{"gene":"DTX4","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":2012,"finding":"DTX4 acts as an E3 ubiquitin ligase that is recruited by the pattern-recognition receptor NLRP4 to TBK1, mediating K48-linked polyubiquitination at Lys670 of TBK1, leading to its proteasomal degradation and suppression of type I interferon signaling.","method":"Co-immunoprecipitation, ubiquitination assays, knockdown experiments, phosphorylation analysis of TBK1 and IRF3","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ubiquitination assays, knockdown with defined molecular phenotype; highly cited foundational paper replicated by multiple subsequent studies","pmids":["22388039"],"is_preprint":false},{"year":2015,"finding":"DYRK2 phosphorylates TBK1 at Ser527, which is essential for recruiting NLRP4 and DTX4 to TBK1, priming TBK1 for K48-linked ubiquitination and degradation by DTX4.","method":"Kinase assay, Co-immunoprecipitation, ubiquitination assay, site-directed mutagenesis of TBK1 Ser527","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 — kinase assay with mutagenesis, Co-IP, and functional ubiquitination readout in a single study","pmids":["26407194"],"is_preprint":false},{"year":2016,"finding":"USP38 deubiquitinase specifically cleaves K33-linked polyubiquitin chains from TBK1 at Lys670, allowing subsequent K48-linked ubiquitination at the same site mediated by DTX4 (and TRIP) within the NLRP4 signalosome, leading to TBK1 degradation.","method":"In vitro deubiquitination assay, Co-immunoprecipitation, knockout mouse experiments, ubiquitination linkage-specific assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro assays, KO mouse model, multiple orthogonal methods; highly cited paper","pmids":["27692986"],"is_preprint":false},{"year":2017,"finding":"Upon ligand binding, DTX4 ubiquitylates Notch1 at the cell surface, triggering bilateral endocytosis of the Notch1 extracellular domain (into the ligand-expressing cell) and of the membrane-anchored fragment with DTX4 (into the Notch1-expressing cell), facilitating subsequent ADAM10-mediated cleavage of Notch1 in an endocytic compartment rather than at the cell surface.","method":"Biochemical analysis (Co-IP, ubiquitination assay), immunofluorescence, live-cell imaging, dynamin inhibition experiments","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including live imaging, biochemistry, and pharmacological inhibition with functional readout","pmids":["28611181"],"is_preprint":false},{"year":2020,"finding":"TRAF3IP3 interacts with endogenous TRAF3 and TBK1, and promotes DTX4-dependent K48-linked ubiquitination of TBK1 at Lys372, leading to its degradation and suppression of cytosolic RNA-triggered type I IFN production in myeloid cells.","method":"Co-immunoprecipitation, ubiquitination assay, Traf3ip3 knockout primary myeloid cells, myeloid-specific gene deletion mouse model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, KO primary cells and in vivo mouse model, site-specific ubiquitination mapping","pmids":["32366851"],"is_preprint":false},{"year":2020,"finding":"The DTC (C-terminal) domain of DELTEX family E3 ligases, including DTX4, harbors an ADP-ribose-binding pocket that recruits poly-ADP-ribose (PAR)-modified proteins for ubiquitination; PAR-binding by the DTC domain is conserved across DTX family members.","method":"Label-free mass spectrometry interactome, structural analysis, biochemical binding assays, cell-based ubiquitination assays, domain mutagenesis","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 — structural, biochemical, and cell-based validation with mutagenesis in a single study","pmids":["32937373"],"is_preprint":false},{"year":2021,"finding":"MAP4K1 (HGK) interacts with TBK1 and recruits DTX4 to promote K48-linked ubiquitination and proteasomal degradation of TBK1 and IKKε, thereby negatively regulating RLR antiviral signaling; knockdown of DTX4 abrogates this ubiquitination and degradation.","method":"Yeast two-hybrid screen, Co-immunoprecipitation, ubiquitination assay, knockdown/knockout experiments, IFN-β reporter assay","journal":"Microbiology spectrum","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ubiquitination assay, and DTX4 knockdown with defined phenotypic rescue; single lab","pmids":["34908452"],"is_preprint":false},{"year":2022,"finding":"Zika virus (ZIKV) infection increases centrosomal accumulation of DTX4, which degrades centrosomal TBK1; ZIKV nonstructural protein NS3 binds CEP63, disrupting its function and allowing DTX4 to accumulate at centrosomes and destabilize TBK1, thereby suppressing the innate immune response.","method":"Immunofluorescence/confocal microscopy, Co-immunoprecipitation, protein stability assays, ZIKV infection experiments, loss-of-function (CEP63 knockdown)","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment tied to functional consequence (TBK1 degradation), Co-IP, and loss-of-function; single lab","pmids":["35793002"],"is_preprint":false},{"year":2023,"finding":"The transcription factor c-Myb negatively regulates DTX4 transcription in Kupffer cells; DTX4 promotes K48-linked ubiquitination of TBK1, and overexpression of c-Myb reduces DTX4-mediated ubiquitination of TBK1, boosting the anti-inflammatory effect of endotoxin tolerance.","method":"Overexpression, knockdown, ubiquitination assay, transcriptional regulation analysis","journal":"Journal of immunology research","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, overexpression/knockdown with ubiquitination