25,"is_preprint":false},{"pmid":"32353736","id":"PMC_32353736","title":"miR-548e Sponged by ZFAS1 Regulates Metastasis and Cisplatin Resistance of OC by Targeting CXCR4 and let-7a/BCL-XL/S Signaling Axis.","date":"2020","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/32353736","citation_count":24,"is_preprint":false},{"pmid":"29511621","id":"PMC_29511621","title":"Robust DNA repair in PAXX-deficient mammalian cells.","date":"2018","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/29511621","citation_count":22,"is_preprint":false},{"pmid":"29511619","id":"PMC_29511619","title":"Normal development of mice lacking PAXX, the paralogue of XRCC4 and XLF.","date":"2018","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/29511619","citation_count":22,"is_preprint":false},{"pmid":"9042772","id":"PMC_9042772","title":"Immunolocalization of Bcl-xL/S in the central nervous system of neonatal and adult rats.","date":"1997","source":"Cell and tissue research","url":"https://pubmed.ncbi.nlm.nih.gov/9042772","citation_count":22,"is_preprint":false},{"pmid":"30579708","id":"PMC_30579708","title":"Synthetic lethality between DNA repair factors Xlf and Paxx is rescued by inactivation of 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to promote DNA double-strand break repair by NHEJ. PAXX promotes Ku-dependent DNA ligation in vitro and facilitates assembly of core NHEJ factors on damaged chromatin in cells.\",\n      \"method\": \"Crystal structure determination, direct binding assay, in vitro ligation assay, RNAi/CRISPR-Cas9 KO with DSB sensitivity phenotype, chromatin fractionation\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure, in vitro reconstitution assay, mutagenesis, and cellular KO phenotype in a single rigorous study\",\n      \"pmids\": [\"25574025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"XLS/PAXX (c9orf142) co-purifies with DNA-PKcs and other core NHEJ factors (identified by affinity purification-mass spectrometry) and interacts with core NHEJ factors; its depletion impairs DSB repair consistent with an NHEJ defect.\",\n      \"method\": \"Affinity purification–mass spectrometry, co-immunoprecipitation, computational structural modeling, siRNA knockdown with DSB repair assay\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal AP-MS plus KD phenotype, single lab, two orthogonal methods\",\n      \"pmids\": [\"25941166\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PAXX forms a stable ternary complex with Ku bound to DNA through a direct interaction specifically with Ku70 (not Ku80), and this complex requires a bare DNA extension for stability. PAXX provides only weak stimulation of LIG4/XRCC4 ligation activity, which is unmasked when XLF is absent.\",\n      \"method\": \"Biochemical complex reconstitution, co-immunoprecipitation, in vitro ligation assay, PAXX-deficient cell lines\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of ternary complex plus ligation assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27705800\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PAXX function in V(D)J recombination depends on its interaction with Ku; PAXX and XLF have redundant functions in NHEJ such that combined deficiency abrogates DSB joining, whereas PAXX deficiency alone does not phenocopy loss of core NHEJ factors. Unlike XLF, PAXX's role does not overlap with ATM or the RAG complex.\",\n      \"method\": \"CRISPR/genetic KO mouse models, V(D)J recombination assays, epistasis analysis with ATM/RAG, Ku-binding mutants\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with multiple defined KO combinations replicated across labs, Ku-binding domain mutants tested functionally\",\n      \"pmids\": [\"27601299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PAXX and XLF are functionally redundant for joining DSBs in G1-arrested pro-B cells during V(D)J recombination; combined PAXX/XLF deficiency abrogates DSB joining and sensitizes cells to ionizing radiation, but PAXX deficiency alone has no impact even in ATM-deficient pro-B lines.\",\n      \"method\": \"CRISPR/genetic KO in G1-arrested mouse pro-B cell lines, V(D)J recombination assay, IR sensitivity assay, class switch recombination assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic KO with defined cellular phenotype, replicated by multiple labs\",\n      \"pmids\": [\"27601633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PAXX promotes accumulation of KU at DSBs in vivo, while XLF enhances LIG4 recruitment without affecting KU dynamics; these represent distinct but critically complementary molecular functions within NHEJ. Paxx/Xlf double-KO mice show severe genomic instability, neuronal apoptosis, and embryonic lethality.