{"gene":"TRIM69","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2018,"finding":"TRIM69 is an interferon-stimulated gene that directly interacts with dengue virus nonstructural protein 3 (NS3) and mediates its K48-linked polyubiquitination and proteasomal degradation, with Lys104 of NS3 identified as the target residue. The RING domain of TRIM69, which confers E3 ubiquitin ligase activity, is required for this antiviral function. TRIM69 does not modulate IFN signaling itself.","method":"Co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis (Lys104 of NS3), RING domain deletion mutants, in vivo mouse infection model","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (Co-IP, in vitro ubiquitination, mutagenesis, in vivo validation) in a single rigorous study","pmids":["30142214"],"is_preprint":false},{"year":2019,"finding":"TRIM69 inhibits vesicular stomatitis Indiana virus (VSIV) replication in an IFN-induced antiviral state. TRIM69 physically associates with the VSIV phosphoprotein (P) through a specific peptide sequence, and by targeting P (a cofactor of the viral polymerase), TRIM69 inhibits pioneer transcription of incoming virion-associated minus-strand RNA, thereby preventing viral mRNA synthesis. Importantly, TRIM69 does not degrade P but requires higher-order TRIM69 multimerization for antiviral activity. A single amino acid substitution in VSIV P can confer resistance to TRIM69.","method":"Arrayed ISG expression screening, loss-of-function experiments, Co-immunoprecipitation, viral RNA synthesis assays, mutagenesis (single amino acid substitution in P protein), multimerization studies","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including functional screen, Co-IP, mechanistic mutagenesis, and RNA synthesis assays in one study","pmids":["31578292"],"is_preprint":false},{"year":2019,"finding":"TRIM69 inhibits VSIV by a transcriptional inhibition mechanism distinct from degradation. TRIM69 was identified as a potent and specific inhibitor of VSIV (but not influenza A, HIV-1, Rift Valley fever virus, or dengue virus) using arrayed ISG expression screening. TRIM69 exhibits signatures of positive selection consistent with an antiviral role and is highly divergent in human populations.","method":"Arrayed ISG expression screening, viral inhibition assays across multiple viruses, evolutionary analysis","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 — arrayed ISG screen plus multi-virus specificity testing; findings replicated across two independent papers (31375575 and 31578292)","pmids":["31375575","31578292"],"is_preprint":false},{"year":2019,"finding":"TRIM69 interacts with p53 and induces its ubiquitination, thereby suppressing UVB-induced apoptosis and reactive oxygen species production in human lens epithelial cells. Foxo3a acts as a transcription factor that drives TRIM69 promoter activity, establishing a Foxo3a/TRIM69/p53 regulatory axis in cataract formation.","method":"Co-immunoprecipitation, ubiquitination assay, overexpression and knockdown experiments, luciferase promoter assay, flow cytometry (apoptosis/ROS)","journal":"Redox biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and ubiquitination assay from a single lab with multiple readouts but no in vitro reconstitution","pmids":["30844644"],"is_preprint":false},{"year":2022,"finding":"TRIM69 mediates polyubiquitination and degradation of ferroptosis suppressor protein 1 (FSP1). The long noncoding RNA lncFAL directly binds FSP1 and competitively abolishes TRIM69-dependent FSP1 polyubiquitination, thereby reducing ferroptosis vulnerability in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation, ubiquitination assay, RNA pulldown, overexpression/knockdown in HCC cells, in vitro and in vivo functional assays","journal":"Redox biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and ubiquitination assays with functional rescue experiments from a single lab","pmids":["36423520"],"is_preprint":false}],"current_model":"TRIM69 is an interferon-stimulated E3 ubiquitin ligase (via its RING domain) that restricts viral replication through at least two distinct mechanisms: (1) it ubiquitinates and degrades dengue virus NS3 at Lys104, and (2) it inhibits VSV transcription by physically associating with the viral phosphoprotein P and blocking viral RNA synthesis through higher-order multimerization rather than target degradation; additionally, TRIM69 ubiquitinates cellular substrates including p53 and FSP1, implicating it in apoptosis regulation and ferroptosis suppression."