readout, transcriptional regulation link established","pmids":["37032653"],"is_preprint":false},{"year":2024,"finding":"HBV upregulates DTX4 via p-STAT3; DTX4 (together with MSL2) mediates ubiquitination-dependent degradation of APOBEC3B, thereby stabilizing HBV cccDNA and promoting viral replication in liver cells.","method":"RNA-seq, Co-immunoprecipitation, ubiquitination assay, HBV-infected liver chimeric mouse model, shRNA knockdown","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP, ubiquitination assay, in vivo mouse model, and RNA-seq; single lab study","pmids":["39346550"],"is_preprint":false},{"year":2024,"finding":"DTX3L, but not DTX4, ubiquitylates DNA and RNA via ester bond formation in vitro, demonstrating that the ability to ubiquitylate nucleic acids is not shared by all DELTEX family members; DTX4 lacks this nucleic acid ubiquitylation activity.","method":"In vitro ubiquitylation assay with purified components, comparison across DTX family members, deubiquitylation assays","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with purified proteins and direct biochemical readout across multiple family members","pmids":["39242775"],"is_preprint":false},{"year":2017,"finding":"DTX4 knockdown in 3T3-L1 preadipocytes inhibits adipogenic differentiation by reducing lipid droplet formation, downregulating C/EBPα, PPARγ, FABP4, and Adipsin expression, arresting mitotic clonal expansion, and elevating Wnt signaling genes (Wnt6, Wnt10b, β-catenin).","method":"shRNA stable knockdown, oil red O staining, qRT-PCR, Western blot, EdU incorporation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — clean KD with defined cellular phenotype and pathway placement (Wnt signaling); single lab","pmids":["28842252"],"is_preprint":false},{"year":2023,"finding":"DTX4 promotes thyroid cancer cell proliferation and migration through regulation of stearoyl-CoA desaturase 1 (SCD); DTX4 knockdown reduces tumor growth in vivo, and SCD inhibition rescues the enhanced growth induced by DTX4 overexpression.","method":"shRNA knockdown, overexpression, CCK-8, colony formation, transwell assay, RNA-seq/KEGG analysis, xenograft mouse model, SCD inhibitor rescue","journal":"Functional & integrative genomics","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods including in vivo, rescue experiment; single lab","pmids":["37612343"],"is_preprint":false},{"year":2023,"finding":"During EBV lytic reactivation, enhanced m6A methylation of DTX4 mRNA (due to ALKBH5 downregulation) increases DTX4 translation efficiency, leading to elevated DTX4 protein that attenuates IFN signaling and promotes viral lytic replication.","method":"MeRIP-seq, RNA-seq, RNA stability assay, polysome analysis, point mutation of m6A sites, Western blotting, qRT-PCR","journal":"Journal of biomedical science","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (epitranscriptomic mapping, translation assay, mutagenesis); single lab","pmids":["36918845"],"is_preprint":false},{"year":2023,"finding":"Postnatal overexpression of DTX4 in the mouse retina reduces the frequency of AII amacrine cells, indicating a role for DTX4 (as a regulator of Notch signaling) in controlling retinal neuron number.","method":"In vivo overexpression, quantitative cell counting, QTL analysis, chromosome substitution strains","journal":"Frontiers in neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo gain-of-function with quantitative cellular phenotype; single lab","pmids":["36816119"],"is_preprint":false},{"year":2025,"finding":"DTX4 sustains radial glia identity and prevents premature transition to intermediate progenitors in the mammalian neocortex by regulating cell cycle length; loss of DTX4 is required for intermediate progenitor generation, and perturbing DTX4 expression in human cerebral organoids and murine neocortex alters progenitor composition, neuronal diversity, and cortical morphology.","method":"In vivo mouse knockdown/overexpression, human cerebral organoid perturbation, single-cell transcriptomics, cell cycle analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — loss- and gain-of-function in vivo and in organoids with mechanistic (cell cycle) readout; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.04.10.648213"],"is_preprint":true}],"current_model":"DTX4 is a RING-domain E3 ubiquitin ligase of the DELTEX family whose best-characterized function is mediating K48-linked polyubiquitination and proteasomal degradation of TBK1 (at Lys670, primed by DYRK2 phosphorylation at Ser527) within an NLRP4 signalosome, thereby negatively regulating type I interferon signaling; DTX4 also ubiquitylates Notch1 to drive bilateral endocytosis and ADAM10-mediated cleavage, promotes degradation of APOBEC3B in the context of HBV infection, and regulates neural progenitor identity and adipogenic differentiation, with its C-terminal DTC domain serving as an ADP-ribose-binding module that recruits PAR-modified proteins for ubiquitination."