{"gene":"TRIM25","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2002,"finding":"TRIM25 (EFP/estrogen-responsive finger protein) is a RING-finger-dependent E3 ubiquitin ligase that targets 14-3-3 sigma for proteasomal degradation, promoting cell cycle progression and breast tumor growth.","method":"In vitro ubiquitination assay, RING domain mutagenesis, antisense knockdown, mouse xenograft model","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro ubiquitination with RING domain mutagenesis, confirmed in vivo with xenograft model","pmids":["12075357"],"is_preprint":false},{"year":2005,"finding":"TRIM25 (EFP) functions as an ISG15 E3 ligase for 14-3-3 sigma in a RING domain-dependent manner, identifying it as a dual ubiquitin and ISG15 E3 ligase.","method":"siRNA knockdown in 293T and MCF-7 cells, interferon treatment, RING domain mutagenesis, in vivo ISGylation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — RING domain mutagenesis plus siRNA knockdown with defined substrate, replicated in multiple cell lines","pmids":["16352599"],"is_preprint":false},{"year":2007,"finding":"TRIM25 (EFP) auto-ISGylates at K117 via its RING domain, and this autoISGylation negatively regulates its ISG15 E3 ligase activity toward 14-3-3 sigma.","method":"Site-directed mutagenesis (K117R), in vivo ISGylation assay, E2 enzyme identification (UbcH6 and UbcH8)","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis of ISGylation site with functional rescue and substrate ubiquitination assay","pmids":["17222803"],"is_preprint":false},{"year":2007,"finding":"TRIM25 (EFP) interacts with and ubiquitylates estrogen receptor alpha (ERα), promoting its ligand-dependent degradation, which paradoxically enhances ERα transcriptional activity through recruitment of the coactivator Tip60.","method":"Co-immunoprecipitation, in vitro and in vivo ubiquitylation assay, dominant-negative RING mutant, reporter assay","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro/in vivo ubiquitylation with RING-domain dominant-negative and transcriptional readout","pmids":["17418098"],"is_preprint":false},{"year":2008,"finding":"TRIM25 binds the first CARD of RIG-I and mediates K63-linked polyubiquitination of the second CARD at K172, which is required for RIG-I interaction with MAVS and downstream IFN-beta production.","method":"Reciprocal co-immunoprecipitation, site-directed mutagenesis (T55I, K172R), IFN-beta reporter assay, RIG-I splice variant analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 — mutagenesis of both binding and ubiquitination sites, orthogonal signaling readouts","pmids":["18948594"],"is_preprint":false},{"year":2011,"finding":"LUBAC (HOIL-1L/HOIP) suppresses TRIM25 by inducing its K48-linked polyubiquitination and proteasomal degradation via RBR ligase domains, and HOIL-1L NZF domain competes with TRIM25 for RIG-I binding, thereby inhibiting RIG-I ubiquitination and antiviral IFN production.","method":"Co-immunoprecipitation, domain mapping, genetic deletion/depletion, IFN production assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP with domain mapping, genetic KO phenotype, multiple orthogonal methods","pmids":["21292167"],"is_preprint":false},{"year":2012,"finding":"TRIM25 ubiquitinates MAVS on K7 and K10, marking it for proteasomal degradation, which is required to release the TBK1/NEMO signaling complex from mitochondria and allow IRF3 phosphorylation.","method":"Co-immunoprecipitation, proteasome inhibitor treatment, IRF3 activation assay, site mapping","journal":"BMC biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — single lab, site mapping and functional readout, but mechanistic model partially inferred","pmids":["22626058"],"is_preprint":false},{"year":2014,"finding":"USP15 deubiquitylates TRIM25, removing K48-linked ubiquitin chains added by LUBAC and thereby stabilizing TRIM25 to sustain RIG-I-mediated type I IFN production.","method":"Protein purification, mass spectrometry, co-immunoprecipitation, catalytically inactive USP15 mutant, siRNA knockdown, IFN production assay","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 1-2 — endogenous interaction by MS, catalytic mutant rescue, orthogonal KD and OE assays","pmids":["24399297"],"is_preprint":false},{"year":2014,"finding":"TRIM25 acts as an RNA-specific cofactor for Lin28a/TuT4-mediated pre-let-7 uridylation by binding the conserved terminal loop of pre-let-7 and activating TuT4, providing substrate specificity for this non-let-7 pre-miRNA.","method":"RNA pulldown coupled with quantitative mass spectrometry, co-immunoprecipitation, in vitro uridylation assay","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 — unbiased MS identification followed by functional reconstitution of uridylation activity","pmids":["25457611"],"is_preprint":false},{"year":2015,"finding":"Dengue virus subgenomic flavivirus RNA (sfRNA) binds TRIM25 in a sequence-dependent manner and prevents its deubiquitylation, thereby blocking TRIM25-dependent sustained RIG-I activation and type I IFN expression.","method":"RNA-protein binding assay, TRIM25 deubiquitylation assay, IFN expression measurement, viral fitness comparison","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — direct RNA-protein interaction with functional IFN suppression, epidemiological validation","pmids":["26138103"],"is_preprint":false},{"year":2016,"finding":"TRIM25 RING domain forms a dimer that engages ubiquitin-charged E2 enzymes; RING dimerization is required for catalysis, K63-linked polyubiquitin synthesis, RIG-I ubiquitination, and IFN induction. Binding of TRIM25 SPRY domain to the RIG-I effector domain promotes RING dimerization and E3 ligase activity.","method":"Crystal structure of RING dimer, in vitro ubiquitination assay with RING dimerization mutants, IFN reporter assay, antiviral activity assay","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — crystal structure combined with mutagenesis and reconstituted ubiquitination assay","pmids":["27425606"],"is_preprint":false},{"year":2017,"finding":"TRIM25 interacts with ZAP (zinc-finger antiviral protein) through its SPRY domain, and both TRIM25 RING domain (ligase activity) and coiled-coil domain (oligomerization) are required for TRIM25 to enhance ZAP's translational inhibition of incoming viral RNA.","method":"Co-immunoprecipitation, genome-wide RNAi screen, TRIM25 RING/coiled-coil deletion mutants, antiviral activity assay, polyubiquitin linkage analysis","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — genome-wide screen with stringent confirmation, domain mutant analysis and functional antiviral readout","pmids":["28060952"],"is_preprint":false},{"year":2017,"finding":"TRIM25 RNA-binding activity is mediated by its PRY/SPRY domain; this RNA-binding activity is required for TRIM25's ubiquitin ligase activity toward itself (autoubiquitination) and its substrate ZAP.","method":"CLIP-seq, SILAC co-immunoprecipitation, RNA-binding domain mutagenesis, in vitro ubiquitination assay","journal":"BMC biology","confidence":"High","confidence_rationale":"Tier 1-2 — CLIP-seq plus in vitro ubiquitination assay with domain mutagenesis","pmids":["29117863"],"is_preprint":false},{"year":2017,"finding":"Nuclear TRIM25 directly binds influenza A virus ribonucleoproteins (vRNPs) via a ubiquitin ligase-independent mechanism and blocks the onset of viral RNA chain elongation without affecting initiation of capped-RNA-primed mRNA synthesis.","method":"Subcellular fractionation, vRNP binding assay, viral RNA synthesis assay with ubiquitin ligase-dead mutant, NS1 antagonism assay","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 2 — direct binding demonstrated, mechanism separated from ubiquitin ligase activity by specific mutant","pmids":["29107643"],"is_preprint":false},{"year":2017,"finding":"Influenza A NS1 protein binds the TRIM25 coiled-coil domain, sterically preventing correct positioning of the PRYSPRY domain required for substrate ubiquitination without affecting unanchored K63-linked polyubiquitin chain synthesis or RING dimerization.","method":"Crystal structures of TRIM25 coiled-coil-PRYSPRY and TRIM25-NS1 complex, in vitro ubiquitination assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — high-resolution crystal structures with functional in vitro ubiquitination validation","pmids":["29739942"],"is_preprint":false},{"year":2017,"finding":"TRIM25 is redistributed to cytoplasmic stress granules upon viral infection; TRIM25 forms homo-complexes and heterocomplexes with RIG-I, and influenza NS1 inhibits TRIM25 homo-complex formation but not RIG-I/TRIM25 heterocomplex formation, preventing downstream RIG-I/MAVS complex assembly.","method":"Bimolecular fluorescence complementation (BiFC), super-resolution microscopy, co-localization analysis in virus-infected cells","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — direct subcellular imaging with functional implication, single lab","pmids":["27807226"],"is_preprint":false},{"year":2017,"finding":"TRIM25 is required for ZAP's antiviral activity; TRIM25 E3 ligase activity mediates ZAP ubiquitination and modulates ZAP's target RNA binding activity.","method":"siRNA knockdown of TRIM25, overexpression of deubiquitinase OTUB1, RNA binding assay, antiviral activity assay","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2-3 — loss-of-function with specific antiviral readout, single lab, indirect ubiquitination mechanism","pmids":["28202764"],"is_preprint":false},{"year":2018,"finding":"HPV16 E6 oncoprotein forms a complex with TRIM25 and USP15, increasing K48-linked ubiquitination and proteasomal degradation of TRIM25, thereby suppressing TRIM25-mediated K63-linked RIG-I ubiquitination and CARD-dependent RIG-I/MAVS interaction.","method":"Co-immunoprecipitation in human cells, ubiquitination assay, IFN-beta reporter assay, CRISPR-Cas9 gene targeting","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP, ubiquitination assay, CRISPR KO with functional readout","pmids":["29263274"],"is_preprint":false},{"year":2018,"finding":"TRIM25 directly ubiquitinates PPARγ, leading to its proteasome-dependent degradation and suppression of adipocyte differentiation; TRIM25 expression is inversely correlated with PPARγ during differentiation.","method":"In vitro ubiquitination assay, TRIM25 stable overexpression, siRNA knockdown, TRIM25-KO MEFs, adipocyte differentiation assay","journal":"Experimental & molecular medicine","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro ubiquitination plus KO MEF phenotype and stable overexpression, multiple methods","pmids":["30323259"],"is_preprint":false},{"year":2019,"finding":"NLRP12 interacts with TRIM25 via its nucleotide-binding domain to prevent TRIM25-mediated K63-linked ubiquitination of RIG-I, and also enhances RNF125-mediated K48-linked degradative ubiquitination of RIG-I, thereby dampening antiviral signaling.","method":"Co-immunoprecipitation, ubiquitination assay, Nlrp12-KO mice, VSV infection model","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 2 — domain mapping, ubiquitination assay, and in vivo KO model with viral infection readout","pmids":["30902577"],"is_preprint":false},{"year":2019,"finding":"14-3-3 