\",\n      \"method\": \"Mouse genetic KO models, live-cell imaging/ChIP for KU and LIG4 dynamics at DSBs, epistasis with ATM/DNA-PK inhibitors\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct measurement of KU accumulation at DSBs in vivo combined with genetic epistasis across multiple KO combinations, replicated across labs\",\n      \"pmids\": [\"28051062\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency in mice, but Paxx/Xlf double-knockout is synthetic-lethal in mammals, with embryonic lethality, genomic instability, CNS cell death, and near-complete block in lymphogenesis phenocopying Xrcc4-/- or Lig4-/- mice.\",\n      \"method\": \"Mouse genetic KO models, epistasis analysis across multiple NHEJ-deficient backgrounds\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genetic epistasis with multiple combinations, replicated across independent labs\",\n      \"pmids\": [\"27798842\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PAXX, XLF, and XRCC4 share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity, and are required for recruitment of Pol λ to laser-induced DNA damage sites. This stimulation requires a direct interaction between the SP/8 kDa domain of Pol λ and the N-terminal head domains of XRCC4 paralogs, facilitating recognition of the 5' end of substrate gaps. PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends.\",\n      \"method\": \"Co-immunoprecipitation/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment assay, incompatible end-joining assay in cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay plus direct protein interaction plus domain mapping plus cellular recruitment assay in a single study\",\n      \"pmids\": [\"30250067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM and X-ray crystallography structures of PAXX C-terminal Ku-binding motif bound to Ku70/80 identify residues critical for the Ku70/PAXX interaction in vitro and in cells. PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK end-bridging dimers (mediated by either Ku80 or XLF), providing complementary advantage for DNA end synapsis and end joining.\",\n      \"method\": \"Cryo-EM, X-ray crystallography, mutagenesis of Ku70/PAXX interface residues, in vitro end-joining assay, cellular end-joining assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution structure plus interface mutagenesis plus functional end-joining assays in vitro and in cells\",\n      \"pmids\": [\"37256950\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PAXX deficiency causes modest sensitivity to DNA damage in human HAP1 cells (unlike XRCC4 or XLF deficiency) and PAXX-deficient murine CH12F3 B cells perform class switch recombination at near-wild-type levels, indicating that PAXX is largely dispensable for CSR and basal NHEJ in these cell systems.\",\n      \"method\": \"Genetic KO (CRISPR, mouse Paxx-/- CH12F3 cells), DSB-inducing agent sensitivity assay, CSR assay, chromosomal break analysis\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic KO with multiple cellular phenotype readouts, single lab\",\n      \"pmids\": [\"29511621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Chemoresistance to doxorubicin or cisplatin in osteosarcoma cells results in enhanced PAXX–Ku70 interaction and elevated NHEJ efficiency; disruption of the PAXX–Ku70 interaction with small molecule M11 re-sensitizes resistant cells to these drugs.\",\n      \"method\": \"Co-immunoprecipitation of PAXX-Ku70 in resistant cells, NHEJ efficiency assay, small-molecule inhibitor (M11) treatment with drug sensitivity assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP plus functional rescue with small molecule, single lab, single study\",\n      \"pmids\": [\"31640855\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PAXX interacts with DNA polymerase β (Pol β) and contributes to base excision repair (BER); PAXX-deficient cells show increased sensitivity to the BER-substrate drug temozolomide in glioma cells.\",\n      \"method\": \"Co-immunoprecipitation of PAXX with Pol β, PAXX-deficient cell lines, TMZ sensitivity assay\",\n      \"journal\": \"Journal of molecular neuroscience\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP plus KD phenotype, single lab, no in vitro reconstitution or domain mapping\",\n      \"pmids\": [\"30238427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PAXX is excluded from the nucleus during HSV-1 infection, and PAXX-/- cells show a defect in viral genome replication efficiency but produce greater numbers of infectious virions, indicating PAXX restricts HSV-1 infection in a manner distinct from other c-NHEJ factors.