{"gene":"TRIM4","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2014,"finding":"TRIM4 associates with RIG-I and targets it for K63-linked polyubiquitination, positively regulating RIG-I-mediated type I interferon induction and activation of IRF3 and NF-κB in response to viral RNA.","method":"Co-immunoprecipitation, overexpression and knockdown with reporter assays for IRF3, NF-κB, and IFN-β activation","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with functional knockdown/overexpression, single lab, two orthogonal approaches","pmids":["24755855"],"is_preprint":false},{"year":2015,"finding":"TRIM4 forms cytoplasmic speckle-like structures that transiently interact with mitochondria, induces mitochondrial aggregation and increased mitochondrial ROS in the presence of H2O2, potentiates loss of mitochondrial transmembrane potential and cytochrome c release, and interacts with peroxiredoxin 1 (PRX1); this interaction is critical for H2O2-induced cell death sensitization.","method":"Subcellular localization imaging, overexpression/knockdown cell death assays, Co-immunoprecipitation/mass spectrometry for PRX1 interaction, mitochondrial ROS and membrane potential measurements","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with functional consequence, Co-IP for binding partner, multiple orthogonal methods in single lab","pmids":["26524401"],"is_preprint":false},{"year":2022,"finding":"TRIM4 interacts with SET via its RING and B-box domains (and SET's carboxyl terminus) and catalyzes K48-linked polyubiquitination of SET at K150 and K172, promoting proteasomal degradation of SET, which releases p53 and PP2A to promote ESR1 transcription and enhance ER-α expression.","method":"Co-immunoprecipitation, domain-mapping experiments, in vitro/cell-based ubiquitination assays with site-specific mutagenesis (K150/K172), in vivo xenograft models","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — ubiquitination assay with site-specific mutagenesis, domain mapping, multiple orthogonal methods (Co-IP, in vivo), single lab","pmids":["35843886"],"is_preprint":false},{"year":2023,"finding":"TRIM4 acts as an E3 ubiquitin ligase for MDA5, mediating K63-linked polyubiquitination of MDA5 to activate antiviral innate immune responses; SARS-CoV-2 Nsp8 binds both MDA5 and TRIM4 to impair this ubiquitination and suppress IFN induction.","method":"Co-immunoprecipitation, ubiquitination assays, reporter assays for IFN-β/NF-κB/ISRE, overexpression/knockdown functional studies","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional ubiquitination assays, single lab with multiple approaches","pmids":["37956198"],"is_preprint":false},{"year":2020,"finding":"TRIM4 interacts with TRPM8 via its SPRY domain and promotes K63-linked ubiquitination of TRPM8 at lysine K423, reducing TRPM8 cell-surface expression and negatively regulating TRPM8-mediated currents; this regulation requires the E1 enzyme UBA1.","method":"Co-immunoprecipitation (SPRY domain mapping), patch-clamp electrophysiology, cell-surface biotinylation, site-directed mutagenesis (K423), UBA1 knockdown","journal":"Journal of cellular physiology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro channel function assay (patch-clamp), site-specific mutagenesis, domain mapping, and surface expression assay in single lab with multiple orthogonal methods","pmids":["33037615"],"is_preprint":false},{"year":2022,"finding":"TRIM4 inhibits PRRSV replication by ubiquitinating and degrading the viral NSP2 protein via the proteasome; TRIM4 knockdown increases virus titers and MG132 treatment blocks TRIM4-driven NSP2 degradation.","method":"Overexpression/siRNA knockdown viral replication assays, ubiquitination assays, proteasome inhibitor (MG132) rescue experiments","journal":"BMC veterinary research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional assays with genetic and pharmacological perturbations, single lab","pmids":["35637527"],"is_preprint":false},{"year":2023,"finding":"TRIM4 uses its E3 ubiquitin ligase activity to degrade influenza A virus NP protein (within incoming vRNP and newly synthesized NP), thereby inhibiting IAV replication; ABTB1 counteracts this by interacting with TRIM4 and promoting TRIM4 degradation through the proteasome.","method":"Immunoprecipitation and mass spectrometry, overexpression/knockdown viral replication assays, ubiquitination assays, proteasome inhibitor rescue","journal":"Emerging microbes & infections","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — IP-MS plus functional assays and pharmacological rescue, single lab","pmids":["37823597"],"is_preprint":false},{"year":2024,"finding":"TRIM4 is the E3 ligase that binds and degrades TPL2 kinase via polyubiquitination at lysines K415 and K439; TRIM4 itself is stabilized by E3 ligase TRIM21, which is regulated by KRAS—mutant KRAS recruits RNF185 to degrade TRIM21, thereby destabilizing TRIM4 and stabilizing TPL2, leading to GSK3β phosphorylation/degradation and β-catenin/Wnt pathway activation.","method":"Proximity-dependent