proteins bind the coiled-coil domain of TRIM25 and mediate Epstein-Barr virus BPLF1 deubiquitinase positioning to induce TRIM25 mono/di-ubiquitination and sequestration into inactive cytosolic aggregates decorated by p62/SQSTM1, suppressing IFN responses.","method":"Co-immunoprecipitation, in vitro pulldown, BPLF1 catalytic and 14-3-3-binding mutants, p62 colocalization, IFN suppression assay","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — multiple mutant complementation, direct pulldown with domain mapping, dual functional readout","pmids":["31710640"],"is_preprint":false},{"year":2019,"finding":"The lncRNA Lnczc3h7a acts as a molecular scaffold that simultaneously binds TRIM25 and activated RIG-I, stabilizing the RIG-I-TRIM25 complex at early stages of infection and facilitating TRIM25-mediated K63-linked ubiquitination of RIG-I.","method":"RNA pulldown, co-immunoprecipitation, Lnczc3h7a depletion in vitro and in vivo, ubiquitination assay","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — RNA scaffold mechanism with in vitro and in vivo knockdown, multiple orthogonal methods","pmids":["31036902"],"is_preprint":false},{"year":2019,"finding":"MAP3K13 phosphorylates TRIM25 at Ser12 to stabilize it by reducing its polyubiquitination and proteasomal degradation; stabilized TRIM25 then directly ubiquitinates FBXW7α at K412 to block Myc ubiquitination, thereby increasing Myc protein levels.","method":"Phosphorylation assay, ubiquitination assay, co-immunoprecipitation, site-directed mutagenesis, tumor xenograft model","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1-2 — phosphorylation and ubiquitination assays with identified sites plus in vivo tumor model","pmids":["31186535"],"is_preprint":false},{"year":2020,"finding":"TRIM25 directly targets Keap1 for K48-linked ubiquitination and proteasomal degradation, leading to Nrf2 nuclear activation, upregulation of antioxidant defense, reduction of IRE1 UPR signaling, and promotion of ER-associated degradation.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, TRIM25 knockdown/overexpression, TRIM25 KO cell lines, xenograft model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro ubiquitination with direct substrate identification, multiple KO/OE approaches, in vivo validation","pmids":["31953436"],"is_preprint":false},{"year":2020,"finding":"RIG-I binds TRIM25 mRNA via its helicase and C-terminal regulatory domains, enhancing TRIM25 transcript stability, and activates ISGylation pathway genes via CARD domain through ISRE, promoting the RIG-I-TRIM25-ISGylation axis required for myeloid differentiation.","method":"RNA immunoprecipitation, mRNA stability assay, domain-deletion mutants, TRIM25 and ISG15 knockdown, ATRA-induced differentiation assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2-3 — RNA-IP and domain mapping with functional differentiation readout, single lab","pmids":["32513696"],"is_preprint":false},{"year":2020,"finding":"TRIM25 interacts with ZAP through its PRY/SPRY domain and controls the cellular level of ZAP; RNA binding by the PRY/SPRY domain is required for TRIM25 ubiquitin ligase activity toward ZAP (autoubiquitination and ZAP ubiquitination).","method":"CLIP-seq, SILAC co-immunoprecipitation, RNA-binding deficient mutant, in vitro ubiquitination assay","journal":"BMC biology","confidence":"High","confidence_rationale":"Tier 1-2 — CLIP-seq and in vitro biochemistry with domain mutant, moderate evidence","pmids":["29117863"],"is_preprint":false},{"year":2021,"finding":"TRIM25 directly interacts with RIP3 through its SPRY domain and mediates K48-linked polyubiquitination of RIP3 at K501 via its RING domain, promoting proteasomal degradation of RIP3 and inhibiting TNF-induced cell necrosis.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, site-directed mutagenesis (K501R), TRIM25 KO/knockdown, necrosis assay","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro ubiquitination with defined residue, KO phenotype, domain mapping","pmids":["33953350"],"is_preprint":false},{"year":2021,"finding":"TRIM25 activates the AKT/mTOR pathway by mediating K63-linked ubiquitination of PTEN at K266, which prevents PTEN plasma membrane translocation and reduces its phosphatase activity.","method":"Co-immunoprecipitation, ubiquitination assay with K266R mutant, membrane fractionation, PTEN phosphatase activity assay, NSCLC cell xenograft","journal":"Acta pharmacologica Sinica","confidence":"High","confidence_rationale":"Tier 1-2 — site-specific mutagenesis, membrane fractionation, phosphatase assay, in vivo model","pmids":["33931764"],"is_preprint":false},{"year":2021,"finding":"SARS-CoV-2 nucleocapsid (N) protein interacts with TRIM25 at its SPRY domain, masking TRIM25's RNA-binding activity and suppressing TRIM25-mediated K63-linked ubiquitination of RIG-I and IFN-beta secretion.","method":"Co-immunoprecipitation, IFN-beta reporter assay, ubiquitination assay, domain mapping","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 3 — co-IP with domain mapping and functional IFN readout, single lab","pmids":["34452305"],"is_preprint":false},{"year":2021,"finding":"JCV small t antigen interacts with TRIM25 and prevents its RNA-binding activity, thereby inhibiting K63-linked ubiquitination of RIG-I and downstream antiviral signaling.","method":"Co-immunoprecipitation, RNA binding assay, ubiquitination assay, IFN reporter assay","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2-3 — RNA binding and ubiquitination assays with viral protein interaction, single lab","pmids":["33849980"],"is_preprint":false},{"year":2021,"finding":"TRIM25 promotes ubiquitination of IBDV structural protein VP3 at K854 via K27-linked polyubiquitination, targeting it for proteasomal degradation and inhibiting IBDV replication.","method":"Immunoprecipitation, ubiquitination assay, site-directed mutagenesis (K854), TRIM25 overexpression/knockdown, in vitro and in vivo viral replication assay","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 — identified ubiquitination site by mutagenesis with in vitro and in vivo replication assays","pmids":["34516573"],"is_preprint":false},{"year":2022,"finding":"TRIM25 R54P mutation traps substrates including G3BP1/2, UPF1, NME1, and PABPC4, and TRIM25's antiviral activity against alphaviruses is independent of host interferon response, being directly mediated by ubiquitination of these substrates.","method":"Substrate trapping with R54P mutant, mass spectrometry interactome, siRNA knockdown of substrates, antiviral assay independent of IFN","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — catalytic trap mutant combined with MS identification and functional knockdown validation","pmids":["36067236"],"is_preprint":false},{"year":2022,"finding":"TRIM25 binds IAV mRNAs and destabilizes them in a manner independent of its ubiquitin ligase or canonical RNA-binding domain activity; direct tethering of TRIM25 to RNA is sufficient to downregulate the targeted RNA.","method":"RNA binding assay with TRIM25ΔRBD and TRIM25ΔRING mutants, IAV replication assay, RNA tethering assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1-2 — specific domain mutants with mechanistic separation of RNA destabilization from ubiquitin ligase, direct tethering experiment","pmids":["35736141"],"is_preprint":false},{"year":2024,"finding":"TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with G3BP1 in a dsRNA-dependent manner at antiviral stress granules, and this co-condensation significantly enhances TRIM25's ubiquitination activity toward multiple antiviral proteins and is critical for activating the RIG-I signaling pathway.","method":"Live-cell imaging, LLPS assay, co-condensation with dsRNA titration, ubiquitination assay in condensates, RIG-I signaling readout","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 — direct LLPS reconstitution with dsRNA-dependence, enhanced ubiquitination in condensates, multiple orthogonal methods","pmids":["38750080"],"is_preprint":false},{"year":2016,"finding":"TRIM25 polyubiquitinates ERG (ETS-related gene) in vitro, and TRIM25 inactivation reduces ERG polyubiquitination and stabilizes ERG protein; ERG in turn upregulates TRIM25 expression, creating a regulatory feedback.","method":"In vitro polyubiquitination assay, TRIM25 inactivation, co-immunoprecipitation of full-length and truncated ERG","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vitro ubiquitination assay with TRIM25 inactivation, single lab","pmids":["27626314"],"is_preprint":false},{"year":2014,"finding":"TRIM25 cooperates with gp78 in polyubiquitylation of AMF/PGI: TRIM25 mediates the initial ubiquitylation while gp78 catalyzes poly-extension; TRIM25 also ubiquitylates gp78 itself, controlling gp78 steady-state levels.","method":"In vitro polyubiquitylation assay with Ub-DHFR model substrate, co-immunoprecipitation, overexpression/degradation assay","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2-3 — in vitro ubiquitylation reconstitution, single lab","pmids":["24810856"],"is_preprint":false},{"year":2011,"finding":"EFP (TRIM25) interacts with and ubiquitylates KLF5, promoting its degradation in an estrogen-dependent manner; only unubiquitinated EFP can interact with KLF5, and auto-ubiquitination of EFP disrupts its interaction with KLF5.","method":"Co-immunoprecipitation, in vitro ubiquitylation, cycloheximide chase, siRNA knockdown and overexpression","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct interaction and ubiquitylation shown, but mechanism of degradation not fully reconstituted","pmids":["21542805"],"is_preprint":false},{"year":2012,"finding":"EFP (TRIM25) interacts with and ubiquitinates ATBF1, promoting its estrogen-induced proteasomal degradation in breast cancer cells.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown and overexpression of EFP, protein half-life analysis","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct interaction and ubiquitination demonstrated, single lab","pmids":["22452784"],"is_preprint":false},{"year":2023,"finding":"TRIM25 interacts with HBx protein and promotes its K90-site ubiquitination via both RING and SPRY domains, leading to proteasomal degradation; additionally, TRIM25 acts as an adaptor (via SPRY domain, independently of RING) to enhance RIG-I recognition of HBV pregenomic RNA and IFN production.","method":"Co-immunoprecipitation, immunofluorescence colocalization, Western blotting with RING and SPRY mutants, RNA-binding protein immunoprecipitation, ELISA for HBV antigens","journal":"Chinese medical journal","confidence":"Medium","confidence_rationale":"Tier 2-3 — domain-specific mutants with ubiquitination site identification and dual functional readout, single lab","pmids":["36975005"],"is_preprint":false}],"current_model":"TRIM25 is a multifunctional E3 ubiquitin (and ISG15) ligase whose RING domain dimerizes to catalyze K63-linked polyubiquitination of RIG-I CARDs (K172), and whose PRY/SPRY domain mediates substrate recognition, RNA-binding, and interaction with viral RNA; these activities are regulated by stabilizing deubiquitylases (USP15), inhibitory ubiquitylases (LUBAC), viral antagonists (influenza NS1, dengue sfRNA, HPV E6, SARS-CoV-2 N), and phase separation into antiviral stress granules, collectively controlling IFN-mediated antiviral innate immunity as well as diverse non-immune functions including Keap1/Nrf2 axis regulation, PTEN inhibition, and modulation of ZAP-dependent viral RNA translational repression."