},"narrative":{"teleology":[{"year":2012,"claim":"Establishing that DTX4 is the effector E3 ligase in a previously uncharacterized NLRP4-dependent mechanism for shutting down type I IFN signaling answered how innate immune activation is restrained at the level of TBK1 turnover.","evidence":"Co-IP, K48-linked ubiquitination assays, and knockdown in human cells showing TBK1 degradation and IFN suppression","pmids":["22388039"],"confidence":"High","gaps":["Upstream signal triggering NLRP4–DTX4 recruitment was unknown","Whether DTX4 targets TBK1 at specific subcellular sites was not addressed","Relative contribution of DTX4 versus other E3 ligases (e.g. TRIP) was unresolved"]},{"year":2015,"claim":"Identification of DYRK2 as the kinase that phosphorylates TBK1 at Ser527 to prime DTX4 recruitment resolved how the NLRP4–DTX4 ubiquitination complex is temporally gated.","evidence":"In vitro kinase assay, mutagenesis of TBK1 Ser527, and Co-IP showing phosphorylation-dependent NLRP4/DTX4 binding","pmids":["26407194"],"confidence":"High","gaps":["Signals activating DYRK2 in the context of infection were undefined","Whether other kinases can substitute for DYRK2 was untested"]},{"year":2016,"claim":"Demonstrating that USP38 must first remove K33-linked ubiquitin from TBK1 Lys670 before DTX4 can attach K48-linked chains at the same site established a chain-editing mechanism governing TBK1 fate.","evidence":"Linkage-specific ubiquitination assays, in vitro deubiquitination, and Usp38-knockout mice","pmids":["27692986"],"confidence":"High","gaps":["Identity of the E3 ligase attaching the initial K33 chains was not determined","Whether chain editing occurs at all DTX4 substrate sites was unknown"]},{"year":2017,"claim":"Showing that DTX4 ubiquitylates Notch1 to drive bilateral endocytosis and redirect ADAM10-mediated S2 cleavage from the cell surface to endosomes expanded DTX4 function beyond innate immunity into Notch signaling mechanics.","evidence":"Live-cell imaging, Co-IP, ubiquitination assays, and dynamin inhibition in signal-sending/receiving cell pairs","pmids":["28611181"],"confidence":"High","gaps":["The specific ubiquitin chain type on Notch1 was not defined","Whether DTX4-mediated Notch regulation is tissue-restricted was unclear"]},{"year":2017,"claim":"DTX4 knockdown blocking adipogenic differentiation and elevating Wnt signaling in preadipocytes revealed a developmental role for DTX4 in lineage commitment beyond immune regulation.","evidence":"Stable shRNA knockdown in 3T3-L1 cells with lipid staining, gene expression, and cell cycle readouts","pmids":["28842252"],"confidence":"Medium","gaps":["Direct ubiquitination substrate driving the adipogenic phenotype was not identified","In vivo adipogenesis data were lacking","Whether the effect is Notch- or TBK1-dependent was not tested"]},{"year":2020,"claim":"Discovery that TRAF3IP3 promotes DTX4-dependent K48-linked ubiquitination of TBK1 at a second lysine (Lys372) in myeloid cells demonstrated cell-type-specific adaptors feeding into the same DTX4 degradation pathway.","evidence":"Co-IP, ubiquitination assay, Traf3ip3-KO primary myeloid cells, and myeloid-specific deletion mouse model","pmids":["32366851"],"confidence":"High","gaps":["How Lys372 and Lys670 ubiquitination are coordinated or independently regulated was unresolved","Whether TRAF3IP3 and NLRP4 act in the same or separate complexes was unknown"]},{"year":2020,"claim":"Structural and biochemical demonstration that the DTC domain of DTX4 binds ADP-ribose and recruits PAR-modified proteins for ubiquitination provided a molecular logic for substrate recognition beyond protein–protein interaction.","evidence":"Label-free mass spectrometry, structural analysis, biochemical binding assays, and domain mutagenesis","pmids":["32937373"],"confidence":"High","gaps":["Whether PAR-binding is required for TBK1 or Notch1 targeting specifically was not tested","Structural resolution of the DTX4 DTC domain itself was not reported"]},{"year":2021,"claim":"Identification of MAP4K1 as another adaptor that recruits DTX4 to TBK1 and IKKε broadened the repertoire of upstream scaffolds converging on DTX4-mediated innate immune suppression.","evidence":"Yeast two-hybrid, Co-IP, ubiquitination assay, DTX4 knockdown rescue, and IFN-β reporter","pmids":["34908452"],"confidence":"Medium","gaps":["Redundancy among NLRP4, TRAF3IP3, and MAP4K1 in physiological settings was not dissected","Single-lab finding without independent replication"]},{"year":2022,"claim":"Showing that ZIKV NS3 disrupts CEP63, enabling centrosomal DTX4 accumulation and local TBK1 degradation, established a spatially resolved viral immune evasion mechanism exploiting DTX4.","evidence":"Confocal microscopy, Co-IP, protein stability assays, and ZIKV infection with CEP63 knockdown","pmids":["35793002"],"confidence":"Medium","gaps":["Whether centrosomal TBK1 pool has distinct signaling roles was not determined","Generalizability to other flaviviruses was untested"]},{"year":2023,"claim":"Multiple findings in 2023 collectively showed that diverse viruses (EBV, HBV) and cancers exploit DTX4 upregulation—via m6A-enhanced translation or STAT3 signaling—to degrade antiviral factors (TBK1, APOBEC3B) or promote tumor growth through SCD regulation.","evidence":"MeRIP-seq and polysome profiling for EBV [PMID:36918845]; Co-IP, ubiquitination, and HBV-infected liver chimeric mice for HBV [PMID:39346550]; xenograft models and SCD inhibitor rescue for thyroid cancer [PMID:37612343]","pmids":["36918845","39346550","37612343"],"confidence":"Medium","gaps":["Whether DTX4 directly ubiquitinates SCD or acts indirectly in thyroid cancer was not established","APOBEC3B ubiquitination site was not mapped","Each study from a single lab"]},{"year":2023,"claim":"DTX4 overexpression in the postnatal mouse retina reduced AII amacrine cell number, linking DTX4-Notch regulation to quantitative control of retinal neuron fate.","evidence":"In vivo retinal overexpression, quantitative cell counting, and QTL analysis","pmids":["36816119"],"confidence":"Medium","gaps":["Whether