},"narrative":{"teleology":[{"year":2018,"claim":"Establishing TRIM69 as a direct antiviral effector resolved how an ISG could target a flavivirus replication protein: TRIM69 ubiquitinates and degrades dengue virus NS3 via K48-linked chains at Lys104, using its RING E3 ligase domain, without modulating IFN signaling itself.","evidence":"Co-IP, ubiquitination assays, K104 mutagenesis, RING deletion mutants, and in vivo mouse dengue infection model","pmids":["30142214"],"confidence":"High","gaps":["E2 ubiquitin-conjugating enzyme partner not identified","Structural basis of TRIM69–NS3 recognition unknown","Whether TRIM69 restricts other flaviviruses beyond dengue not tested"]},{"year":2019,"claim":"Demonstrating that TRIM69 inhibits VSV through a degradation-independent mechanism showed the protein has two distinct antiviral modes: it blocks pioneer transcription of VSV genomic RNA by binding the phosphoprotein P and multimerizing, with a single P mutation conferring resistance, indicating direct and specific targeting.","evidence":"Arrayed ISG screen, Co-IP, viral RNA synthesis assays, multimerization studies, resistance-conferring P mutant, and evolutionary positive-selection analysis across two independent studies","pmids":["31375575","31578292"],"confidence":"High","gaps":["Molecular interface between TRIM69 multimer and P protein unresolved","Whether TRIM69 multimerization is required for dengue NS3 degradation not addressed","TRIM69 did not inhibit influenza A, HIV-1, RVFV, or dengue in the VSV-focused screen, leaving the full spectrum of antiviral activity unclear"]},{"year":2019,"claim":"Identifying p53 as a cellular ubiquitination substrate of TRIM69 expanded its role beyond antiviral defense: TRIM69 ubiquitinates p53 to suppress UVB-induced apoptosis and ROS in lens epithelial cells, under transcriptional control by Foxo3a.","evidence":"Co-IP, ubiquitination assay, Foxo3a promoter-reporter assay, overexpression/knockdown, flow cytometry for apoptosis and ROS in human lens epithelial cells","pmids":["30844644"],"confidence":"Medium","gaps":["No in vitro reconstitution of TRIM69-mediated p53 ubiquitination","Ubiquitin chain type on p53 not determined","Findings from a single lab without independent replication"]},{"year":2022,"claim":"Identification of FSP1 as another TRIM69 degradation substrate linked the E3 ligase to ferroptosis regulation: TRIM69 polyubiquitinates FSP1, and the lncRNA lncFAL competitively blocks this interaction to protect hepatocellular carcinoma cells from ferroptosis.","evidence":"Co-IP, ubiquitination assay, RNA pulldown for lncFAL–FSP1 interaction, overexpression/knockdown in HCC cells, in vivo xenograft assays","pmids":["36423520"],"confidence":"Medium","gaps":["Ubiquitin chain linkage type on FSP1 not specified","Whether TRIM69-FSP1 axis operates in non-cancer contexts unknown","Findings from a single lab without independent replication"]},{"year":null,"claim":"Unresolved: how TRIM69 achieves substrate selectivity across diverse viral and cellular targets, what structural features govern the switch between degradation-dependent (NS3, p53, FSP1) and degradation-independent (VSV P) mechanisms, and what E2 conjugating enzymes cooperate with TRIM69.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural data for TRIM69 or any of its substrate complexes","E2 partner(s) remain unidentified","Relative physiological importance of antiviral vs. cellular substrate functions not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3,4]}],"localization":[],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3,4]}],"complexes":[],"partners":["NS3","TP53","FSP1"],"other_free_text":[]},"mechanistic_narrative":"TRIM69 is an interferon-stimulated E3 ubiquitin ligase that restricts viral replication through mechanistically distinct pathways and ubiquitinates cellular substrates involved in apoptosis and ferroptosis. Its RING domain-dependent K48-linked polyubiquitination targets dengue virus NS3 at Lys104 for proteasomal degradation [PMID:30142214], whereas it inhibits vesicular stomatitis virus (VSV) pioneer transcription by physically associating with the viral phosphoprotein P and forming higher-order multimers, without degrading P [PMID:31578292]. TRIM69 also ubiquitinates and promotes degradation of the cellular substrates p53 and ferroptosis suppressor protein 1 (FSP1), linking it to suppression of UVB-induced apoptosis and modulation of ferroptosis sensitivity in hepatocellular carcinoma [PMID:30844644, PMID:36423520]."},"prefetch_data":{"uniprot":{"accession":"Q86WT6","full_name":"E3 ubiquitin-protein ligase TRIM69","aliases":["RFP-like domain-containing protein trimless","RING finger protein 36","RING-type E3 ubiquitin transferase TRIM69","Tripartite motif-containing protein 69"],"length_aa":500,"mass_kda":57.4,"function":"E3 ubiquitin ligase that plays an important role in antiviral immunity by restricting different viral infections including dengue virus or vesicular stomatitis indiana virus (PubMed:23131556, PubMed:30142214, PubMed:31375575, PubMed:31578292). Ubiquitinates viral proteins such as dengue virus NS3 thereby limiting infection (PubMed:30844644). In addition, acts as a key mediator of type I interferon induced microtubule stabilization by directly associating to microtubules independently of its E3 ligase activity (PubMed:36251989). Also plays a role in cataract formation together with TP53 (PubMed:30844644). Mechanistically, inhibits UVB-induced cell apoptosis and reactive oxygen species (ROS) production by inducing TP53 ubiquitination (PubMed:30844644). Regulates centrosome dynamics and mitotic progression by ubiquitinating STK3/MST2; leading to its redistribution to the perinuclear cytoskeleton and subsequent phosphorylation by PLK1 (PubMed:37739411)","subcellular_location":"Cytoplasm; Nucleus; Nucleus speckle; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome","url":"https://www.uniprot.org/uniprotkb/Q86WT6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM69","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/TRIM69","total_profiled":1310},"omim":[{"mim_id":"616017","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 