},"narrative":{"teleology":[{"year":2002,"claim":"Establishing TRIM25 as a RING-dependent E3 ubiquitin ligase resolved the question of whether this TRIM family member possessed intrinsic catalytic activity and identified 14-3-3σ as its first substrate linking it to cell proliferation.","evidence":"In vitro ubiquitination reconstitution with RING mutagenesis and mouse xenograft tumor model","pmids":["12075357"],"confidence":"High","gaps":["Ubiquitin chain linkage type on 14-3-3σ not determined","E2 enzyme specificity not identified"]},{"year":2005,"claim":"Demonstrating that TRIM25 also functions as an ISG15 E3 ligase for 14-3-3σ revealed dual modifier specificity, connecting TRIM25 to interferon-stimulated pathways beyond canonical ubiquitination.","evidence":"siRNA knockdown in 293T and MCF-7 cells with interferon treatment and RING domain mutagenesis","pmids":["16352599"],"confidence":"High","gaps":["Physiological contexts in which ISGylation vs. ubiquitination is favored were unclear","Auto-ISGylation consequences not yet known"]},{"year":2007,"claim":"Discovery that TRIM25 auto-ISGylates at K117 as a negative-feedback mechanism, and that it ubiquitinates ERα to paradoxically enhance transcription, expanded the substrate repertoire and revealed automodification as a regulatory switch.","evidence":"K117R mutagenesis with ISGylation assay; co-IP and ubiquitination assay with dominant-negative RING for ERα","pmids":["17222803","17418098"],"confidence":"High","gaps":["Other auto-modification sites not mapped","Structural basis for ERα recognition unknown"]},{"year":2008,"claim":"Identification of TRIM25 as the E3 ligase that K63-polyubiquitinates RIG-I CARD at K172 to enable MAVS interaction established the central axis of TRIM25 in antiviral innate immunity.","evidence":"Reciprocal co-IP, K172R and T55I mutagenesis, IFN-β reporter assay","pmids":["18948594"],"confidence":"High","gaps":["Whether unanchored K63-Ub chains also contribute was unresolved","Structural basis for CARD recognition not determined"]},{"year":2011,"claim":"Discovery that LUBAC targets TRIM25 for K48-linked degradation and that HOIL-1L competes for RIG-I binding revealed a dedicated negative regulatory circuit controlling TRIM25 protein levels and substrate access.","evidence":"Domain mapping, genetic deletion, IFN production assay","pmids":["21292167"],"confidence":"High","gaps":["Quantitative threshold of TRIM25 degradation needed to suppress IFN unknown","Whether other E3 ligases compensate in LUBAC absence untested"]},{"year":2014,"claim":"USP15 was identified as the deubiquitylase that counteracts LUBAC-mediated K48 ubiquitination of TRIM25, establishing a stabilizing DUB–E3 axis that sustains RIG-I signaling; separately, TRIM25 was found to act as an RNA-binding cofactor for Lin28a/TuT4-mediated pre-let-7 uridylation, revealing a non-immune RNA regulatory function.","evidence":"Endogenous interaction by mass spectrometry with catalytic-dead USP15 mutant; RNA pulldown with quantitative MS and in vitro uridylation reconstitution","pmids":["24399297","25457611"],"confidence":"High","gaps":["Whether USP15 regulation is tissue-specific was unknown","Full spectrum of TRIM25's RNA targets not mapped"]},{"year":2015,"claim":"Dengue sfRNA was shown to bind TRIM25 directly and prevent its deubiquitylation, establishing the first viral RNA antagonist of TRIM25 and explaining sfRNA-mediated immune evasion.","evidence":"RNA-protein binding assay, TRIM25 deubiquitylation assay, IFN suppression, epidemiological validation","pmids":["26138103"],"confidence":"High","gaps":["Exact binding site on TRIM25 for sfRNA not mapped","Whether other flavivirus sfRNAs use the same mechanism unknown"]},{"year":2016,"claim":"Crystal structure of the TRIM25 RING dimer demonstrated that dimerization is essential for E2 engagement and catalysis, and that SPRY domain binding to RIG-I allosterically promotes RING dimerization, providing the first structural framework for TRIM25 activation.","evidence":"X-ray crystallography of RING dimer, RING dimerization mutants in ubiquitination and IFN assays","pmids":["27425606"],"confidence":"High","gaps":["Full-length TRIM25 structure not available","How coiled-coil antiparallel architecture positions two SPRY domains relative to RING dimer unresolved"]},{"year":2017,"claim":"A cluster of studies revealed that TRIM25 partners with ZAP via its SPRY domain to restrict viral RNA translation, that RNA binding by the PRY/SPRY domain is required for TRIM25 ligase activity, that influenza NS1 disrupts TRIM25 by binding its coiled-coil to misposition the SPRY domain, and that nuclear TRIM25 directly inhibits vRNP RNA elongation independently of ubiquitin ligase activity — collectively showing TRIM25 operates through both ligase-dependent and ligase-independent antiviral mechanisms in distinct subcellular compartments.","evidence":"Crystal structures of TRIM25 CC-SPRY and CC-NS1 complex; CLIP-seq; genome-wide RNAi screen; vRNP binding with ligase-dead mutant; BiFC and super-resolution imaging in infected cells","pmids":["28060952","29117863","29739942","29107643","27807226"],"confidence":"High","gaps":["How nuclear vs. cytoplasmic TRIM25 pools are regulated remained unclear","Whether TRIM25 RNA binding activates ligase by an allosteric or proximity mechanism was unresolved","Full repertoire of ZAP-targeted viral RNAs requiring TRIM25 not defined"]},{"year":2018,"claim":"Multiple viral antagonists were shown to converge on TRIM25: HPV16 E6 promotes K48-linked TRIM25 degradation through a complex with USP15, while TRIM25 was also demonstrated to ubiquitinate PPARγ for proteasomal degradation, expanding its non-immune substrate repertoire to adipocyte differentiation.","evidence":"Co-IP, ubiquitination assay, CRISPR KO; in vitro ubiquitination with TRIM25-KO MEFs and adipocyte differentiation assay","pmids":["29263274","30323259"],"confidence":"High","gaps":["Whether E6-mediated TRIM25 suppression contributes to HPV-driven oncogenesis in vivo untested","Ubiquitin chain type on PPARγ not determined"]},{"year":2019,"claim":"New regulatory layers were uncovered: NLRP12 blocks TRIM25-mediated RIG-I ubiquitination, MAP3K13 phosphorylates TRIM25 at S12 to stabilize it and enable FBXW7α ubiquitination (increasing Myc), EBV BPLF1 uses 14-3-3 proteins to sequester TRIM25 into inactive aggregates, and lncRNA Lnczc3h7a scaffolds the RIG-I–TRIM25 complex.","evidence":"KO mice with viral infection; phosphorylation site mutagenesis and xenograft; BPLF1 catalytic mutants with p62 colocalization; RNA pulldown and in vivo knockdown","pmids":["30902577","31186535","31710640","31036902"],"confidence":"High","gaps":["Interplay between these multiple regulators under physiological infection conditions not modeled","Whether MAP3K13-S12 phosphorylation affects antiviral functions of TRIM25 unknown"]},{"year":2021,"claim":"TRIM25's substrate repertoire was further expanded to include RIP3 (K48-linked ubiquitination at K501 inhibiting necroptosis), PTEN (K63-linked at K266 activating AKT/mTOR), and IBDV VP3 (K27-linked at K854), while viral antagonism was extended to SARS-CoV-2 N protein and JCV small t antigen targeting TRIM25 RNA-binding activity.","evidence":"In vitro ubiquitination with site-directed mutagenesis and KO cells; co-IP and domain mapping with IFN readout","pmids":["33953350","33931764","34516573","34452305","33849980"],"confidence":"High","gaps":["K27-linked ubiquitination mechanism by TRIM25 is unusual and structural basis unknown","Whether PTEN ubiquitination is relevant outside NSCLC not tested"]},{"year":2022,"claim":"Substrate-trapping (R54P mutant) combined with mass spectrometry identified G3BP1/2, UPF1, NME1, and PABPC4 as direct TRIM25 substrates mediating IFN-independent antiviral activity against alphaviruses, and separate work showed TRIM25 destabilizes IAV mRNAs through a mechanism independent of both its ligase and canonical RNA-binding domain.","evidence":"Catalytic trap mutant interactome by MS with siRNA validation; RNA tethering assay with ΔRING and ΔRBD mutants","pmids":["36067236","35736141"],"confidence":"High","gaps":["Ubiquitin chain type and sites on G3BP1/2 and UPF1 not mapped","Molecular mechanism of ligase-independent RNA destabilization unclear"]},{"year":2024,"claim":"TRIM25 was shown to undergo dsRNA-dependent liquid–liquid phase separation and co-condense with G3BP1 in antiviral stress granules, with phase separation significantly enhancing its ubiquitination activity, providing a biophysical mechanism for spatiotemporal activation of TRIM25 during infection.","evidence":"Live-cell imaging, in vitro LLPS reconstitution with dsRNA titration, ubiquitination assay in condensates","pmids":["38750080"],"confidence":"High","gaps":["Which TRIM25 domains drive phase separation not fully mapped","Whether LLPS is required for all TRIM25 antiviral functions or only RIG-I signaling is unknown","Post-translational modifications regulating LLPS not identified"]},{"year":null,"claim":"A full-length structural model of TRIM25 showing how the B-box, coiled-coil, and SPRY domains coordinate RING dimerization, RNA binding, substrate engagement, and phase separation remains unresolved, as does the in vivo hierarchy among its many substrates and the tissue-specific regulation of its immune versus non-immune functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No full-length structure available","In vivo substrate hierarchy and competition not determined","Tissue-specific regulation of immune vs. metabolic TRIM25 functions not characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,3,4,10,18,23,26,27,30]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1,10]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8,12,25,32]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[11,16]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[15,20,33]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[4,5,7,9,10,14,17,19,21,28,29]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,3,18,23,26,27,30]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[27,23]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[8,32]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[26]}],"complexes":[],"partners":["RIG-I","ZAP","USP15","G3BP1","MAVS","NS1","NLRP12","14-3-3"],"other_free_text":[]},"mechanistic_narrative":"TRIM25 is a RING-type E3 ubiquitin and ISG15 ligase that serves as a central hub in innate antiviral immunity, stress granule-based signaling, and diverse protein turnover pathways. Its RING domain dimerizes to catalyze K63-linked polyubiquitination of RIG-I at K172, an event essential for RIG-I–MAVS interaction and type I interferon induction, while multiple viral antagonists (influenza NS1, dengue sfRNA, SARS-CoV-2 N, HPV E6, EBV BPLF1) converge on TRIM25 to block this pathway by disrupting its coiled-coil-mediated oligomerization, RNA binding via the PRY/SPRY domain, or protein stability [PMID:18948594, PMID:27425606, PMID:29739942, PMID:26138103, PMID:29263274, PMID:31710640]. Beyond RIG-I signaling, TRIM25 ubiquitinates substrates including Keap1 (K48-linked, activating Nrf2 antioxidant defense), PTEN (K63-linked, activating AKT/mTOR), RIP3 (K48-linked, inhibiting necroptosis), PPARγ (suppressing adipogenesis), and 14-3-3σ, and it cooperates with ZAP to restrict viral RNA translation through SPRY-mediated interaction and ligase-dependent ZAP activation [PMID:31953436, PMID:33931764, PMID:33953350, PMID:30323259, PMID:12075357, PMID:28060952]. TRIM25 also possesses ubiquitin-ligase-independent antiviral functions: it binds and destabilizes viral mRNAs directly, restricts influenza vRNP RNA chain elongation in the nucleus, and undergoes dsRNA-dependent liquid–liquid phase separation with G3BP1 at stress granules to enhance its catalytic output [PMID:35736141, PMID:29107643, PMID:38750080]."