the effect is Notch-dependent was assumed but not formally tested","Loss-of-function data in the retina were absent"]},{"year":2024,"claim":"Demonstrating that DTX4, unlike DTX3L, cannot ubiquitylate nucleic acids via ester bonds clarified the functional boundaries within the DELTEX family despite their shared DTC domain architecture.","evidence":"In vitro ubiquitylation assays with purified DELTEX family members comparing nucleic acid substrates","pmids":["39242775"],"confidence":"High","gaps":["Whether DTX4 has unique substrates not shared with DTX3L was not explored","The structural basis for differential nucleic acid ubiquitylation activity was not resolved"]},{"year":null,"claim":"A unified model explaining how DTX4 partitions between its TBK1-degradation, Notch-regulatory, and PAR-dependent substrate recognition functions—and whether these represent independent or interconnected pathways—remains unestablished.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of full-length DTX4 exists","Relative importance of PAR-binding versus adaptor-mediated substrate recruitment in vivo is unknown","Comprehensive identification of DTX4 substrates beyond TBK1, Notch1, and APOBEC3B has not been performed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,4,5,6,9]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,3,5]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[7]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,4]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,2,4,6,7,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,14]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,14,15]}],"complexes":["NLRP4 signalosome"],"partners":["TBK1","NLRP4","DYRK2","USP38","TRAF3IP3","MAP4K1","NOTCH1","APOBEC3B"],"other_free_text":[]},"mechanistic_narrative":"DTX4 is a RING-domain E3 ubiquitin ligase of the DELTEX family that functions as a critical negative regulator of type I interferon signaling and a modulator of Notch pathway-dependent cell fate decisions. Its best-characterized activity is K48-linked polyubiquitination of TBK1, which it performs within an NLRP4 signalosome following DYRK2-mediated phosphorylation of TBK1 at Ser527 and USP38-dependent removal of competing K33-linked ubiquitin chains at Lys670, leading to proteasomal degradation of TBK1 and suppression of IFN-β production [PMID:22388039, PMID:26407194, PMID:27692986]. DTX4 also ubiquitylates Notch1 at the cell surface to drive bilateral endocytosis and ADAM10-mediated cleavage in endocytic compartments [PMID:28611181], and its C-terminal DTC domain functions as a conserved ADP-ribose-binding module that recruits poly-ADP-ribosylated proteins for ubiquitination [PMID:32937373]. Multiple viruses exploit DTX4-mediated TBK1 degradation to evade innate immunity—Zika virus promotes centrosomal DTX4 accumulation via NS3-CEP63 disruption [PMID:35793002], EBV lytic reactivation upregulates DTX4 translation through enhanced m6A methylation of its mRNA [PMID:36918845], and HBV induces DTX4 via p-STAT3 to degrade the antiviral factor APOBEC3B [PMID:39346550]."},"prefetch_data":{"uniprot":{"accession":"Q9Y2E6","full_name":"E3 ubiquitin-protein ligase DTX4","aliases":["Protein deltex-4","Deltex4","RING finger protein 155","RING-type E3 ubiquitin transferase DTX4"],"length_aa":619,"mass_kda":67.3,"function":"Regulator of Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations (By similarity). Functions as a ubiquitin ligase protein in vivo, mediating 'Lys48'-linked polyubiquitination and promoting degradation of TBK1, targeting to TBK1 requires interaction with NLRP4","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9Y2E6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DTX4","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DTX4","total_profiled":1310},"omim":[{"mim_id":"616110","title":"DELTEX E3 UBIQUITIN LIGASE 4; DTX4","url":"https://www.omim.org/entry/616110"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":55.5}],"url":"https://www.proteinatlas.org/search/DTX4"},"hgnc":{"alias_symbol":["KIAA0937","RNF155"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2E6","domains":[{"cath_id":"3.30.720.50","chopping":"6-166","consensus_level":"medium","plddt":90.5833,"start":6,"end":166},{"cath_id":"-","chopping":"316-350","consensus_level":"high","plddt":64.332,"start":316,"end":350},{"cath_id":"3.30.390.130","chopping":"364-378_477-617","consensus_level":"high","plddt":91.9915,"start":364,"end":617},{"cath_id":"3.30.40.10","chopping":"391-459","consensus_level":"high","plddt":89.0716,"start":391,"end":459}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2E6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2E6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2E6-F1-predicted_aligned_error_v6.png","plddt_mean":75.