biotin identification (BioID), Co-immunoprecipitation, ubiquitination assays with site-specific mutagenesis (K415, K439), genetic perturbation of KRAS/TRIM21/RNF185","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — BioID proximity labeling plus site-specific mutagenesis and Co-IP, multiple orthogonal methods in single rigorous study","pmids":["39178114"],"is_preprint":false},{"year":2024,"finding":"TRIM4 binds hnRNPDL via its RING and B-box domains and promotes K48-linked ubiquitination and proteasomal degradation of hnRNPDL; hnRNPDL in turn binds CDKN2C isoform 2 mRNA and suppresses its expression via alternative splicing, thereby weakening sensitivity to CDK4/6 inhibitors.","method":"Co-immunoprecipitation, GST pull-down (domain mapping), ubiquitination assays, RIP (RNA immunoprecipitation) assay, in vivo siTRIM4 experiments","journal":"Frontiers of medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and GST pull-down domain mapping plus RIP and in vivo experiments, single lab","pmids":["39643799"],"is_preprint":false},{"year":2024,"finding":"TRIM4 promotes ABTB1 degradation through K6, K27, K29, and K33-linked ubiquitination (mediated by the TRIM4 53–500 aa region), thereby preventing ABTB1 from ubiquitinating CDK1 (via K27-linked ubiquitination) and stabilizing CDK1 to promote G2/M progression in glioblastoma.","method":"Co-immunoprecipitation, ubiquitination assays with domain/lysine-specific mutagenesis, protein turnover assays, flow cytometry (cell cycle), xenograft tumor models","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple ubiquitination and domain-mapping experiments plus in vivo models, single lab","pmids":["42034143"],"is_preprint":false},{"year":2024,"finding":"TRIM4 acts as an E3 ligase (atypical neddylation pathway) facilitating the neddylation and proteasomal degradation of CORO1A when bound to the small molecule Aurovertin B, functioning as a molecular glue mechanism; TRIM4-CORO1A interaction was confirmed by Co-IP, mass spectrometry, and SPPIER assay.","method":"Co-immunoprecipitation, mass spectrometry, SPPIER (separation of phases-based protein interaction reporter), phenotypic drug screen with multi-omics, patient-derived organoids","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus MS and orthogonal SPPIER method, single lab with functional organoid validation","pmids":["39629122"],"is_preprint":false},{"year":2022,"finding":"Macaca mulatta TRIM4 overexpression upregulates IFN-alpha, IFN-beta, RIG-I, MAVS, IRF3, IRF7, and antiviral gene expression, and increases IFN-β, NF-κB, and ISRE reporter activity; siRNA knockdown of TRIM4 downregulates the IFN pathway, confirming a conserved positive regulatory role in the interferon signaling pathway.","method":"Overexpression and siRNA knockdown with luciferase reporter assays and qRT-PCR in primate cells","journal":"Frontiers in veterinary science","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional reporter assays in a single study without mechanistic dissection of direct substrate interactions","pmids":["35242838"],"is_preprint":false}],"current_model":"TRIM4 is a RING-domain E3 ubiquitin ligase that targets multiple substrates for K48-linked (proteasomal) or K63-linked (signaling) ubiquitination: it promotes antiviral innate immunity by K63-ubiquitinating RIG-I and MDA5 to activate IRF3/NF-κB/IFN-β signaling; degrades viral proteins (influenza NP, PRRSV NSP2) and cellular substrates (SET, TPL2, hnRNPDL, ABTB1, CORO1A) via the proteasome; negatively regulates the TRPM8 ion channel via K63-ubiquitination at K423; interacts transiently with mitochondria and PRX1 to sensitize cells to oxidative stress-induced death; and its own stability is regulated by TRIM21/RNF185 downstream of oncogenic KRAS signaling."},"narrative":{"mechanistic_narrative":"TRIM4 is a RING-domain E3 ubiquitin ligase that governs both antiviral innate immunity and proteostasis by directing distinct polyubiquitin linkages onto multiple substrates [PMID:24755855, PMID:35843886]. In the RIG-I/MDA5 sensing pathway it catalyzes K63-linked polyubiquitination of RIG-I and MDA5, driving IRF3/NF-κB activation and type I interferon induction [PMID:24755855, PMID:37956198]. This antiviral arm is targeted by pathogens: SARS-CoV-2 Nsp8 bridges MDA5 and TRIM4 to block the modification and suppress IFN [PMID:37956198], while TRIM4 directly degrades viral proteins including influenza A NP and PRRSV NSP2 through the proteasome to restrict replication [PMID:35637527, PMID:37823597]. In its degradative mode TRIM4 catalyzes K48-linked ubiquitination of cellular substrates at defined lysines—SET at K150/K172, engaging the p53/PP2A/ESR1 axis, and TPL2 at K415/K439, controlling GSK3β and β-catenin/Wnt signaling—and additionally degrades hnRNPDL and ABTB1 to influence CDK4/6-inhibitor sensitivity and CDK1-dependent G2/M progression [PMID:35843886, PMID:39178114, PMID:39643799, PMID:42034143]. TRIM4 substrate selection is achieved through discrete domains (RING and B-box for SET and