},"prefetch_data":{"uniprot":{"accession":"Q14258","full_name":"E3 ubiquitin/ISG15 ligase TRIM25","aliases":["Estrogen-responsive finger protein","RING finger protein 147","RING-type E3 ubiquitin transferase","RING-type E3 ubiquitin transferase TRIM25","Tripartite motif-containing protein 25","Ubiquitin/ISG15-conjugating enzyme TRIM25","Zinc finger protein 147"],"length_aa":630,"mass_kda":71.0,"function":"Functions as a ubiquitin E3 ligase and as an ISG15 E3 ligase (PubMed:16352599). Involved in innate immune defense against viruses by mediating ubiquitination of RIGI and IFIH1 (PubMed:17392790, PubMed:29357390, PubMed:30193849, PubMed:31710640, PubMed:33849980, PubMed:36045682). Mediates 'Lys-63'-linked polyubiquitination of the RIGI N-terminal CARD-like region and may play a role in signal transduction that leads to the production of interferons in response to viral infection (PubMed:17392790, PubMed:23950712). Mediates 'Lys-63'-linked polyubiquitination of IFIH1 (PubMed:30193849). Promotes ISGylation of 14-3-3 sigma (SFN), an adapter protein implicated in the regulation of a large spectrum signaling pathway (PubMed:16352599, PubMed:17069755). Mediates estrogen action in various target organs (PubMed:22452784). Mediates the ubiquitination and subsequent proteasomal degradation of ZFHX3 (PubMed:22452784). Plays a role in promoting the restart of stalled replication forks via interaction with the KHDC3L-OOEP scaffold and subsequent ubiquitination of BLM, resulting in the recruitment and retainment of BLM at DNA replication forks (By similarity). Plays an essential role in the antiviral activity of ZAP/ZC3HAV1; an antiviral protein which inhibits the replication of certain viruses. Mechanistically, mediates 'Lys-63'-linked polyubiquitination of ZAP/ZC3HAV1 that is required for its optimal binding to target mRNA (PubMed:28060952, PubMed:28202764). Also mediates the ubiquitination of various substrates implicated in stress granule formation, nonsense-mediated mRNA decay, nucleoside synthesis and mRNA translation and stability (PubMed:36067236)","subcellular_location":"Cytoplasm; Cytoplasm, Stress granule; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q14258/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRIM25","classification":"Not Classified","n_dependent_lines":14,"n_total_lines":1208,"dependency_fraction":0.011589403973509934},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRIM25","total_profiled":1310},"omim":[{"mim_id":"621451","title":"SMALL NUCLEOLAR RNA HOST GENE 12; SNHG12","url":"https://www.omim.org/entry/621451"},{"mim_id":"619579","title":"KH DOMAIN- AND NYN DOMAIN-CONTAINING PROTEIN; KHNYN","url":"https://www.omim.org/entry/619579"},{"mim_id":"618326","title":"ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 3; ZCCHC3","url":"https://www.omim.org/entry/618326"},{"mim_id":"614371","title":"DENGUE VIRUS, SUSCEPTIBILITY TO","url":"https://www.omim.org/entry/614371"},{"mim_id":"609631","title":"RNA SENSOR RIGI; RIGI","url":"https://www.omim.org/entry/609631"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRIM25"},"hgnc":{"alias_symbol":["EFP","RNF147"],"prev_symbol":["ZNF147"]},"alphafold":{"accession":"Q14258","domains":[{"cath_id":"3.30.40.10","chopping":"5-83","consensus_level":"high","plddt":87.6781,"start":5,"end":83},{"cath_id":"3.30.160.60","chopping":"118-194","consensus_level":"medium","plddt":90.8335,"start":118,"end":194},{"cath_id":"-","chopping":"195-354","consensus_level":"medium","plddt":92.9614,"start":195,"end":354},{"cath_id":"2.60.120.920","chopping":"446-628","consensus_level":"high","plddt":96.4547,"start":446,"end":628}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14258","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q14258-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q14258-F1-predicted_aligned_error_v6.png","plddt_mean":84.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRIM25","jax_strain_url":"https://www.jax.org/strain/search?query=TRIM25"},"sequence":{"accession":"Q14258","fasta_url":"https://rest.uniprot.org/uniprotkb/Q14258.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q14258/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14258"}},"corpus_meta":[{"pmid":"28266114","id":"PMC_28266114","title":"Interaction of lifestyle, behaviour or systemic diseases with dental caries and periodontal diseases: consensus report of group 2 of the joint EFP/ORCA workshop on the boundaries between caries and periodontal diseases.","date":"2017","source":"Journal of clinical periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/28266114","citation_count":372,"is_preprint":false},{"pmid":"23631572","id":"PMC_23631572","title":"Diabetes and periodontal diseases: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases.","date":"2013","source":"Journal of periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/23631572","citation_count":364,"is_preprint":false},{"pmid":"23631582","id":"PMC_23631582","title":"Periodontitis and atherosclerotic cardiovascular disease: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases.","date":"2013","source":"Journal of periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/23631582","citation_count":364,"is_preprint":false},{"pmid":"26138103","id":"PMC_26138103","title":"Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness.","date":"2015","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/26138103","citation_count":337,"is_preprint":false},{"pmid":"12075357","id":"PMC_12075357","title":"Efp targets 14-3-3 sigma for proteolysis and promotes breast tumour growth.","date":"2002","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/12075357","citation_count":322,"is_preprint":false},{"pmid":"23627322","id":"PMC_23627322","title":"Diabetes and periodontal diseases: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases.","date":"2013","source":"Journal of clinical periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/23627322","citation_count":305,"is_preprint":false},{"pmid":"23627332","id":"PMC_23627332","title":"Periodontitis and atherosclerotic cardiovascular disease: consensus report of the Joint EFP/AAP Workshop on Periodontitis and Systemic Diseases.","date":"2013","source":"Journal of clinical periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/23627332","citation_count":261,"is_preprint":false},{"pmid":"16352599","id":"PMC_16352599","title":"The interferon-inducible ubiquitin-protein isopeptide ligase (E3) EFP also functions as an ISG15 E3 ligase.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16352599","citation_count":240,"is_preprint":false},{"pmid":"31953436","id":"PMC_31953436","title":"TRIM25 promotes the cell survival and growth of hepatocellular carcinoma through targeting Keap1-Nrf2 pathway.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31953436","citation_count":224,"is_preprint":false},{"pmid":"29537596","id":"PMC_29537596","title":"Periodontitis and atherosclerotic cardiovascular disease: consensus report of the Joint EFP/AAPWorkshop on Periodontitis and Systemic Diseases.","date":"2013","source":"Journal of periodontology","url":"https://pubmed.ncbi.nlm.nih.gov/29537596","citation_count":220,"is_preprint":false},{"pmid":"18948594","id":"PMC_18948594","title":"Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated antiviral signal transduction.","date":"2008","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/18948594","citation_count":209,"is_preprint":false},{"pmid":"21292167","id":"PMC_21292167","title":"Linear ubiquitin assembly complex negatively regulates RIG-I- and TRIM25-mediated type I interferon induction.","date":"2011","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/21292167","citation_count":185,"is_preprint":false},{"pmid":"22626058","id":"PMC_22626058","title":"MAVS ubiquitination by the E3 ligase TRIM25 and degradation by the proteasome is involved in type I interferon production after activation of the antiviral RIG-I-like receptors.","date":"2012","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/22626058","citation_count":180,"is_preprint":false},{"pmid":"28060952","id":"PMC_28060952","title":"TRIM25 Enhances the Antiviral Action of Zinc-Finger Antiviral Protein (ZAP).","date":"2017","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/28060952","citation_count":173,"is_preprint":false},{"pmid":"31036902","id":"PMC_31036902","title":"The long noncoding RNA Lnczc3h7a promotes a TRIM25-mediated RIG-I antiviral innate immune response.","date":"2019","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31036902","citation_count":158,"is_preprint":false},{"pmid":"29739942","id":"PMC_29739942","title":"Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29739942","citation_count":155,"is_preprint":false},{"pmid":"24399297","id":"PMC_24399297","title":"The ubiquitin-specific protease USP15 promotes RIG-I-mediated antiviral signaling by deubiquitylating TRIM25.","date":"2014","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/24399297","citation_count":139,"is_preprint":false},{"pmid":"29117863","id":"PMC_29117863","title":"RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination.","date":"2017","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/29117863","citation_count":133,"is_preprint":false},{"pmid":"29100052","id":"PMC_29100052","title":"Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29100052","citation_count":124,"is_preprint":false},{"pmid":"29263274","id":"PMC_29263274","title":"The Human Papillomavirus E6 Oncoprotein Targets USP15 and TRIM25 To Suppress RIG-I-Mediated Innate Immune Signaling.