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DTX4","jax_strain_url":"https://www.jax.org/strain/search?query=DTX4"},"sequence":{"accession":"Q9Y2E6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2E6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2E6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2E6"}},"corpus_meta":[{"pmid":"22388039","id":"PMC_22388039","title":"NLRP4 negatively regulates type I interferon signaling by targeting the kinase TBK1 for degradation via the ubiquitin ligase DTX4.","date":"2012","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/22388039","citation_count":247,"is_preprint":false},{"pmid":"27692986","id":"PMC_27692986","title":"USP38 Inhibits Type I Interferon Signaling by Editing TBK1 Ubiquitination through NLRP4 Signalosome.","date":"2016","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/27692986","citation_count":119,"is_preprint":false},{"pmid":"32937373","id":"PMC_32937373","title":"DELTEX2 C-terminal domain recognizes and recruits ADP-ribosylated proteins for ubiquitination.","date":"2020","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/32937373","citation_count":63,"is_preprint":false},{"pmid":"26407194","id":"PMC_26407194","title":"DYRK2 Negatively Regulates Type I Interferon Induction by Promoting TBK1 Degradation via Ser527 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okadaic acid and DTX-1: Self-protective precursors of diarrhetic shellfish poisoning (DSP) toxins.","date":"2017","source":"Harmful algae","url":"https://pubmed.ncbi.nlm.nih.gov/28366404","citation_count":23,"is_preprint":false},{"pmid":"39242775","id":"PMC_39242775","title":"Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L.","date":"2024","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/39242775","citation_count":19,"is_preprint":false},{"pmid":"27350400","id":"PMC_27350400","title":"Identification of miRNA/mRNA-Negative Regulation Pairs in Nasopharyngeal Carcinoma.","date":"2016","source":"Medical science monitor : international medical journal of experimental and clinical research","url":"https://pubmed.ncbi.nlm.nih.gov/27350400","citation_count":19,"is_preprint":false},{"pmid":"36918845","id":"PMC_36918845","title":"Attenuation of IFN signaling due to m6A modification of the host epitranscriptome promotes EBV lytic 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     \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ubiquitination assays, knockdown with defined molecular phenotype; highly cited foundational paper replicated by multiple subsequent studies\",\n      \"pmids\": [\"22388039\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"DYRK2 phosphorylates TBK1 at Ser527, which is essential for recruiting NLRP4 and DTX4 to TBK1, priming TBK1 for K48-linked ubiquitination and degradation by DTX4.\",\n      \"method\": \"Kinase assay, Co-immunoprecipitation, ubiquitination assay, site-directed mutagenesis of TBK1 Ser527\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — kinase assay with mutagenesis, Co-IP, and functional ubiquitination readout in a single study\",\n      \"pmids\": [\"26407194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"USP38 deubiquitinase specifically cleaves K33-linked polyubiquitin chains from TBK1 at Lys670, allowing subsequent K48-linked ubiquitination at the same site mediated by DTX4 (and TRIP) within the NLRP4 signalosome, leading to TBK1 degradation.\",\n      \"method\": \"In vitro deubiquitination assay, Co-immunoprecipitation, knockout mouse experiments, ubiquitination linkage-specific assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro assays, KO mouse model, multiple orthogonal methods; highly cited paper\",\n      \"pmids\": [\"27692986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Upon ligand binding, DTX4 ubiquitylates Notch1 at the cell surface, triggering bilateral endocytosis of the Notch1 extracellular domain (into the ligand-expressing cell) and of the membrane-anchored fragment with DTX4 (into the Notch1-expressing cell), facilitating subsequent ADAM10-mediated cleavage of Notch1 in an endocytic compartment rather than at the cell surface.\",\n      \"method\": \"Biochemical analysis (Co-IP, ubiquitination assay), immunofluorescence, live-cell imaging, dynamin inhibition experiments\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including live imaging, biochemistry, and pharmacological inhibition with functional readout\",\n      \"pmids\": [\"28611181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRAF3IP3 interacts with endogenous TRAF3 and TBK1, and promotes DTX4-dependent K48-linked ubiquitination of TBK1 at Lys372, leading to its degradation and suppression of cytosolic RNA-triggered type I IFN production in myeloid cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Traf3ip3 knockout primary myeloid cells, myeloid-specific gene deletion mouse model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, KO primary cells and in vivo mouse model, site-specific ubiquitination mapping\",\n      \"pmids\": [\"32366851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The DTC (C-terminal) domain of DELTEX family E3 ligases, including DTX4, harbors an ADP-ribose-binding pocket that recruits poly-ADP-ribose (PAR)-modified proteins for ubiquitination; PAR-binding by the DTC domain is conserved across DTX family members.\",\n      \"method\": \"Label-free mass spectrometry interactome, structural analysis, biochemical binding assays, cell-based ubiquitination assays, domain mutagenesis\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural, biochemical, and cell-based validation with mutagenesis in a single study\",\n      \"pmids\": [\"32937373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MAP4K1 (HGK) interacts with TBK1 and recruits DTX4 to promote K48-linked ubiquitination and proteasomal degradation of TBK1 and IKKε, thereby negatively regulating RLR antiviral signaling; knockdown of DTX4 abrogates this ubiquitination and degradation.