69; TRIM69","url":"https://www.omim.org/entry/616017"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":33.7}],"url":"https://www.proteinatlas.org/search/TRIM69"},"hgnc":{"alias_symbol":["Trif","TRIMLESS"],"prev_symbol":["RNF36"]},"alphafold":{"accession":"Q86WT6","domains":[{"cath_id":"3.30.40.10","chopping":"28-112","consensus_level":"medium","plddt":84.2675,"start":28,"end":112},{"cath_id":"-","chopping":"114-128_135-154","consensus_level":"medium","plddt":84.3403,"start":114,"end":154},{"cath_id":"2.60.120.920","chopping":"337-498","consensus_level":"high","plddt":94.1496,"start":337,"end":498},{"cath_id":"1.20.5","chopping":"201-287","consensus_level":"high","plddt":94.6372,"start":201,"end":287}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86WT6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86WT6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86WT6-F1-predicted_aligned_error_v6.png","plddt_mean":88.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM69","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM69"},"sequence":{"accession":"Q86WT6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86WT6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86WT6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86WT6"}},"corpus_meta":[{"pmid":"12855817","id":"PMC_12855817","title":"Role 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The RING domain of TRIM69, which confers E3 ubiquitin ligase activity, is required for this antiviral function. TRIM69 does not modulate IFN signaling itself.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis (Lys104 of NS3), RING domain deletion mutants, in vivo mouse infection model\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (Co-IP, in vitro ubiquitination, mutagenesis, in vivo validation) in a single rigorous study\",\n      \"pmids\": [\"30142214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM69 inhibits vesicular stomatitis Indiana virus (VSIV) replication in an IFN-induced antiviral state. TRIM69 physically associates with the VSIV phosphoprotein (P) through a specific peptide sequence, and by targeting P (a cofactor of the viral polymerase), TRIM69 inhibits pioneer transcription of incoming virion-associated minus-strand RNA, thereby preventing viral mRNA synthesis. Importantly, TRIM69 does not degrade P but requires higher-order TRIM69 multimerization for antiviral activity. A single amino acid substitution in VSIV P can confer resistance to TRIM69.\",\n      \"method\": \"Arrayed ISG expression screening, loss-of-function experiments, Co-immunoprecipitation, viral RNA synthesis assays, mutagenesis (single amino acid substitution in P protein), multimerization studies\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including functional screen, Co-IP, mechanistic mutagenesis, and RNA synthesis assays in one study\",\n      \"pmids\": [\"31578292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM69 inhibits VSIV by a transcriptional inhibition mechanism distinct from degradation. TRIM69 was identified as a potent and specific inhibitor of VSIV (but not influenza A, HIV-1, Rift Valley fever virus, or dengue virus) using arrayed ISG expression screening. TRIM69 exhibits signatures of positive selection consistent with an antiviral role and is highly divergent in human populations.\",\n      \"method\": \"Arrayed ISG expression screening, viral inhibition assays across multiple viruses, evolutionary analysis\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — arrayed ISG screen plus multi-virus specificity testing; findings replicated across two independent papers (31375575 and 31578292)\",\n      \"pmids\": [\"31375575\", \"31578292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM69 interacts with p53 and induces its ubiquitination, thereby suppressing UVB-induced apoptosis and reactive oxygen species production in human lens epithelial cells. Foxo3a acts as a transcription factor that drives TRIM69 promoter activity, establishing a Foxo3a/TRIM69/p53 regulatory axis in cataract formation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, overexpression and knockdown experiments, luciferase promoter assay, flow cytometry (apoptosis/ROS)\",\n      \"journal\": \"Redox biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and ubiquitination assay from a single lab with multiple readouts but no in vitro reconstitution\",\n      \"pmids\": [\"30844644\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM69 mediates polyubiquitination and degradation of ferroptosis suppressor protein 1 (FSP1). The long noncoding RNA lncFAL directly binds FSP1 and competitively abolishes TRIM69-dependent FSP1 polyubiquitination, thereby reducing ferroptosis vulnerability in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, RNA pulldown, overexpression/knockdown in HCC cells, in vitro and in vivo functional assays\",\n      \"journal\": \"Redox biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and ubiquitination assays with functional rescue experiments from a single lab\",\n      \"pmids\": [\"36423520\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRIM69 is an interferon-stimulated E3 ubiquitin ligase (via its RING domain) that restricts viral replication through at least two distinct mechanisms: (1) it ubiquitinates and degrades dengue virus NS3 at Lys104, and (2) it inhibits VSV transcription by physically associating with the viral phosphoprotein P and blocking viral RNA synthesis through higher-order multimerization rather than target degradation; additionally, TRIM69 ubiquitinates cellular substrates including p53 and FSP1, implicating it in apoptosis regulation and ferroptosis suppression.