hnRNPDL, SPRY for TRPM8), and its own abundance is controlled by a KRAS–RNF185–TRIM21 stabilization circuit and by ABTB1-driven turnover [PMID:35843886, PMID:33037615, PMID:39178114, PMID:37823597]. Beyond ubiquitination, TRIM4 forms cytoplasmic speckles that transiently engage mitochondria and binds PRX1 to sensitize cells to H2O2-induced death [PMID:26524401], and it negatively regulates the TRPM8 ion channel via K63-ubiquitination at K423 [PMID:33037615].","teleology":[{"year":2014,"claim":"Established TRIM4 as a positive regulator of antiviral signaling, answering whether this TRIM acts on a nucleic-acid sensor rather than acting only as a degradative ligase.","evidence":"Reciprocal Co-IP plus overexpression/knockdown with IRF3, NF-κB and IFN-β reporters in response to viral RNA","pmids":["24755855"],"confidence":"Medium","gaps":["Direct in vitro reconstitution of RIG-I K63-ubiquitination not shown","Ubiquitin-acceptor lysines on RIG-I not mapped"]},{"year":2015,"claim":"Defined a ubiquitination-independent role linking TRIM4 to mitochondrial oxidative-stress responses and identified PRX1 as a partner mediating death sensitization.","evidence":"Subcellular imaging, mitochondrial ROS/membrane-potential assays, Co-IP/MS for PRX1 in H2O2-treated cells","pmids":["26524401"],"confidence":"Medium","gaps":["Whether PRX1 is a ubiquitination substrate unresolved","Molecular trigger of mitochondrial speckle association unknown"]},{"year":2020,"claim":"Showed TRIM4 regulates ion-channel surface expression, broadening its substrate repertoire to a membrane channel via the SPRY domain and a defined acceptor lysine.","evidence":"SPRY-domain Co-IP mapping, patch-clamp, surface biotinylation, K423 mutagenesis and UBA1 knockdown","pmids":["33037615"],"confidence":"High","gaps":["Physiological context of TRPM8 regulation in cold/pain signaling untested","Whether K63-ubiquitination drives internalization mechanistically not dissected"]},{"year":2022,"claim":"Demonstrated a K48-linked degradative function with site-specific resolution, connecting TRIM4 to the SET/p53/PP2A/ESR1 axis in cancer.","evidence":"Domain mapping, in vitro/cell ubiquitination with K150/K172 mutagenesis, xenografts","pmids":["35843886"],"confidence":"High","gaps":["Tissue specificity of the SET-ERα axis not defined","Upstream signals regulating TRIM4-SET engagement unknown"]},{"year":2022,"claim":"Extended the antiviral degradative role to a non-human virus, showing TRIM4 directly degrades a viral protein to restrict replication.","evidence":"Knockdown/overexpression PRRSV replication assays, ubiquitination assays, MG132 rescue","pmids":["35637527"],"confidence":"Medium","gaps":["NSP2 acceptor lysines not mapped","Ubiquitin linkage type on NSP2 not determined"]},{"year":2022,"claim":"Confirmed conservation of TRIM4's positive IFN-pathway role across primates.","evidence":"Overexpression/siRNA with IFN-β/NF-κB/ISRE reporters and qRT-PCR in Macaca mulatta cells","pmids":["35242838"],"confidence":"Low","gaps":["No mechanistic dissection of direct substrate interactions in this system","Human relevance inferred not tested here"]},{"year":2023,"claim":"Identified MDA5 as a second sensor substrate and revealed a viral evasion strategy targeting TRIM4-MDA5 ubiquitination.","evidence":"Co-IP, ubiquitination assays, IFN-β/NF-κB/ISRE reporters; SARS-CoV-2 Nsp8 binding studies","pmids":["37956198"],"confidence":"Medium","gaps":["MDA5 acceptor lysines not mapped","Stoichiometry of the Nsp8-MDA5-TRIM4 ternary interaction unresolved"]},{"year":2023,"claim":"Showed TRIM4 restricts influenza by degrading NP and revealed ABTB1 as a regulator of TRIM4 stability.","evidence":"IP-MS, viral replication assays, ubiquitination assays, proteasome rescue","pmids":["37823597"],"confidence":"Medium","gaps":["NP degradation lysines not defined","Whether ABTB1 directly ubiquitinates TRIM4 not established here"]},{"year":2024,"claim":"Placed TRIM4 within an oncogenic KRAS circuit, defining TPL2 as a substrate and a KRAS-RNF185-TRIM21 cascade controlling TRIM4 levels.","evidence":"BioID, Co-IP, K415/K439 mutagenesis, genetic perturbation of KRAS/TRIM21/RNF185","pmids":["39178114"],"confidence":"High","gaps":["Direct TRIM21-mediated TRIM4 ubiquitination sites not mapped","Generality of the KRAS circuit across tumor types untested"]},{"year":2024,"claim":"Linked TRIM4 to CDK4/6-inhibitor sensitivity through K48-degradation of hnRNPDL and its downstream control of CDKN2C splicing.","evidence":"Co-IP, GST pull-down domain mapping, ubiquitination assays, RIP, in vivo siTRIM4","pmids":["39643799"],"confidence":"Medium","gaps":["hnRNPDL acceptor lysines not mapped","Direct vs indirect effects on CDKN2C splicing not fully separated"]},{"year":2024,"claim":"Demonstrated atypical multi-linkage ubiquitination of ABTB1 by TRIM4, coupling TRIM4 to CDK1 stabilization and G2/M progression in glioblastoma.","evidence":"Co-IP, domain/lysine-specific ubiquitination assays, cell-cycle flow cytometry, xenografts","pmids":["42034143"],"confidence":"Medium","gaps":["Functional