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/29263274","citation_count":123,"is_preprint":false},{"pmid":"28202764","id":"PMC_28202764","title":"TRIM25 Is Required for the Antiviral Activity of Zinc Finger Antiviral Protein.","date":"2017","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/28202764","citation_count":122,"is_preprint":false},{"pmid":"29018447","id":"PMC_29018447","title":"TRIM25 in the Regulation of the Antiviral Innate Immunity.","date":"2017","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29018447","citation_count":121,"is_preprint":false},{"pmid":"27425606","id":"PMC_27425606","title":"Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27425606","citation_count":115,"is_preprint":false},{"pmid":"29107643","id":"PMC_29107643","title":"Nuclear TRIM25 Specifically Targets Influenza Virus Ribonucleoproteins to Block the Onset of RNA Chain Elongation.","date":"2017","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/29107643","citation_count":101,"is_preprint":false},{"pmid":"31335993","id":"PMC_31335993","title":"RIPLET, and not TRIM25, is required for endogenous RIG-I-dependent antiviral responses.","date":"2019","source":"Immunology and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/31335993","citation_count":84,"is_preprint":false},{"pmid":"26009254","id":"PMC_26009254","title":"Maintenance of protein synthesis reading frame by EF-P and m(1)G37-tRNA.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/26009254","citation_count":82,"is_preprint":false},{"pmid":"30902577","id":"PMC_30902577","title":"NLRP12 Regulates Anti-viral RIG-I Activation via Interaction with TRIM25.","date":"2019","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/30902577","citation_count":82,"is_preprint":false},{"pmid":"27807226","id":"PMC_27807226","title":"Subcellular Localizations of RIG-I, TRIM25, and MAVS Complexes.","date":"2017","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/27807226","citation_count":78,"is_preprint":false},{"pmid":"37269686","id":"PMC_37269686","title":"EETs alleviate alveolar epithelial cell senescence by inhibiting endoplasmic reticulum stress through the Trim25/Keap1/Nrf2 axis.","date":"2023","source":"Redox biology","url":"https://pubmed.ncbi.nlm.nih.gov/37269686","citation_count":73,"is_preprint":false},{"pmid":"25457611","id":"PMC_25457611","title":"Trim25 Is an RNA-Specific Activator of Lin28a/TuT4-Mediated Uridylation.","date":"2014","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/25457611","citation_count":71,"is_preprint":false},{"pmid":"29321315","id":"PMC_29321315","title":"Paramyxovirus V Proteins Interact with the RIG-I/TRIM25 Regulatory Complex and Inhibit RIG-I Signaling.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/29321315","citation_count":69,"is_preprint":false},{"pmid":"383483","id":"PMC_383483","title":"Peptide bond formation stimulated by protein synthesis factor EF-P depends on the aminoacyl moiety of the acceptor.","date":"1979","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/383483","citation_count":68,"is_preprint":false},{"pmid":"30558248","id":"PMC_30558248","title":"Human Respiratory Syncytial Virus NS 1 Targets TRIM25 to Suppress RIG-I Ubiquitination and Subsequent RIG-I-Mediated Antiviral Signaling.","date":"2018","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/30558248","citation_count":67,"is_preprint":false},{"pmid":"26416626","id":"PMC_26416626","title":"Stall no more at polyproline stretches with the translation elongation factors EF-P and IF-5A.","date":"2015","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/26416626","citation_count":66,"is_preprint":false},{"pmid":"32471869","id":"PMC_32471869","title":"A RIG-I-like receptor directs antiviral responses to a bunyavirus and is antagonized by virus-induced blockade of TRIM25-mediated ubiquitination.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32471869","citation_count":64,"is_preprint":false},{"pmid":"31186535","id":"PMC_31186535","title":"The MAP3K13-TRIM25-FBXW7α axis affects c-Myc protein stability and tumor development.","date":"2019","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/31186535","citation_count":63,"is_preprint":false},{"pmid":"34452305","id":"PMC_34452305","title":"SARS-CoV-2 N Protein Targets TRIM25-Mediated RIG-I Activation to Suppress Innate Immunity.","date":"2021","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/34452305","citation_count":61,"is_preprint":false},{"pmid":"10781795","id":"PMC_10781795","title":"Efp as a primary estrogen-responsive gene in human breast cancer.","date":"2000","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/10781795","citation_count":61,"is_preprint":false},{"pmid":"28194021","id":"PMC_28194021","title":"Type I IFN augments IL-27-dependent TRIM25 expression to inhibit HBV replication.","date":"2017","source":"Cellular & molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/28194021","citation_count":59,"is_preprint":false},{"pmid":"28674614","id":"PMC_28674614","title":"An eFP browser for visualizing strawberry fruit and flower transcriptomes.","date":"2017","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/28674614","citation_count":55,"is_preprint":false},{"pmid":"26754079","id":"PMC_26754079","title":"TRIM25 blockade by RNA interference inhibited migration and invasion of gastric cancer cells through TGF-β signaling.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26754079","citation_count":54,"is_preprint":false},{"pmid":"31990130","id":"PMC_31990130","title":"TRIM25 and its emerging RNA-binding roles in antiviral defense.","date":"2020","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/31990130","citation_count":49,"is_preprint":false},{"pmid":"27528750","id":"PMC_27528750","title":"The role of Trim25 in development, disease and RNA metabolism.","date":"2016","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/27528750","citation_count":49,"is_preprint":false},{"pmid":"17222803","id":"PMC_17222803","title":"Negative regulation of ISG15 E3 ligase EFP through its autoISGylation.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17222803","citation_count":48,"is_preprint":false},{"pmid":"32513696","id":"PMC_32513696","title":"RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation.","date":"2020","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/32513696","citation_count":47,"is_preprint":false},{"pmid":"33931764","id":"PMC_33931764","title":"TRIM25 activates AKT/mTOR by inhibiting PTEN via K63-linked polyubiquitination in non-small cell lung cancer.","date":"2021","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/33931764","citation_count":47,"is_preprint":false},{"pmid":"32576271","id":"PMC_32576271","title":"JP3, an antiangiogenic peptide, inhibits growth and metastasis of gastric cancer through TRIM25/SP1/MMP2 axis.","date":"2020","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/32576271","citation_count":47,"is_preprint":false},{"pmid":"26113559","id":"PMC_26113559","title":"Overexpression of TRIM25 in Lung Cancer Regulates Tumor Cell Progression.","date":"2015","source":"Technology in cancer research & treatment","url":"https://pubmed.ncbi.nlm.nih.gov/26113559","citation_count":46,"is_preprint":false},{"pmid":"26299329","id":"PMC_26299329","title":"Regulation of MDA5-MAVS Antiviral Signaling Axis by TRIM25 through TRAF6-Mediated NF-κB Activation.","date":"2015","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/26299329","citation_count":45,"is_preprint":false},{"pmid":"33953350","id":"PMC_33953350","title":"E3 ligase TRIM25 ubiquitinates RIP3 to inhibit TNF induced cell necrosis.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/33953350","citation_count":44,"is_preprint":false},{"pmid":"32826889","id":"PMC_32826889","title":"OTUD5 cooperates with TRIM25 in transcriptional regulation and tumor progression via deubiquitination activity.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32826889","citation_count":44,"is_preprint":false},{"pmid":"34516573","id":"PMC_34516573","title":"TRIM25 inhibits infectious bursal disease virus replication by targeting VP3 for ubiquitination and degradation.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34516573","citation_count":44,"is_preprint":false},{"pmid":"30775439","id":"PMC_30775439","title":"NDR2 promotes the antiviral immune response via facilitating TRIM25-mediated RIG-I activation in macrophages.","date":"2019","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/30775439","citation_count":43,"is_preprint":false},{"pmid":"31710640","id":"PMC_31710640","title":"14-3-3 scaffold proteins mediate the inactivation of trim25 and inhibition of the type I interferon response by herpesvirus deconjugases.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/31710640","citation_count":43,"is_preprint":false},{"pmid":"33990776","id":"PMC_33990776","title":"Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/33990776","citation_count":41,"is_preprint":false},{"pmid":"24402910","id":"PMC_24402910","title":"eIF5A and EF-P: two unique translation factors are now traveling the same road.","date":"2014","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/24402910","citation_count":40,"is_preprint":false},{"pmid":"30323259","id":"PMC_30323259","title":"The E3 ubiquitin ligase TRIM25 regulates adipocyte differentiation via proteasome-mediated degradation of PPARγ.","date":"2018","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30323259","citation_count":40,"is_preprint":false},{"pmid":"21542805","id":"PMC_21542805","title":"Oestrogen causes degradation of KLF5 by inducing the E3 ubiquitin ligase EFP in ER-positive breast cancer cells.","date":"2011","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/21542805","citation_count":40,"is_preprint":false},{"pmid":"31237466","id":"PMC_31237466","title":"RNA Helicase LGP2 Negatively Regulates RIG-I Signaling by Preventing TRIM25-Mediated Caspase Activation and Recruitment Domain Ubiquitination.","date":"2019","source":"Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research","url":"https://pubmed.ncbi.nlm.nih.gov/31237466","citation_count":39,"is_preprint":false},{"pmid":"17418098","id":"PMC_17418098","title":"Ligand-dependent transcription of estrogen receptor alpha is mediated by the ubiquitin ligase EFP.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17418098","citation_count":39,"is_preprint":false},{"pmid":"31350781","id":"PMC_31350781","title":"An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data.","date":"2019","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31350781","citation_count":38,"is_preprint":false},{"pmid":"33858324","id":"PMC_33858324","title":"LncRNA XIST upregulates TRIM25 via negatively regulating miR-192 in hepatitis B virus-related hepatocellular carcinoma.","date":"2021","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/33858324","citation_count":38,"is_preprint":false},{"pmid":"27276113","id":"PMC_27276113","title":"RING domain is essential for the antiviral activity of TRIM25 from orange spotted grouper.","date":"2016","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/27276113","citation_count":37,"is_preprint":false},{"pmid":"38438346","id":"PMC_38438346","title":"Suppression of ITPKB degradation by Trim25 confers TMZ resistance in glioblastoma through ROS homeostasis.","date":"2024","source":"Signal transduction and targeted therapy","url":"https://pubmed.ncbi.nlm.nih.gov/38438346","citation_count":36,"is_preprint":false},{"pmid":"35736141","id":"PMC_35736141","title":"TRIM25 inhibits influenza A virus infection, destabilizes viral mRNA, but is redundant for activating the RIG-I pathway.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35736141","citation_count":36,"is_preprint":false},{"pmid":"17069755","id":"PMC_17069755","title":"A ubiquitin E3 ligase Efp is up-regulated by interferons and conjugated with ISG15.