\",\n      \"method\": \"PAXX-/- cell lines, immunofluorescence localization during HSV-1 infection, viral replication and infectious virion production assays\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiment plus functional KO phenotype in viral context, single lab\",\n      \"pmids\": [\"29144403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In human HAP1 cells, XLF but not PAXX genetically interacts with DNA-PKcs (i.e., XLF/DNA-PKcs double KO is more severe than either single KO, whereas PAXX/DNA-PKcs double KO phenocopies DNA-PKcs single KO). ATM has overlapping functions with DNA-PKcs, XLF, and XRCC4, but not with PAXX, in response to DSBs.\",\n      \"method\": \"CRISPR-generated human HAP1 single and double KO cell lines, DSB-inducing agent sensitivity assay, chromosomal break analysis, genetic epistasis\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic epistasis in human cells with multiple KO combinations, single lab\",\n      \"pmids\": [\"31141305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A single conserved amino acid substitution in PAXX at the Ku70/80 contact interface dramatically stabilizes the PAXX–Ku repair complex, causes co-dependent mislocalization of PAXX and Ku to the nucleoli, and accelerates NHEJ repair specifically of DSBs requiring end processing (radiation-induced DSBs), revealing that repair complex stability at the Ku70/PAXX interface is rate-limiting for NHEJ of complex DSBs.\",\n      \"method\": \"Structure-guided mutagenesis of PAXX Ku70/80 interface, live-cell imaging of PAXX and Ku localization, NHEJ repair kinetics assay with radiation-induced vs. restriction enzyme DSBs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structure-guided mutagenesis with functional repair assay, single lab, single study\",\n      \"pmids\": [\"40659092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PAXX promotes DSB end synapsis during NHEJ in a manner partially redundant with DNA-PKcs and XLF; PAXX becomes important for blunt DSB end joining when DNA-PKcs or XLF is disrupted, but PAXX loss does not magnify the DNA-PKcs-mediated suppression of microhomology-mediated deletions, distinguishing its function from DNA-PKcs in end-use fidelity.\",\n      \"method\": \"Cas9-reporter end-joining assay in PAXX-/-, DNA-PKcs-inhibited, and XLF-/- single and combined-deficient human cell lines; indel profiling\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic KO/inhibitor epistasis with defined molecular readout, single lab, multiple combined deficiency conditions\",\n      \"pmids\": [\"40546969\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"An XRCC4 separation-of-function mutation (M61R) that abolishes XRCC4–XLF filament formation while preserving LIG4 stabilization reveals that PAXX is functionally redundant with XRCC4-XLF filaments during V(D)J recombination; crossing Xrcc4-M61R mice onto Paxx-/- background causes severe immunodeficiency and embryonic lethality, identifying a direct functional interplay between XRCC4 and PAXX in NHEJ.\",\n      \"method\": \"Xrcc4 separation-of-function knock-in mouse crossed onto Paxx-/- background; V(D)J recombination assay; CNS apoptosis analysis; genetic epistasis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined separation-of-function allele combined with Paxx-/- in vivo genetic epistasis, single lab with multiple phenotypic readouts\",\n      \"pmids\": [\"34519267\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PAXX is an accessory NHEJ factor and structural paralog of XRCC4 and XLF that directly binds Ku70 via its C-terminal motif (structurally defined by cryo-EM/crystallography), recruits and stabilizes KU at DSBs, promotes DNA end synapsis in alternate DNA-PK end-bridging dimers together with XLF, stimulates DNA polymerase λ activity through its N-terminal head domain to facilitate gap-filling, and is functionally redundant with XLF (and partially with DNA-PKcs) such that combined loss causes synthetic lethality in mice due to catastrophic failure of NHEJ-dependent neurogenesis and lymphocyte development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PAXX (C9orf142) is an accessory factor of the classical non-homologous end-joining (NHEJ) pathway and a structural paralog of XRCC4 