consequence of each individual linkage type unresolved","Reciprocal TRIM4/ABTB1 regulation across contexts not reconciled with the influenza ABTB1 finding"]},{"year":2024,"claim":"Revealed a drug-induced molecular-glue/neddylation mechanism, showing TRIM4 can be redirected to degrade CORO1A in the presence of Aurovertin B.","evidence":"Co-IP, MS, SPPIER, phenotypic drug screen with multi-omics, patient-derived organoids","pmids":["39629122"],"confidence":"Medium","gaps":["Neddylation versus ubiquitination contributions not biochemically separated","Endogenous (drug-independent) relevance of CORO1A targeting unknown"]},{"year":null,"claim":"How TRIM4 selects between K48-degradative and K63/signaling outputs on different substrates, and what upstream signals partition these activities, remains undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of substrate engagement","Linkage-determining cofactors (E2 enzymes) largely unidentified","Cell-type-specific regulation of competing functions unmapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,2,3,4,7,8,9]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,4,7,8,9]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[0,3,4]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,3,5,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[2,7,8,9]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3,7]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8,9]}],"complexes":[],"partners":["RIG-I","MDA5","TRPM8","SET","TPL2","HNRNPDL","ABTB1","PRX1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C037","full_name":"E3 ubiquitin-protein ligase TRIM4","aliases":["RING finger protein 87","RING-type E3 ubiquitin transferase TRIM4","Tripartite motif-containing protein 4"],"length_aa":500,"mass_kda":57.5,"function":"E3 ubiquitin-protein ligase. Mediates 'Lys-63'-linked polyubiquitination of the innate immune receptor RIGI, this linkage doesn't lead to proteasomal degradation but seems to enhance IFN induction","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9C037/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM4","classification":"Not Classified","n_dependent_lines":20,"n_total_lines":1208,"dependency_fraction":0.016556291390728478},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRIM4","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRIM4"},"hgnc":{"alias_symbol":["RNF87"],"prev_symbol":[]},"alphafold":{"accession":"Q9C037","domains":[{"cath_id":"3.30.40.10","chopping":"2-64","consensus_level":"medium","plddt":83.1405,"start":2,"end":64},{"cath_id":"-","chopping":"173-292","consensus_level":"medium","plddt":91.2589,"start":173,"end":292},{"cath_id":"2.60.120.920","chopping":"299-345_363-433_441-493","consensus_level":"high","plddt":86.0019,"start":299,"end":493}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C037","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C037-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C037-F1-predicted_aligned_error_v6.png","plddt_mean":83.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM4","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM4"},"sequence":{"accession":"Q9C037","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C037.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C037/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C037"}},"corpus_meta":[{"pmid":"24755855","id":"PMC_24755855","title":"TRIM4 modulates type I interferon induction and cellular antiviral response by targeting RIG-I for K63-linked ubiquitination.","date":"2014","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24755855","citation_count":185,"is_preprint":false},{"pmid":"26524401","id":"PMC_26524401","title":"TRIM4; a novel mitochondrial interacting RING E3 ligase, sensitizes the cells to hydrogen peroxide (H2O2) induced cell death.","date":"2015","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26524401","citation_count":34,"is_preprint":false},{"pmid":"35843886","id":"PMC_35843886","title":"The E3 Ligase TRIM4 Facilitates SET Ubiquitin-Mediated Degradation to Enhance ER-α Action in Breast Cancer.","date":"2022","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/35843886","citation_count":27,"is_preprint":false},{"pmid":"37956198","id":"PMC_37956198","title":"SARS-CoV-2 Nsp8 suppresses MDA5 antiviral immune responses by impairing TRIM4-mediated K63-linked polyubiquitination.","date":"2023","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/37956198","citation_count":27,"is_preprint":false},{"pmid":"30709423","id":"PMC_30709423","title":"TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis.","date":"2019","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/30709423","citation_count":17,"is_preprint":false},{"pmid":"37823597","id":"PMC_37823597","title":"ABTB1 facilitates the replication of influenza A virus by counteracting TRIM4-mediated degradation of viral NP protein.","date":"2023","source":"Emerging microbes & infections","url":"https://pubmed.ncbi.nlm.nih.gov/37823597","citation_count":12,"is_preprint":false},{"pmid":"33037615","id":"PMC_33037615","title":"TRIM4 interacts with TRPM8 and regulates its channel function through K423-mediated ubiquitination.","date":"2020","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/33037615","citation_count":9,"is_preprint":false},{"pmid":"39629122","id":"PMC_39629122","title":"TRIM4 enhances small-molecule-induced neddylated-degradation of CORO1A for triple negative breast cancer therapy.","date":"2024","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/39629122","citation_count":7,"is_preprint":false},{"pmid":"35637527","id":"PMC_35637527","title":"TRIM4-mediated ubiquitination of NSP2 restricts porcine reproductive and respiratory syndrome virus proliferation.","date":"2022","source":"BMC veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/35637527","citation_count":5,"is_preprint":false},{"pmid":"37115387","id":"PMC_37115387","title":"TRIM4 Expression Related to Malignant Progression and Cisplatin Resistance in Osteosarcoma.","date":"2023","source":"Applied biochemistry and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/37115387","citation_count":2,"is_preprint":false},{"pmid":"35242838","id":"PMC_35242838","title":"Sequence Analysis of Macaca mulatta TRIM4 and Its Role in the Interferon Pathway.","date":"2022","source":"Frontiers in veterinary science","url":"https://pubmed.ncbi.nlm.nih.gov/35242838","citation_count":2,"is_preprint":false},{"pmid":"39178114","id":"PMC_39178114","title":"The TRIM4 E3 ubiquitin ligase degrades TPL2 and is modulated by oncogenic KRAS.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39178114","citation_count":1,"is_preprint":false},{"pmid":"39643799","id":"PMC_39643799","title":"TRIM4 modulates the ubiquitin-mediated degradation of hnRNPDL and weakens sensitivity to CDK4/6 inhibitor in ovarian cancer.","date":"2024","source":"Frontiers of medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39643799","citation_count":1,"is_preprint":false},{"pmid":"42034143","id":"PMC_42034143","title":"The E3 ubiquitin ligase TRIM4 promotes the proliferation of glioblastoma by inhibiting ABTB1-mediated CDK1 ubiquitination.","date":"2026","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/42034143","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8926,"output_tokens":3163,"usd":0.037111,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10605,"output_tokens":4014,"usd":0.076688,"stage2_stop_reason":"end_turn"},"total_usd":0.113799,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"TRIM4 associates with RIG-I and targets it for K63-linked polyubiquitination, positively regulating RIG-I-mediated type I interferon induction and activation of IRF3 and NF-κB in response to viral RNA.\",\n      \"method\": \"Co-immunoprecipitation, overexpression and knockdown with reporter assays for IRF3, NF-κB, and IFN-β activation\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with functional knockdown/overexpression, single lab, two orthogonal approaches\",\n      \"pmids\": [\"24755855\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TRIM4 forms cytoplasmic speckle-like structures that transiently interact with mitochondria, induces mitochondrial aggregation and increased mitochondrial ROS in the presence of H2O2, potentiates loss of mitochondrial transmembrane potential and cytochrome c release, and interacts with peroxiredoxin 1 (PRX1); this interaction is critical for H2O2-induced cell death sensitization.\",\n      \"method\": \"Subcellular localization imaging, overexpression/knockdown cell death assays, Co-immunoprecipitation/mass spectrometry for PRX1 interaction, mitochondrial ROS and membrane potential measurements\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with functional consequence, Co-IP for binding partner, multiple orthogonal methods in single lab\",\n      \"pmids\": [\"26524401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM4 interacts with SET via its RING and B-box domains (and SET's carboxyl terminus) and catalyzes K48-linked polyubiquitination of SET at K150 and K172, promoting proteasomal degradation of SET, which releases p53 and PP2A to promote ESR1 transcription and enhance ER-α expression.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping experiments, in vitro/cell-based ubiquitination assays with site-specific mutagenesis (K150/K172), in vivo xenograft models\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — ubiquitination assay with site-specific mutagenesis, domain mapping, multiple orthogonal methods (Co-IP, in vivo), single lab\",\n      \"pmids\": [\"35843886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM4 acts as an E3 ubiquitin ligase for MDA5, mediating K63-linked polyubiquitination of MDA5 to activate antiviral innate immune responses; SARS-CoV-2 Nsp8 binds both MDA5 and TRIM4 to impair this ubiquitination and suppress IFN induction.