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17069755","citation_count":35,"is_preprint":false},{"pmid":"16140366","id":"PMC_16140366","title":"Expression of estrogen-responsive finger protein (Efp) is associated with advanced disease in human epithelial ovarian cancer.","date":"2005","source":"Gynecologic oncology","url":"https://pubmed.ncbi.nlm.nih.gov/16140366","citation_count":34,"is_preprint":false},{"pmid":"27626314","id":"PMC_27626314","title":"The ubiquitin ligase TRIM25 targets ERG for degradation in prostate cancer.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27626314","citation_count":34,"is_preprint":false},{"pmid":"22452784","id":"PMC_22452784","title":"Oestrogen causes ATBF1 protein degradation through the oestrogen-responsive E3 ubiquitin ligase EFP.","date":"2012","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/22452784","citation_count":34,"is_preprint":false},{"pmid":"24466302","id":"PMC_24466302","title":"Activation of duck RIG-I by TRIM25 is independent of anchored ubiquitin.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24466302","citation_count":34,"is_preprint":false},{"pmid":"32011712","id":"PMC_32011712","title":"Translation elongation factor P (EF-P).","date":"2020","source":"FEMS microbiology reviews","url":"https://pubmed.ncbi.nlm.nih.gov/32011712","citation_count":31,"is_preprint":false},{"pmid":"38502885","id":"PMC_38502885","title":"Morusin Alleviates Aortic Valve Calcification by Inhibiting Valve Interstitial Cell Senescence Through Ccnd1/Trim25/Nrf2 Axis.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/38502885","citation_count":30,"is_preprint":false},{"pmid":"36067236","id":"PMC_36067236","title":"Elucidation of TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/36067236","citation_count":30,"is_preprint":false},{"pmid":"31849979","id":"PMC_31849979","title":"Zebrafish TRIM25 Promotes Innate Immune Response to RGNNV Infection by Targeting 2CARD and RD Regions of RIG-I for K63-Linked Ubiquitination.","date":"2019","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31849979","citation_count":29,"is_preprint":false},{"pmid":"1956781","id":"PMC_1956781","title":"Cloning, sequencing and overexpression of the gene for prokaryotic factor EF-P involved in peptide bond synthesis.","date":"1991","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/1956781","citation_count":29,"is_preprint":false},{"pmid":"10987361","id":"PMC_10987361","title":"Peptide bond synthesis: function of the efp gene product.","date":"2000","source":"Biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10987361","citation_count":28,"is_preprint":false},{"pmid":"9195040","id":"PMC_9195040","title":"Molecular characterization of the prokaryotic efp gene product involved in a peptidyltransferase reaction.","date":"1997","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/9195040","citation_count":27,"is_preprint":false},{"pmid":"28301380","id":"PMC_28301380","title":"Nitroxoline shows antimyeloma activity by targeting the TRIM25/p53 axle.","date":"2017","source":"Anti-cancer drugs","url":"https://pubmed.ncbi.nlm.nih.gov/28301380","citation_count":26,"is_preprint":false},{"pmid":"38303029","id":"PMC_38303029","title":"TRIM25 promotes glioblastoma cell growth and invasion via regulation of the PRMT1/c-MYC pathway by targeting the splicing factor NONO.","date":"2024","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/38303029","citation_count":26,"is_preprint":false},{"pmid":"38926803","id":"PMC_38926803","title":"Neddylation activated TRIM25 desensitizes triple-negative breast cancer to paclitaxel via TFEB-mediated autophagy.","date":"2024","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/38926803","citation_count":25,"is_preprint":false},{"pmid":"28867193","id":"PMC_28867193","title":"TRIM25 is associated with cisplatin resistance in non-small-cell lung carcinoma A549 cell line via downregulation of 14-3-3σ.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/28867193","citation_count":24,"is_preprint":false},{"pmid":"38750080","id":"PMC_38750080","title":"TRIM25 predominately associates with anti-viral stress granules.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38750080","citation_count":23,"is_preprint":false},{"pmid":"35800389","id":"PMC_35800389","title":"The Role of ZAP and TRIM25 RNA Binding in Restricting Viral Translation.","date":"2022","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/35800389","citation_count":23,"is_preprint":false},{"pmid":"27084108","id":"PMC_27084108","title":"Safety pharmacology studies using EFP and impedance.","date":"2016","source":"Journal of pharmacological and toxicological methods","url":"https://pubmed.ncbi.nlm.nih.gov/27084108","citation_count":23,"is_preprint":false},{"pmid":"36635499","id":"PMC_36635499","title":"Hepatitis B virus X protein promotes MAN1B1 expression by enhancing stability of GRP78 via TRIM25 to facilitate hepatocarcinogenesis.","date":"2023","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/36635499","citation_count":23,"is_preprint":false},{"pmid":"28861931","id":"PMC_28861931","title":"The ubiquitin ligase TRIM25 inhibits hepatocellular carcinoma progression by targeting metastasis associated 1 protein.","date":"2017","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/28861931","citation_count":23,"is_preprint":false},{"pmid":"33849980","id":"PMC_33849980","title":"The Small t Antigen of JC Virus Antagonizes RIG-I-Mediated Innate Immunity by Inhibiting TRIM25's RNA Binding Ability.","date":"2021","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/33849980","citation_count":22,"is_preprint":false},{"pmid":"31237868","id":"PMC_31237868","title":"Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P.","date":"2019","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31237868","citation_count":22,"is_preprint":false},{"pmid":"34445801","id":"PMC_34445801","title":"TRIM25 and DEAD-Box RNA Helicase DDX3X Cooperate to Regulate RIG-I-Mediated Antiviral Immunity.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34445801","citation_count":21,"is_preprint":false},{"pmid":"24810856","id":"PMC_24810856","title":"Polyubiquitylation of AMF requires cooperation between the gp78 and TRIM25 ubiquitin ligases.","date":"2014","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/24810856","citation_count":21,"is_preprint":false},{"pmid":"29654742","id":"PMC_29654742","title":"The E3 ligase for metastasis associated 1 protein, TRIM25, is targeted by microRNA-873 in hepatocellular carcinoma.","date":"2018","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/29654742","citation_count":21,"is_preprint":false},{"pmid":"37437700","id":"PMC_37437700","title":"The role of TRIM25 in the occurrence and development of cancers and inflammatory diseases.","date":"2023","source":"Biochimica et biophysica acta. Reviews on cancer","url":"https://pubmed.ncbi.nlm.nih.gov/37437700","citation_count":20,"is_preprint":false},{"pmid":"37188737","id":"PMC_37188737","title":"TRIM25 promotes temozolomide resistance in glioma by regulating oxidative stress and ferroptotic cell death via the ubiquitination of keap1.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37188737","citation_count":20,"is_preprint":false},{"pmid":"33298177","id":"PMC_33298177","title":"Regulatory effects of chicken TRIM25 on the replication of ALV-A and the MDA5-mediated type I interferon response.","date":"2020","source":"Veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/33298177","citation_count":20,"is_preprint":false},{"pmid":"30586414","id":"PMC_30586414","title":"Efp promotes in vitro and in vivo growth of endometrial cancer cells along with the activation of nuclear factor-κB signaling.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30586414","citation_count":19,"is_preprint":false},{"pmid":"36045682","id":"PMC_36045682","title":"Human metapneumovirus M2-2 protein inhibits RIG-I signaling by preventing TRIM25-mediated RIG-I ubiquitination.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36045682","citation_count":18,"is_preprint":false},{"pmid":"33406425","id":"PMC_33406425","title":"Attenuation of Antiviral Immune Response Caused by Perturbation of TRIM25-Mediated RIG-I Activation under Simulated Microgravity.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33406425","citation_count":18,"is_preprint":false},{"pmid":"31842382","id":"PMC_31842382","title":"Identification of TRIM25 as a Negative Regulator of Caspase-2 Expression Reveals a Novel Target for Sensitizing Colon Carcinoma Cells to Intrinsic Apoptosis.","date":"2019","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/31842382","citation_count":18,"is_preprint":false},{"pmid":"10425199","id":"PMC_10425199","title":"Molecular cloning of rat efp: expression and regulation in primary osteoblasts.","date":"1999","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/10425199","citation_count":17,"is_preprint":false},{"pmid":"36975005","id":"PMC_36975005","title":"TRIM25 inhibits HBV replication by promoting HBx degradation and the RIG-I-mediated pgRNA recognition.","date":"2023","source":"Chinese medical journal","url":"https://pubmed.ncbi.nlm.nih.gov/36975005","citation_count":17,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49610,"output_tokens":8389,"usd":0.137332},"stage2":{"model":"claude-opus-4-6","input_tokens":12248,"output_tokens":4141,"usd":0.247147},"total_usd":0.384479,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"TRIM25 (EFP/estrogen-responsive finger protein) is a RING-finger-dependent E3 ubiquitin ligase that targets 14-3-3 sigma for proteasomal degradation, promoting cell cycle progression and breast tumor growth.\",\n      \"method\": \"In vitro ubiquitination assay, RING domain mutagenesis, antisense knockdown, mouse xenograft model\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro ubiquitination with RING domain mutagenesis, confirmed in vivo with xenograft model\",\n      \"pmids\": [\"12075357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TRIM25 (EFP) functions as an ISG15 E3 ligase for 14-3-3 sigma in a RING domain-dependent manner, identifying it as a dual ubiquitin and ISG15 E3 ligase.\",\n      \"method\": \"siRNA knockdown in 293T and MCF-7 cells, interferon treatment, RING domain mutagenesis, in vivo ISGylation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — RING domain mutagenesis plus siRNA knockdown with defined substrate, replicated in multiple cell lines\",\n      \"pmids\": [\"16352599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"TRIM25 (EFP) auto-ISGylates at K117 via its RING domain, and this autoISGylation negatively regulates its ISG15 E3 ligase activity toward 14-3-3 sigma.\",\n      \"method\": \"Site-directed mutagenesis (K117R), in vivo ISGylation assay, E2 enzyme identification (UbcH6 and UbcH8)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis of ISGylation site with functional rescue and substrate ubiquitination assay\",\n      \"pmids\": [\"17222803\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"TRIM25 (EFP) interacts with and ubiquitylates estrogen receptor alpha (ERα), promoting its ligand-dependent degradation, which paradoxically enhances ERα transcriptional activity through recruitment of the coactivator Tip60.