\",\n      \"method\": \"Yeast two-hybrid screen, Co-immunoprecipitation, ubiquitination assay, knockdown/knockout experiments, IFN-β reporter assay\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ubiquitination assay, and DTX4 knockdown with defined phenotypic rescue; single lab\",\n      \"pmids\": [\"34908452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Zika virus (ZIKV) infection increases centrosomal accumulation of DTX4, which degrades centrosomal TBK1; ZIKV nonstructural protein NS3 binds CEP63, disrupting its function and allowing DTX4 to accumulate at centrosomes and destabilize TBK1, thereby suppressing the innate immune response.\",\n      \"method\": \"Immunofluorescence/confocal microscopy, Co-immunoprecipitation, protein stability assays, ZIKV infection experiments, loss-of-function (CEP63 knockdown)\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment tied to functional consequence (TBK1 degradation), Co-IP, and loss-of-function; single lab\",\n      \"pmids\": [\"35793002\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The transcription factor c-Myb negatively regulates DTX4 transcription in Kupffer cells; DTX4 promotes K48-linked ubiquitination of TBK1, and overexpression of c-Myb reduces DTX4-mediated ubiquitination of TBK1, boosting the anti-inflammatory effect of endotoxin tolerance.\",\n      \"method\": \"Overexpression, knockdown, ubiquitination assay, transcriptional regulation analysis\",\n      \"journal\": \"Journal of immunology research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, overexpression/knockdown with ubiquitination readout, transcriptional regulation link established\",\n      \"pmids\": [\"37032653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HBV upregulates DTX4 via p-STAT3; DTX4 (together with MSL2) mediates ubiquitination-dependent degradation of APOBEC3B, thereby stabilizing HBV cccDNA and promoting viral replication in liver cells.\",\n      \"method\": \"RNA-seq, Co-immunoprecipitation, ubiquitination assay, HBV-infected liver chimeric mouse model, shRNA knockdown\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ubiquitination assay, in vivo mouse model, and RNA-seq; single lab study\",\n      \"pmids\": [\"39346550\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DTX3L, but not DTX4, ubiquitylates DNA and RNA via ester bond formation in vitro, demonstrating that the ability to ubiquitylate nucleic acids is not shared by all DELTEX family members; DTX4 lacks this nucleic acid ubiquitylation activity.\",\n      \"method\": \"In vitro ubiquitylation assay with purified components, comparison across DTX family members, deubiquitylation assays\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with purified proteins and direct biochemical readout across multiple family members\",\n      \"pmids\": [\"39242775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"DTX4 knockdown in 3T3-L1 preadipocytes inhibits adipogenic differentiation by reducing lipid droplet formation, downregulating C/EBPα, PPARγ, FABP4, and Adipsin expression, arresting mitotic clonal expansion, and elevating Wnt signaling genes (Wnt6, Wnt10b, β-catenin).\",\n      \"method\": \"shRNA stable knockdown, oil red O staining, qRT-PCR, Western blot, EdU incorporation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KD with defined cellular phenotype and pathway placement (Wnt signaling); single lab\",\n      \"pmids\": [\"28842252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DTX4 promotes thyroid cancer cell proliferation and migration through regulation of stearoyl-CoA desaturase 1 (SCD); DTX4 knockdown reduces tumor growth in vivo, and SCD inhibition rescues the enhanced growth induced by DTX4 overexpression.\",\n      \"method\": \"shRNA knockdown, overexpression, CCK-8, colony formation, transwell assay, RNA-seq/KEGG analysis, xenograft mouse model, SCD inhibitor rescue\",\n      \"journal\": \"Functional & integrative genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including in vivo, rescue experiment; single lab\",\n      \"pmids\": [\"37612343\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"During EBV lytic reactivation, enhanced m6A methylation of DTX4 mRNA (due to ALKBH5 downregulation) increases DTX4 translation efficiency, leading to elevated DTX4 protein that attenuates IFN signaling and promotes viral lytic replication.\",\n      \"method\": \"MeRIP-seq, RNA-seq, RNA stability assay, polysome analysis, point mutation of m6A sites, Western blotting, qRT-PCR\",\n      \"journal\": \"Journal of biomedical science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (epitranscriptomic mapping, translation assay, mutagenesis); single lab\",\n      \"pmids\": [\"36918845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Postnatal overexpression of DTX4 in the mouse retina reduces the frequency of AII amacrine cells, indicating a role for DTX4 (as a regulator of Notch signaling) in controlling retinal neuron number.\",\n      \"method\": \"In vivo overexpression, quantitative cell counting, QTL analysis, chromosome substitution strains\",\n      \"journal\": \"Frontiers in neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo gain-of-function with quantitative cellular phenotype; single lab\",\n      \"pmids\": [\"36816119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DTX4 sustains radial glia identity and prevents premature transition to intermediate progenitors in the mammalian neocortex by regulating cell cycle length; loss of DTX4 is required for intermediate progenitor generation, and perturbing DTX4 expression in human cerebral organoids and murine neocortex alters progenitor composition, neuronal diversity, and cortical morphology.