that promotes repair of DNA double-strand breaks (DSBs) [#0]. Its principal molecular role is to engage the DSB-recognition machinery directly: PAXX binds Ku through a C-terminal motif that contacts Ku70 specifically, forming a stable PAXX–Ku–DNA ternary complex that requires a bare DNA extension and that drives accumulation of Ku at breaks in cells [#2, #5, #8]. High-resolution cryo-EM and crystallographic analysis define the Ku70/PAXX interface and show that PAXX and XLF can bind the Ku heterodimer simultaneously, acting as alternative structural bridges in DNA-PK end-bridging dimers to promote DNA end synapsis [#8, #15]. Through its N-terminal head domain, PAXX—like its paralogs XRCC4 and XLF—interacts with and stimulates DNA polymerase λ and is required for its recruitment to damage sites, facilitating gap-filling and joining of incompatible ends [#7]. Functionally, PAXX is largely redundant with XLF and partially with DNA-PKcs: loss of PAXX alone produces only modest DSB-repair defects, but combined PAXX/XLF deficiency abolishes end joining and is synthetic-lethal in mice, causing embryonic lethality, genomic instability, CNS apoptosis, and a near-complete block in lymphocyte development that phenocopies Xrcc4 or Lig4 loss [#3, #4, #6]. Genetic interplay extends to XRCC4 itself, as PAXX is redundant with XRCC4–XLF filaments during V(D)J recombination [#16]. The stability of the PAXX–Ku interface is rate-limiting for NHEJ of complex, end-processing-requiring DSBs, with interface-stabilizing mutations accelerating repair of radiation-induced breaks [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Established PAXX as a previously unrecognized NHEJ factor by showing it is a structural paralog of XRCC4 that binds Ku and promotes Ku-dependent end ligation, defining its place in the core repair machinery.\",\n      \"evidence\": \"Crystal structure, direct binding and in vitro ligation assays, and CRISPR/RNAi KO with DSB-sensitivity and chromatin-assembly readouts\",\n      \"pmids\": [\"25574025\", \"25941166\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which Ku subunit PAXX contacts\", \"Magnitude of contribution relative to XLF/XRCC4 not established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the molecular basis of PAXX's Ku engagement, showing a Ku70-specific, DNA-dependent ternary complex and that its ligation-stimulating role is weak and unmasked only when XLF is absent.\",\n      \"evidence\": \"Biochemical reconstitution of PAXX–Ku–DNA complex, co-IP, in vitro ligation assays in PAXX-deficient cells\",\n      \"pmids\": [\"27705800\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution interface not yet defined\", \"Quantitative redundancy with XLF not mapped genetically\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved why PAXX single loss is mild by demonstrating functional redundancy with XLF—combined deficiency abolishes DSB joining and V(D)J recombination, while PAXX alone does not phenocopy core factor loss and acts independently of ATM/RAG.\",\n      \"evidence\": \"CRISPR/genetic KO mouse models and G1-arrested pro-B cell lines, V(D)J and class-switch assays, IR sensitivity, epistasis with ATM/RAG, Ku-binding mutants\",\n      \"pmids\": [\"27601299\", \"27601633\", \"27798842\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic distinction between PAXX and XLF activities not yet defined\", \"Basis for synthetic lethality at the molecular level unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Assigned PAXX and XLF distinct, complementary molecular tasks—PAXX promotes Ku accumulation at DSBs whereas XLF enhances LIG4 recruitment—and confirmed the developmental consequences of combined loss in vivo.\",\n      \"evidence\": \"Mouse KO models with live-cell imaging/ChIP of Ku and LIG4 dynamics, epistasis with ATM/DNA-PK inhibitors\",\n      \"pmids\": [\"28051062\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How PAXX stabilizes Ku mechanistically not structurally explained\", \"Whether the two functions are strictly separable or overlap partially\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended PAXX function beyond Ku tethering to gap-filling, showing PAXX (with XRCC4 and XLF) binds and stimulates DNA polymerase λ via its N-terminal head domain and is required for Pol λ recruitment to damage.