\",\n      \"method\": \"Co-immunoprecipitation, in vitro and in vivo ubiquitylation assay, dominant-negative RING mutant, reporter assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro/in vivo ubiquitylation with RING-domain dominant-negative and transcriptional readout\",\n      \"pmids\": [\"17418098\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TRIM25 binds the first CARD of RIG-I and mediates K63-linked polyubiquitination of the second CARD at K172, which is required for RIG-I interaction with MAVS and downstream IFN-beta production.\",\n      \"method\": \"Reciprocal co-immunoprecipitation, site-directed mutagenesis (T55I, K172R), IFN-beta reporter assay, RIG-I splice variant analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — mutagenesis of both binding and ubiquitination sites, orthogonal signaling readouts\",\n      \"pmids\": [\"18948594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"LUBAC (HOIL-1L/HOIP) suppresses TRIM25 by inducing its K48-linked polyubiquitination and proteasomal degradation via RBR ligase domains, and HOIL-1L NZF domain competes with TRIM25 for RIG-I binding, thereby inhibiting RIG-I ubiquitination and antiviral IFN production.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, genetic deletion/depletion, IFN production assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP with domain mapping, genetic KO phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"21292167\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TRIM25 ubiquitinates MAVS on K7 and K10, marking it for proteasomal degradation, which is required to release the TBK1/NEMO signaling complex from mitochondria and allow IRF3 phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation, proteasome inhibitor treatment, IRF3 activation assay, site mapping\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — single lab, site mapping and functional readout, but mechanistic model partially inferred\",\n      \"pmids\": [\"22626058\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"USP15 deubiquitylates TRIM25, removing K48-linked ubiquitin chains added by LUBAC and thereby stabilizing TRIM25 to sustain RIG-I-mediated type I IFN production.\",\n      \"method\": \"Protein purification, mass spectrometry, co-immunoprecipitation, catalytically inactive USP15 mutant, siRNA knockdown, IFN production assay\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — endogenous interaction by MS, catalytic mutant rescue, orthogonal KD and OE assays\",\n      \"pmids\": [\"24399297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRIM25 acts as an RNA-specific cofactor for Lin28a/TuT4-mediated pre-let-7 uridylation by binding the conserved terminal loop of pre-let-7 and activating TuT4, providing substrate specificity for this non-let-7 pre-miRNA.\",\n      \"method\": \"RNA pulldown coupled with quantitative mass spectrometry, co-immunoprecipitation, in vitro uridylation assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — unbiased MS identification followed by functional reconstitution of uridylation activity\",\n      \"pmids\": [\"25457611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Dengue virus subgenomic flavivirus RNA (sfRNA) binds TRIM25 in a sequence-dependent manner and prevents its deubiquitylation, thereby blocking TRIM25-dependent sustained RIG-I activation and type I IFN expression.\",\n      \"method\": \"RNA-protein binding assay, TRIM25 deubiquitylation assay, IFN expression measurement, viral fitness comparison\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct RNA-protein interaction with functional IFN suppression, epidemiological validation\",\n      \"pmids\": [\"26138103\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TRIM25 RING domain forms a dimer that engages ubiquitin-charged E2 enzymes; RING dimerization is required for catalysis, K63-linked polyubiquitin synthesis, RIG-I ubiquitination, and IFN induction. Binding of TRIM25 SPRY domain to the RIG-I effector domain promotes RING dimerization and E3 ligase activity.\",\n      \"method\": \"Crystal structure of RING dimer, in vitro ubiquitination assay with RING dimerization mutants, IFN reporter assay, antiviral activity assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with mutagenesis and reconstituted ubiquitination assay\",\n      \"pmids\": [\"27425606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM25 interacts with ZAP (zinc-finger antiviral protein) through its SPRY domain, and both TRIM25 RING domain (ligase activity) and coiled-coil domain (oligomerization) are required for TRIM25 to enhance ZAP's translational inhibition of incoming viral RNA.\",\n      \"method\": \"Co-immunoprecipitation, genome-wide RNAi screen, TRIM25 RING/coiled-coil deletion mutants, antiviral activity assay, polyubiquitin linkage analysis\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide screen with stringent confirmation, domain mutant analysis and functional antiviral readout\",\n      \"pmids\": [\"28060952\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM25 RNA-binding activity is mediated by its PRY/SPRY domain; this RNA-binding activity is required for TRIM25's ubiquitin ligase activity toward itself (autoubiquitination) and its substrate ZAP.\",\n      \"method\": \"CLIP-seq, SILAC co-immunoprecipitation, RNA-binding domain mutagenesis, in vitro ubiquitination assay\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — CLIP-seq plus in vitro ubiquitination assay with domain mutagenesis\",\n      \"pmids\": [\"29117863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Nuclear TRIM25 directly binds influenza A virus ribonucleoproteins (vRNPs) via a ubiquitin ligase-independent mechanism and blocks the onset of viral RNA chain elongation without affecting initiation of capped-RNA-primed mRNA synthesis.\",\n      \"method\": \"Subcellular fractionation, vRNP binding assay, viral RNA synthesis assay with ubiquitin ligase-dead mutant, NS1 antagonism assay\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding demonstrated, mechanism separated from ubiquitin ligase activity by specific mutant\",\n      \"pmids\": [\"29107643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Influenza A NS1 protein binds the TRIM25 coiled-coil domain, sterically preventing correct positioning of the PRYSPRY domain required for substrate ubiquitination without affecting unanchored K63-linked polyubiquitin chain synthesis or RING dimerization.\",\n      \"method\": \"Crystal structures of TRIM25 coiled-coil-PRYSPRY and TRIM25-NS1 complex, in vitro ubiquitination assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structures with functional in vitro ubiquitination validation\",\n      \"pmids\": [\"29739942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM25 is redistributed to cytoplasmic stress granules upon viral infection; TRIM25 forms homo-complexes and heterocomplexes with RIG-I, and influenza NS1 inhibits TRIM25 homo-complex formation but not RIG-I/TRIM25 heterocomplex formation, preventing downstream RIG-I/MAVS complex assembly.\",\n      \"method\": \"Bimolecular fluorescence complementation (BiFC), super-resolution microscopy, co-localization analysis in virus-infected cells\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct subcellular imaging with functional implication, single lab\",\n      \"pmids\": [\"27807226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"TRIM25 is required for ZAP's antiviral activity; TRIM25 E3 ligase activity mediates ZAP ubiquitination and modulates ZAP's target RNA binding activity.\",\n      \"method\": \"siRNA knockdown of TRIM25, overexpression of deubiquitinase OTUB1, RNA binding assay, antiviral activity assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — loss-of-function with specific antiviral readout, single lab, indirect ubiquitination mechanism\",\n      \"pmids\": [\"28202764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HPV16 E6 oncoprotein forms a complex with TRIM25 and USP15, increasing K48-linked ubiquitination and proteasomal degradation of TRIM25, thereby suppressing TRIM25-mediated K63-linked RIG-I ubiquitination and CARD-dependent RIG-I/MAVS interaction.\",\n      \"method\": \"Co-immunoprecipitation in human cells, ubiquitination assay, IFN-beta reporter assay, CRISPR-Cas9 gene targeting\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP, ubiquitination assay, CRISPR KO with functional readout\",\n      \"pmids\": [\"29263274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TRIM25 directly ubiquitinates PPARγ, leading to its proteasome-dependent degradation and suppression of adipocyte differentiation; TRIM25 expression is inversely correlated with PPARγ during differentiation.\",\n      \"method\": \"In vitro ubiquitination assay, TRIM25 stable overexpression, siRNA knockdown, TRIM25-KO MEFs, adipocyte differentiation assay\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro ubiquitination plus KO MEF phenotype and stable overexpression, multiple methods\",\n      \"pmids\": [\"30323259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NLRP12 interacts with TRIM25 via its nucleotide-binding domain to prevent TRIM25-mediated K63-linked ubiquitination of RIG-I, and also enhances RNF125-mediated K48-linked degradative ubiquitination of RIG-I, thereby dampening antiviral signaling.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, Nlrp12-KO mice, VSV infection model\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — domain mapping, ubiquitination assay, and in vivo KO model with viral infection readout\",\n      \"pmids\": [\"30902577\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"14-3-3 proteins bind the coiled-coil domain of TRIM25 and mediate Epstein-Barr virus BPLF1 deubiquitinase positioning to induce TRIM25 mono/di-ubiquitination and sequestration into inactive cytosolic aggregates decorated by p62/SQSTM1, suppressing IFN responses.\",\n      \"method\": \"Co-immunoprecipitation, in vitro pulldown, BPLF1 catalytic and 14-3-3-binding mutants, p62 colocalization, IFN suppression assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple mutant complementation, direct pulldown with domain mapping, dual functional readout\",\n      \"pmids\": [\"31710640\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The lncRNA Lnczc3h7a acts as a molecular scaffold that simultaneously binds TRIM25 and activated RIG-I, stabilizing the RIG-I-TRIM25 complex at early stages of infection and facilitating TRIM25-mediated K63-linked ubiquitination of RIG-I.\",\n      \"method\": \"RNA pulldown, co-immunoprecipitation, Lnczc3h7a depletion in vitro and in vivo, ubiquitination assay\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — RNA scaffold mechanism with in vitro and in vivo knockdown, multiple orthogonal methods\",\n      \"pmids\": [\"31036902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MAP3K13 phosphorylates TRIM25 at Ser12 to stabilize it by reducing its polyubiquitination and proteasomal degradation; stabilized TRIM25 then directly ubiquitinates FBXW7α at K412 to block Myc ubiquitination, thereby increasing Myc protein levels.