\",\n      \"method\": \"In vivo mouse knockdown/overexpression, human cerebral organoid perturbation, single-cell transcriptomics, cell cycle analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss- and gain-of-function in vivo and in organoids with mechanistic (cell cycle) readout; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.04.10.648213\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DTX4 is a RING-domain E3 ubiquitin ligase of the DELTEX family whose best-characterized function is mediating K48-linked polyubiquitination and proteasomal degradation of TBK1 (at Lys670, primed by DYRK2 phosphorylation at Ser527) within an NLRP4 signalosome, thereby negatively regulating type I interferon signaling; DTX4 also ubiquitylates Notch1 to drive bilateral endocytosis and ADAM10-mediated cleavage, promotes degradation of APOBEC3B in the context of HBV infection, and regulates neural progenitor identity and adipogenic differentiation, with its C-terminal DTC domain serving as an ADP-ribose-binding module that recruits PAR-modified proteins for ubiquitination.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"DTX4 is a RING-domain E3 ubiquitin ligase of the DELTEX family that functions as a critical negative regulator of type I interferon signaling and a modulator of Notch pathway-dependent cell fate decisions. Its best-characterized activity is K48-linked polyubiquitination of TBK1, which it performs within an NLRP4 signalosome following DYRK2-mediated phosphorylation of TBK1 at Ser527 and USP38-dependent removal of competing K33-linked ubiquitin chains at Lys670, leading to proteasomal degradation of TBK1 and suppression of IFN-β production [PMID:22388039, PMID:26407194, PMID:27692986]. DTX4 also ubiquitylates Notch1 at the cell surface to drive bilateral endocytosis and ADAM10-mediated cleavage in endocytic compartments [PMID:28611181], and its C-terminal DTC domain functions as a conserved ADP-ribose-binding module that recruits poly-ADP-ribosylated proteins for ubiquitination [PMID:32937373]. Multiple viruses exploit DTX4-mediated TBK1 degradation to evade innate immunity—Zika virus promotes centrosomal DTX4 accumulation via NS3-CEP63 disruption [PMID:35793002], EBV lytic reactivation upregulates DTX4 translation through enhanced m6A methylation of its mRNA [PMID:36918845], and HBV induces DTX4 via p-STAT3 to degrade the antiviral factor APOBEC3B [PMID:39346550].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing that DTX4 is the effector E3 ligase in a previously uncharacterized NLRP4-dependent mechanism for shutting down type I IFN signaling answered how innate immune activation is restrained at the level of TBK1 turnover.\",\n      \"evidence\": \"Co-IP, K48-linked ubiquitination assays, and knockdown in human cells showing TBK1 degradation and IFN suppression\",\n      \"pmids\": [\"22388039\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signal triggering NLRP4–DTX4 recruitment was unknown\", \"Whether DTX4 targets TBK1 at specific subcellular sites was not addressed\", \"Relative contribution of DTX4 versus other E3 ligases (e.g. TRIP) was unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identification of DYRK2 as the kinase that phosphorylates TBK1 at Ser527 to prime DTX4 recruitment resolved how the NLRP4–DTX4 ubiquitination complex is temporally gated.\",\n      \"evidence\": \"In vitro kinase assay, mutagenesis of TBK1 Ser527, and Co-IP showing phosphorylation-dependent NLRP4/DTX4 binding\",\n      \"pmids\": [\"26407194\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals activating DYRK2 in the context of infection were undefined\", \"Whether other kinases can substitute for DYRK2 was untested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrating that USP38 must first remove K33-linked ubiquitin from TBK1 Lys670 before DTX4 can attach K48-linked chains at the same site established a chain-editing mechanism governing TBK1 fate.\",\n      \"evidence\": \"Linkage-specific ubiquitination assays, in vitro deubiquitination, and Usp38-knockout mice\",\n      \"pmids\": [\"27692986\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the E3 ligase attaching the initial K33 chains was not determined\", \"Whether chain editing occurs at all DTX4 substrate sites was unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showing that DTX4 ubiquitylates Notch1 to drive bilateral endocytosis and redirect ADAM10-mediated S2 cleavage from the cell surface to endosomes expanded DTX4 function beyond innate immunity into Notch signaling mechanics.\",\n      \"evidence\": \"Live-cell imaging, Co-IP, ubiquitination assays, and dynamin inhibition in signal-sending/receiving cell pairs\",\n      \"pmids\": [\"28611181\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The specific ubiquitin chain type on Notch1 was not defined\", \"Whether DTX4-mediated Notch regulation is tissue-restricted was unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"DTX4 knockdown blocking adipogenic differentiation and elevating Wnt signaling in preadipocytes revealed a developmental role for DTX4 in lineage commitment beyond immune regulation.\",\n      \"evidence\": \"Stable shRNA knockdown in 3T3-L1 cells with lipid staining, gene expression, and cell cycle readouts\",\n      \"pmids\": [\"28842252\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitination substrate driving the adipogenic phenotype was not identified\", \"In vivo adipogenesis data were lacking\", \"Whether the effect is Notch- or TBK1-dependent was not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discovery that TRAF3IP3 promotes DTX4-dependent K48-linked ubiquitination of TBK1 at a second lysine (Lys372) in myeloid cells demonstrated cell-type-specific adaptors feeding into the same DTX4 degradation pathway.