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TRIM69 is an interferon-stimulated E3 ubiquitin ligase that restricts viral replication through mechanistically distinct pathways and ubiquitinates cellular substrates involved in apoptosis and ferroptosis. Its RING domain-dependent K48-linked polyubiquitination targets dengue virus NS3 at Lys104 for proteasomal degradation [PMID:30142214], whereas it inhibits vesicular stomatitis virus (VSV) pioneer transcription by physically associating with the viral phosphoprotein P and forming higher-order multimers, without degrading P [PMID:31578292]. TRIM69 also ubiquitinates and promotes degradation of the cellular substrates p53 and ferroptosis suppressor protein 1 (FSP1), linking it to suppression of UVB-induced apoptosis and modulation of ferroptosis sensitivity in hepatocellular carcinoma [PMID:30844644, PMID:36423520].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Establishing TRIM69 as a direct antiviral effector resolved how an ISG could target a flavivirus replication protein: TRIM69 ubiquitinates and degrades dengue virus NS3 via K48-linked chains at Lys104, using its RING E3 ligase domain, without modulating IFN signaling itself.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, K104 mutagenesis, RING deletion mutants, and in vivo mouse dengue infection model\",\n      \"pmids\": [\"30142214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"E2 ubiquitin-conjugating enzyme partner not identified\",\n        \"Structural basis of TRIM69–NS3 recognition unknown\",\n        \"Whether TRIM69 restricts other flaviviruses beyond dengue not tested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that TRIM69 inhibits VSV through a degradation-independent mechanism showed the protein has two distinct antiviral modes: it blocks pioneer transcription of VSV genomic RNA by binding the phosphoprotein P and multimerizing, with a single P mutation conferring resistance, indicating direct and specific targeting.\",\n      \"evidence\": \"Arrayed ISG screen, Co-IP, viral RNA synthesis assays, multimerization studies, resistance-conferring P mutant, and evolutionary positive-selection analysis across two independent studies\",\n      \"pmids\": [\"31375575\", \"31578292\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular interface between TRIM69 multimer and P protein unresolved\",\n        \"Whether TRIM69 multimerization is required for dengue NS3 degradation not addressed\",\n        \"TRIM69 did not inhibit influenza A, HIV-1, RVFV, or dengue in the VSV-focused screen, leaving the full spectrum of antiviral activity unclear\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identifying p53 as a cellular ubiquitination substrate of TRIM69 expanded its role beyond antiviral defense: TRIM69 ubiquitinates p53 to suppress UVB-induced apoptosis and ROS in lens epithelial cells, under transcriptional control by Foxo3a.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, Foxo3a promoter-reporter assay, overexpression/knockdown, flow cytometry for apoptosis and ROS in human lens epithelial cells\",\n      \"pmids\": [\"30844644\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vitro reconstitution of TRIM69-mediated p53 ubiquitination\",\n        \"Ubiquitin chain type on p53 not determined\",\n        \"Findings from a single lab without independent replication\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of FSP1 as another TRIM69 degradation substrate linked the E3 ligase to ferroptosis regulation: TRIM69 polyubiquitinates FSP1, and the lncRNA lncFAL competitively blocks this interaction to protect hepatocellular carcinoma cells from ferroptosis.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, RNA pulldown for lncFAL–FSP1 interaction, overexpression/knockdown in HCC cells, in vivo xenograft assays\",\n      \"pmids\": [\"36423520\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Ubiquitin chain linkage type on FSP1 not specified\",\n        \"Whether TRIM69-FSP1 axis operates in non-cancer contexts unknown\",\n        \"Findings from a single lab without independent replication\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Unresolved: how TRIM69 achieves substrate selectivity across diverse viral and cellular targets, what structural features govern the switch between degradation-dependent (NS3, p53, FSP1) and degradation-independent (VSV P) mechanisms, and what E2 conjugating enzymes cooperate with TRIM69.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural data for TRIM69 or any of its substrate complexes\",\n        \"E2 partner(s) remain unidentified\",\n        \"Relative physiological importance of antiviral vs. cellular substrate functions not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3, 4]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NS3\", \"TP53\", \"FSP1\"],\n    \"other_free_text\": []\n  }\n}\n```"}