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, reporter assays for IFN-β/NF-κB/ISRE, overexpression/knockdown functional studies\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional ubiquitination assays, single lab with multiple approaches\",\n      \"pmids\": [\"37956198\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIM4 interacts with TRPM8 via its SPRY domain and promotes K63-linked ubiquitination of TRPM8 at lysine K423, reducing TRPM8 cell-surface expression and negatively regulating TRPM8-mediated currents; this regulation requires the E1 enzyme UBA1.\",\n      \"method\": \"Co-immunoprecipitation (SPRY domain mapping), patch-clamp electrophysiology, cell-surface biotinylation, site-directed mutagenesis (K423), UBA1 knockdown\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro channel function assay (patch-clamp), site-specific mutagenesis, domain mapping, and surface expression assay in single lab with multiple orthogonal methods\",\n      \"pmids\": [\"33037615\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM4 inhibits PRRSV replication by ubiquitinating and degrading the viral NSP2 protein via the proteasome; TRIM4 knockdown increases virus titers and MG132 treatment blocks TRIM4-driven NSP2 degradation.\",\n      \"method\": \"Overexpression/siRNA knockdown viral replication assays, ubiquitination assays, proteasome inhibitor (MG132) rescue experiments\",\n      \"journal\": \"BMC veterinary research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional assays with genetic and pharmacological perturbations, single lab\",\n      \"pmids\": [\"35637527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM4 uses its E3 ubiquitin ligase activity to degrade influenza A virus NP protein (within incoming vRNP and newly synthesized NP), thereby inhibiting IAV replication; ABTB1 counteracts this by interacting with TRIM4 and promoting TRIM4 degradation through the proteasome.\",\n      \"method\": \"Immunoprecipitation and mass spectrometry, overexpression/knockdown viral replication assays, ubiquitination assays, proteasome inhibitor rescue\",\n      \"journal\": \"Emerging microbes & infections\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — IP-MS plus functional assays and pharmacological rescue, single lab\",\n      \"pmids\": [\"37823597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM4 is the E3 ligase that binds and degrades TPL2 kinase via polyubiquitination at lysines K415 and K439; TRIM4 itself is stabilized by E3 ligase TRIM21, which is regulated by KRAS—mutant KRAS recruits RNF185 to degrade TRIM21, thereby destabilizing TRIM4 and stabilizing TPL2, leading to GSK3β phosphorylation/degradation and β-catenin/Wnt pathway activation.\",\n      \"method\": \"Proximity-dependent biotin identification (BioID), Co-immunoprecipitation, ubiquitination assays with site-specific mutagenesis (K415, K439), genetic perturbation of KRAS/TRIM21/RNF185\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — BioID proximity labeling plus site-specific mutagenesis and Co-IP, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"39178114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM4 binds hnRNPDL via its RING and B-box domains and promotes K48-linked ubiquitination and proteasomal degradation of hnRNPDL; hnRNPDL in turn binds CDKN2C isoform 2 mRNA and suppresses its expression via alternative splicing, thereby weakening sensitivity to CDK4/6 inhibitors.\",\n      \"method\": \"Co-immunoprecipitation, GST pull-down (domain mapping), ubiquitination assays, RIP (RNA immunoprecipitation) assay, in vivo siTRIM4 experiments\",\n      \"journal\": \"Frontiers of medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and GST pull-down domain mapping plus RIP and in vivo experiments, single lab\",\n      \"pmids\": [\"39643799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM4 promotes ABTB1 degradation through K6, K27, K29, and K33-linked ubiquitination (mediated by the TRIM4 53–500 aa region), thereby preventing ABTB1 from ubiquitinating CDK1 (via K27-linked ubiquitination) and stabilizing CDK1 to promote G2/M progression in glioblastoma.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays with domain/lysine-specific mutagenesis, protein turnover assays, flow cytometry (cell cycle), xenograft tumor models\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple ubiquitination and domain-mapping experiments plus in vivo models, single lab\",\n      \"pmids\": [\"42034143\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM4 acts as an E3 ligase (atypical neddylation pathway) facilitating the neddylation and proteasomal degradation of CORO1A when bound to the small molecule Aurovertin B, functioning as a molecular glue mechanism; TRIM4-CORO1A interaction was confirmed by Co-IP, mass spectrometry, and SPPIER assay.