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, Traf3ip3-KO primary myeloid cells, and myeloid-specific deletion mouse model\",\n      \"pmids\": [\"32366851\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Lys372 and Lys670 ubiquitination are coordinated or independently regulated was unresolved\", \"Whether TRAF3IP3 and NLRP4 act in the same or separate complexes was unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Structural and biochemical demonstration that the DTC domain of DTX4 binds ADP-ribose and recruits PAR-modified proteins for ubiquitination provided a molecular logic for substrate recognition beyond protein–protein interaction.\",\n      \"evidence\": \"Label-free mass spectrometry, structural analysis, biochemical binding assays, and domain mutagenesis\",\n      \"pmids\": [\"32937373\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PAR-binding is required for TBK1 or Notch1 targeting specifically was not tested\", \"Structural resolution of the DTX4 DTC domain itself was not reported\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of MAP4K1 as another adaptor that recruits DTX4 to TBK1 and IKKε broadened the repertoire of upstream scaffolds converging on DTX4-mediated innate immune suppression.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, ubiquitination assay, DTX4 knockdown rescue, and IFN-β reporter\",\n      \"pmids\": [\"34908452\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Redundancy among NLRP4, TRAF3IP3, and MAP4K1 in physiological settings was not dissected\", \"Single-lab finding without independent replication\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showing that ZIKV NS3 disrupts CEP63, enabling centrosomal DTX4 accumulation and local TBK1 degradation, established a spatially resolved viral immune evasion mechanism exploiting DTX4.\",\n      \"evidence\": \"Confocal microscopy, Co-IP, protein stability assays, and ZIKV infection with CEP63 knockdown\",\n      \"pmids\": [\"35793002\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether centrosomal TBK1 pool has distinct signaling roles was not determined\", \"Generalizability to other flaviviruses was untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Multiple findings in 2023 collectively showed that diverse viruses (EBV, HBV) and cancers exploit DTX4 upregulation—via m6A-enhanced translation or STAT3 signaling—to degrade antiviral factors (TBK1, APOBEC3B) or promote tumor growth through SCD regulation.\",\n      \"evidence\": \"MeRIP-seq and polysome profiling for EBV [PMID:36918845]; Co-IP, ubiquitination, and HBV-infected liver chimeric mice for HBV [PMID:39346550]; xenograft models and SCD inhibitor rescue for thyroid cancer [PMID:37612343]\",\n      \"pmids\": [\"36918845\", \"39346550\", \"37612343\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DTX4 directly ubiquitinates SCD or acts indirectly in thyroid cancer was not established\", \"APOBEC3B ubiquitination site was not mapped\", \"Each study from a single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"DTX4 overexpression in the postnatal mouse retina reduced AII amacrine cell number, linking DTX4-Notch regulation to quantitative control of retinal neuron fate.\",\n      \"evidence\": \"In vivo retinal overexpression, quantitative cell counting, and QTL analysis\",\n      \"pmids\": [\"36816119\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the effect is Notch-dependent was assumed but not formally tested\", \"Loss-of-function data in the retina were absent\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrating that DTX4, unlike DTX3L, cannot ubiquitylate nucleic acids via ester bonds clarified the functional boundaries within the DELTEX family despite their shared DTC domain architecture.\",\n      \"evidence\": \"In vitro ubiquitylation assays with purified DELTEX family members comparing nucleic acid substrates\",\n      \"pmids\": [\"39242775\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DTX4 has unique substrates not shared with DTX3L was not explored\", \"The structural basis for differential nucleic acid ubiquitylation activity was not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A unified model explaining how DTX4 partitions between its TBK1-degradation, Notch-regulatory, and PAR-dependent substrate recognition functions—and whether these represent independent or interconnected pathways—remains unestablished.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of full-length DTX4 exists\", \"Relative importance of PAR-binding versus adaptor-mediated substrate recruitment in vivo is unknown\", \"Comprehensive identification of DTX4 substrates beyond TBK1, Notch1, and APOBEC3B has not been performed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 5, 6, 9]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 2, 4, 6, 7, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 14]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 14, 15]}\n    ],\n    \"complexes\": [\n      \"NLRP4 signalosome\"\n    ],\n    \"partners\": [\n      \"TBK1\",\n      \"NLRP4\",\n      \"DYRK2\",\n      \"USP38\",\n      \"TRAF3IP3\",\n      \"MAP4K1\",\n      \"NOTCH1\",\n      \"APOBEC3B\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}