\",\n      \"evidence\": \"Co-IP/interactome mapping, in vitro polymerase activity assay, laser micro-irradiation recruitment, incompatible end-joining assay\",\n      \"pmids\": [\"30250067\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of each paralog to Pol λ stimulation in vivo not quantified\", \"Structural basis of the head domain–Pol λ contact not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Probed cell-context dependence of PAXX, finding it largely dispensable for CSR and basal NHEJ in some human and mouse systems, and reported lower-confidence links to base excision repair via Pol β and a viral restriction role against HSV-1.\",\n      \"evidence\": \"Genetic KO with DSB/CSR and chromosomal-break readouts; Co-IP with Pol β and TMZ sensitivity; HSV-1 infection localization and replication assays\",\n      \"pmids\": [\"29511621\", \"30238427\", \"29144403\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pol β/BER link rests on a single Co-IP without reconstitution or domain mapping\", \"HSV-1 restriction mechanism distinct from NHEJ not defined\", \"Cell-type basis for variable PAXX dependence unexplained\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Refined the epistatic map in human cells, showing PAXX—unlike XLF—does not genetically interact with DNA-PKcs or overlap with ATM, distinguishing its functional niche from other accessory factors.\",\n      \"evidence\": \"CRISPR single/double KO HAP1 cells, DSB sensitivity, chromosomal break analysis, genetic epistasis; plus Co-IP/small-molecule (M11) chemoresistance study\",\n      \"pmids\": [\"31141305\", \"31640855\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic reason for lack of DNA-PKcs interaction not explained\", \"M11/chemoresistance link is single-lab Co-IP plus inhibitor rescue\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Delivered the atomic-resolution view of the Ku70/PAXX interface and showed PAXX and XLF can co-occupy Ku to form alternate DNA-PK end-bridging dimers, providing a structural model for redundant end-synapsis bridging.\",\n      \"evidence\": \"Cryo-EM, X-ray crystallography, interface mutagenesis, in vitro and cellular end-joining assays\",\n      \"pmids\": [\"37256950\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of switching between PAXX- and XLF-bridged dimers in cells not resolved\", \"Contribution of each bridging mode to repair fidelity not quantified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected PAXX–Ku complex stability to repair kinetics, showing an interface-stabilizing substitution accelerates NHEJ of end-processing-requiring DSBs and that PAXX promotes end synapsis partially redundantly with DNA-PKcs and XLF for blunt-end joining.\",\n      \"evidence\": \"Structure-guided interface mutagenesis with live-cell imaging and repair kinetics; Cas9-reporter end-joining with indel profiling across PAXX/DNA-PKcs/XLF-deficient cells\",\n      \"pmids\": [\"40659092\", \"40546969\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab studies awaiting independent confirmation\", \"Physiological significance of nucleolar mislocalization unclear\", \"How interface stability tunes repair rate mechanistically not fully defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated direct functional interplay between PAXX and XRCC4, showing PAXX is redundant with XRCC4–XLF filaments in V(D)J recombination via a filament-deficient XRCC4 separation-of-function allele.\",\n      \"evidence\": \"Xrcc4-M61R knock-in mouse crossed onto Paxx-/- background, V(D)J and CNS apoptosis assays, genetic epistasis\",\n      \"pmids\": [\"34519267\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PAXX substitutes structurally for XRCC4-XLF filaments not shown biochemically\", \"Molecular basis of the rescue not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the alternate PAXX- and XLF-bridged DNA-PK synaptic complexes are dynamically selected and coordinated during repair of different break types, and whether PAXX's reported BER and viral-restriction roles reflect genuine NHEJ-independent functions, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No real-time structural data on bridging-mode selection in cells\", \"BER/Pol β link unconfirmed by reconstitution\", \"HSV-1 restriction mechanism undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 12]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 3, 6, 8]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 4, 6, 16]}\n    ],\n    \"complexes\": [\"DNA-PK end-bridging dimer\", \"PAXX-Ku-DNA ternary complex\"],\n    \"partners\": [\"XRCC6\", \"XRCC5\", \"DNA-PKcs\", \"XLF\", \"XRCC4\", \"POLL\", \"POLB\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":7,"faith_pct":71.42857142857143}}