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, SPPIER (separation of phases-based protein interaction reporter), phenotypic drug screen with multi-omics, patient-derived organoids\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus MS and orthogonal SPPIER method, single lab with functional organoid validation\",\n      \"pmids\": [\"39629122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Macaca mulatta TRIM4 overexpression upregulates IFN-alpha, IFN-beta, RIG-I, MAVS, IRF3, IRF7, and antiviral gene expression, and increases IFN-β, NF-κB, and ISRE reporter activity; siRNA knockdown of TRIM4 downregulates the IFN pathway, confirming a conserved positive regulatory role in the interferon signaling pathway.\",\n      \"method\": \"Overexpression and siRNA knockdown with luciferase reporter assays and qRT-PCR in primate cells\",\n      \"journal\": \"Frontiers in veterinary science\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional reporter assays in a single study without mechanistic dissection of direct substrate interactions\",\n      \"pmids\": [\"35242838\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRIM4 is a RING-domain E3 ubiquitin ligase that targets multiple substrates for K48-linked (proteasomal) or K63-linked (signaling) ubiquitination: it promotes antiviral innate immunity by K63-ubiquitinating RIG-I and MDA5 to activate IRF3/NF-κB/IFN-β signaling; degrades viral proteins (influenza NP, PRRSV NSP2) and cellular substrates (SET, TPL2, hnRNPDL, ABTB1, CORO1A) via the proteasome; negatively regulates the TRPM8 ion channel via K63-ubiquitination at K423; interacts transiently with mitochondria and PRX1 to sensitize cells to oxidative stress-induced death; and its own stability is regulated by TRIM21/RNF185 downstream of oncogenic KRAS signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRIM4 is a RING-domain E3 ubiquitin ligase that governs both antiviral innate immunity and proteostasis by directing distinct polyubiquitin linkages onto multiple substrates [#0, #2]. In the RIG-I/MDA5 sensing pathway it catalyzes K63-linked polyubiquitination of RIG-I and MDA5, driving IRF3/NF-\\u03baB activation and type I interferon induction [#0, #3]. This antiviral arm is targeted by pathogens: SARS-CoV-2 Nsp8 bridges MDA5 and TRIM4 to block the modification and suppress IFN [#3], while TRIM4 directly degrades viral proteins including influenza A NP and PRRSV NSP2 through the proteasome to restrict replication [#5, #6]. In its degradative mode TRIM4 catalyzes K48-linked ubiquitination of cellular substrates at defined lysines\\u2014SET at K150/K172, engaging the p53/PP2A/ESR1 axis, and TPL2 at K415/K439, controlling GSK3\\u03b2 and \\u03b2-catenin/Wnt signaling\\u2014and additionally degrades hnRNPDL and ABTB1 to influence CDK4/6-inhibitor sensitivity and CDK1-dependent G2/M progression [#2, #7, #8, #9]. TRIM4 substrate selection is achieved through discrete domains (RING and B-box for SET and hnRNPDL, SPRY for TRPM8), and its own abundance is controlled by a KRAS\\u2013RNF185\\u2013TRIM21 stabilization circuit and by ABTB1-driven turnover [#2, #4, #7, #6]. Beyond ubiquitination, TRIM4 forms cytoplasmic speckles that transiently engage mitochondria and binds PRX1 to sensitize cells to H2O2-induced death [#1], and it negatively regulates the TRPM8 ion channel via K63-ubiquitination at K423 [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established TRIM4 as a positive regulator of antiviral signaling, answering whether this TRIM acts on a nucleic-acid sensor rather than acting only as a degradative ligase.\",\n      \"evidence\": \"Reciprocal Co-IP plus overexpression/knockdown with IRF3, NF-\\u03baB and IFN-\\u03b2 reporters in response to viral RNA\",\n      \"pmids\": [\"24755855\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct in vitro reconstitution of RIG-I K63-ubiquitination not shown\", \"Ubiquitin-acceptor lysines on RIG-I not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined a ubiquitination-independent role linking TRIM4 to mitochondrial oxidative-stress responses and identified PRX1 as a partner mediating death sensitization.\",\n      \"evidence\": \"Subcellular imaging, mitochondrial ROS/membrane-potential assays, Co-IP/MS for PRX1 in H2O2-treated cells\",\n      \"pmids\": [\"26524401\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PRX1 is a ubiquitination substrate unresolved\", \"Molecular trigger of mitochondrial speckle association unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed TRIM4 regulates ion-channel surface expression, broadening its substrate repertoire to a membrane channel via the SPRY domain and a defined acceptor lysine.\",\n      \"evidence\": \"SPRY-domain Co-IP mapping, patch-clamp, surface biotinylation, K423 mutagenesis and UBA1 knockdown\",\n      \"pmids\": [\"33037615\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological context of TRPM8 regulation in cold/pain signaling untested\", \"Whether K63-ubiquitination drives internalization mechanistically not dissected\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated a K48-linked degradative function with site-specific resolution, connecting TRIM4 to the SET/p53/PP2A/ESR1 axis in cancer.\",\n      \"evidence\": \"Domain mapping, in vitro/cell ubiquitination with K150/K172 mutagenesis, xenografts\",\n      \"pmids\": [\"35843886\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tissue specificity of the SET-ER\\u03b1 axis not defined\", \"Upstream signals regulating TRIM4-SET engagement unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended the antiviral degradative role to a non-human virus, showing TRIM4 directly degrades a viral protein to restrict replication.\",\n      \"evidence\": \"Knockdown/overexpression PRRSV replication assays, ubiquitination assays, MG132 rescue\",\n      \"pmids\": [\"35637527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"NSP2 acceptor lysines not mapped\", \"Ubiquitin linkage type on NSP2 not determined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Confirmed conservation of TRIM4's positive IFN-pathway role across primates.\",\n      \"evidence\": \"Overexpression/siRNA with IFN-\\u03b2/NF-\\u03baB/ISRE reporters and qRT-PCR in Macaca mulatta cells\",\n      \"pmids\": [\"35242838\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic dissection of direct substrate interactions in this system\", \"Human relevance inferred not tested here\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified MDA5 as a second sensor substrate and revealed a viral evasion strategy targeting TRIM4-MDA5 ubiquitination.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, IFN-\\u03b2/NF-\\u03baB/ISRE reporters; SARS-CoV-2 Nsp8 binding studies\",\n      \"pmids\": [\"37956198\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"MDA5 acceptor lysines not mapped\", \"Stoichiometry of the Nsp8-MDA5-TRIM4 ternary interaction unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed TRIM4 restricts influenza by degrading NP and revealed ABTB1 as a regulator of TRIM4 stability.\",\n      \"evidence\": \"IP-MS, viral replication assays, ubiquitination assays, proteasome rescue\",\n      \"pmids\": [\"37823597\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"NP degradation lysines not defined\", \"Whether ABTB1 directly ubiquitinates TRIM4 not established here\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed TRIM4 within an oncogenic KRAS circuit, defining TPL2 as a substrate and a KRAS-RNF185-TRIM21 cascade controlling TRIM4 levels.\",\n      \"evidence\": \"BioID, Co-IP, K415/K439 mutagenesis, genetic perturbation of KRAS/TRIM21/RNF185\",\n      \"pmids\": [\"39178114\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct TRIM21-mediated TRIM4 ubiquitination sites not mapped\", \"Generality of the KRAS circuit across tumor types untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked TRIM4 to CDK4/6-inhibitor sensitivity through K48-degradation of hnRNPDL and its downstream control of CDKN2C splicing.\",\n      \"evidence\": \"Co-IP, GST pull-down domain mapping, ubiquitination assays, RIP, in vivo siTRIM4\",\n      \"pmids\": [\"39643799\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"hnRNPDL acceptor lysines not mapped\", \"Direct vs indirect effects on CDKN2C splicing not fully separated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated atypical multi-linkage ubiquitination of ABTB1 by TRIM4, coupling TRIM4 to CDK1 stabilization and G2/M progression in glioblastoma.\",\n      \"evidence\": \"Co-IP, domain/lysine-specific ubiquitination assays, cell-cycle flow cytometry, xenografts\",\n      \"pmids\": [\"42034143\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of each individual linkage type unresolved\", \"Reciprocal TRIM4/ABTB1 regulation across contexts not reconciled with the influenza ABTB1 finding\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed a drug-induced molecular-glue/neddylation mechanism, showing TRIM4 can be redirected to degrade CORO1A in the presence of Aurovertin B.\",\n      \"evidence\": \"Co-IP, MS, SPPIER, phenotypic drug screen with multi-omics, patient-derived organoids\",\n      \"pmids\": [\"39629122\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Neddylation versus ubiquitination contributions not biochemically separated\", \"Endogenous (drug-independent) relevance of CORO1A targeting unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TRIM4 selects between K48-degradative and K63/signaling outputs on different substrates, and what upstream signals partition these activities, remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of substrate engagement\", \"Linkage-determining cofactors (E2 enzymes) largely unidentified\", \"Cell-type-specific regulation of competing functions unmapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 2, 3, 4, 7, 8, 9]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 4, 7, 8, 9]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [0, 3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 3, 5, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2, 7, 8, 9]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3, 7]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RIG-I\", \"MDA5\", \"TRPM8\", \"SET\", \"TPL2\", \"hnRNPDL\", \"ABTB1\", \"PRX1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}