\",\n      \"method\": \"Phosphorylation assay, ubiquitination assay, co-immunoprecipitation, site-directed mutagenesis, tumor xenograft model\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — phosphorylation and ubiquitination assays with identified sites plus in vivo tumor model\",\n      \"pmids\": [\"31186535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIM25 directly targets Keap1 for K48-linked ubiquitination and proteasomal degradation, leading to Nrf2 nuclear activation, upregulation of antioxidant defense, reduction of IRE1 UPR signaling, and promotion of ER-associated degradation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, TRIM25 knockdown/overexpression, TRIM25 KO cell lines, xenograft model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro ubiquitination with direct substrate identification, multiple KO/OE approaches, in vivo validation\",\n      \"pmids\": [\"31953436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RIG-I binds TRIM25 mRNA via its helicase and C-terminal regulatory domains, enhancing TRIM25 transcript stability, and activates ISGylation pathway genes via CARD domain through ISRE, promoting the RIG-I-TRIM25-ISGylation axis required for myeloid differentiation.\",\n      \"method\": \"RNA immunoprecipitation, mRNA stability assay, domain-deletion mutants, TRIM25 and ISG15 knockdown, ATRA-induced differentiation assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — RNA-IP and domain mapping with functional differentiation readout, single lab\",\n      \"pmids\": [\"32513696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIM25 interacts with ZAP through its PRY/SPRY domain and controls the cellular level of ZAP; RNA binding by the PRY/SPRY domain is required for TRIM25 ubiquitin ligase activity toward ZAP (autoubiquitination and ZAP ubiquitination).\",\n      \"method\": \"CLIP-seq, SILAC co-immunoprecipitation, RNA-binding deficient mutant, in vitro ubiquitination assay\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — CLIP-seq and in vitro biochemistry with domain mutant, moderate evidence\",\n      \"pmids\": [\"29117863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM25 directly interacts with RIP3 through its SPRY domain and mediates K48-linked polyubiquitination of RIP3 at K501 via its RING domain, promoting proteasomal degradation of RIP3 and inhibiting TNF-induced cell necrosis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, site-directed mutagenesis (K501R), TRIM25 KO/knockdown, necrosis assay\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro ubiquitination with defined residue, KO phenotype, domain mapping\",\n      \"pmids\": [\"33953350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM25 activates the AKT/mTOR pathway by mediating K63-linked ubiquitination of PTEN at K266, which prevents PTEN plasma membrane translocation and reduces its phosphatase activity.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with K266R mutant, membrane fractionation, PTEN phosphatase activity assay, NSCLC cell xenograft\",\n      \"journal\": \"Acta pharmacologica Sinica\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — site-specific mutagenesis, membrane fractionation, phosphatase assay, in vivo model\",\n      \"pmids\": [\"33931764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SARS-CoV-2 nucleocapsid (N) protein interacts with TRIM25 at its SPRY domain, masking TRIM25's RNA-binding activity and suppressing TRIM25-mediated K63-linked ubiquitination of RIG-I and IFN-beta secretion.\",\n      \"method\": \"Co-immunoprecipitation, IFN-beta reporter assay, ubiquitination assay, domain mapping\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — co-IP with domain mapping and functional IFN readout, single lab\",\n      \"pmids\": [\"34452305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"JCV small t antigen interacts with TRIM25 and prevents its RNA-binding activity, thereby inhibiting K63-linked ubiquitination of RIG-I and downstream antiviral signaling.\",\n      \"method\": \"Co-immunoprecipitation, RNA binding assay, ubiquitination assay, IFN reporter assay\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — RNA binding and ubiquitination assays with viral protein interaction, single lab\",\n      \"pmids\": [\"33849980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM25 promotes ubiquitination of IBDV structural protein VP3 at K854 via K27-linked polyubiquitination, targeting it for proteasomal degradation and inhibiting IBDV replication.\",\n      \"method\": \"Immunoprecipitation, ubiquitination assay, site-directed mutagenesis (K854), TRIM25 overexpression/knockdown, in vitro and in vivo viral replication assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — identified ubiquitination site by mutagenesis with in vitro and in vivo replication assays\",\n      \"pmids\": [\"34516573\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM25 R54P mutation traps substrates including G3BP1/2, UPF1, NME1, and PABPC4, and TRIM25's antiviral activity against alphaviruses is independent of host interferon response, being directly mediated by ubiquitination of these substrates.\",\n      \"method\": \"Substrate trapping with R54P mutant, mass spectrometry interactome, siRNA knockdown of substrates, antiviral assay independent of IFN\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — catalytic trap mutant combined with MS identification and functional knockdown validation\",\n      \"pmids\": [\"36067236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM25 binds IAV mRNAs and destabilizes them in a manner independent of its ubiquitin ligase or canonical RNA-binding domain activity; direct tethering of TRIM25 to RNA is sufficient to downregulate the targeted RNA.\",\n      \"method\": \"RNA binding assay with TRIM25ΔRBD and TRIM25ΔRING mutants, IAV replication assay, RNA tethering assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — specific domain mutants with mechanistic separation of RNA destabilization from ubiquitin ligase, direct tethering experiment\",\n      \"pmids\": [\"35736141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with G3BP1 in a dsRNA-dependent manner at antiviral stress granules, and this co-condensation significantly enhances TRIM25's ubiquitination activity toward multiple antiviral proteins and is critical for activating the RIG-I signaling pathway.\",\n      \"method\": \"Live-cell imaging, LLPS assay, co-condensation with dsRNA titration, ubiquitination assay in condensates, RIG-I signaling readout\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct LLPS reconstitution with dsRNA-dependence, enhanced ubiquitination in condensates, multiple orthogonal methods\",\n      \"pmids\": [\"38750080\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TRIM25 polyubiquitinates ERG (ETS-related gene) in vitro, and TRIM25 inactivation reduces ERG polyubiquitination and stabilizes ERG protein; ERG in turn upregulates TRIM25 expression, creating a regulatory feedback.\",\n      \"method\": \"In vitro polyubiquitination assay, TRIM25 inactivation, co-immunoprecipitation of full-length and truncated ERG\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vitro ubiquitination assay with TRIM25 inactivation, single lab\",\n      \"pmids\": [\"27626314\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRIM25 cooperates with gp78 in polyubiquitylation of AMF/PGI: TRIM25 mediates the initial ubiquitylation while gp78 catalyzes poly-extension; TRIM25 also ubiquitylates gp78 itself, controlling gp78 steady-state levels.\",\n      \"method\": \"In vitro polyubiquitylation assay with Ub-DHFR model substrate, co-immunoprecipitation, overexpression/degradation assay\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — in vitro ubiquitylation reconstitution, single lab\",\n      \"pmids\": [\"24810856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"EFP (TRIM25) interacts with and ubiquitylates KLF5, promoting its degradation in an estrogen-dependent manner; only unubiquitinated EFP can interact with KLF5, and auto-ubiquitination of EFP disrupts its interaction with KLF5.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitylation, cycloheximide chase, siRNA knockdown and overexpression\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct interaction and ubiquitylation shown, but mechanism of degradation not fully reconstituted\",\n      \"pmids\": [\"21542805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"EFP (TRIM25) interacts with and ubiquitinates ATBF1, promoting its estrogen-induced proteasomal degradation in breast cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown and overexpression of EFP, protein half-life analysis\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct interaction and ubiquitination demonstrated, single lab\",\n      \"pmids\": [\"22452784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRIM25 interacts with HBx protein and promotes its K90-site ubiquitination via both RING and SPRY domains, leading to proteasomal degradation; additionally, TRIM25 acts as an adaptor (via SPRY domain, independently of RING) to enhance RIG-I recognition of HBV pregenomic RNA and IFN production.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence colocalization, Western blotting with RING and SPRY mutants, RNA-binding protein immunoprecipitation, ELISA for HBV antigens\",\n      \"journal\": \"Chinese medical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — domain-specific mutants with ubiquitination site identification and dual functional readout, single lab\",\n      \"pmids\": [\"36975005\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRIM25 is a multifunctional E3 ubiquitin (and ISG15) ligase whose RING domain dimerizes to catalyze K63-linked polyubiquitination of RIG-I CARDs (K172), and whose PRY/SPRY domain mediates substrate recognition, RNA-binding, and interaction with viral RNA; these activities are regulated by stabilizing deubiquitylases (USP15), inhibitory ubiquitylases (LUBAC), viral antagonists (influenza NS1, dengue sfRNA, HPV E6, SARS-CoV-2 N), and phase separation into antiviral stress granules, collectively controlling IFN-mediated antiviral innate immunity as well as diverse non-immune functions including Keap1/Nrf2 axis regulation, PTEN inhibition, and modulation of ZAP-dependent viral RNA translational repression.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TRIM25 is a RING-type E3 ubiquitin and ISG15 ligase that serves as a central hub in innate antiviral immunity, stress granule-based signaling, and diverse protein turnover pathways. Its RING domain dimerizes to catalyze K63-linked polyubiquitination of RIG-I at K172, an event essential for RIG-I–MAVS interaction and type I interferon induction, while multiple viral antagonists (influenza NS1, dengue sfRNA, SARS-CoV-2 N, HPV E6, EBV BPLF1) converge on TRIM25 to block this pathway by disrupting its coiled-coil-mediated oligomerization, RNA binding via the PRY/SPRY domain, or protein stability [PMID:18948594, PMID:27425606, PMID:29739942, PMID:26138103, PMID:29263274, PMID:31710640]. Beyond RIG-I signaling, TRIM25 ubiquitinates substrates including Keap1 (K48-linked, activating Nrf2 antioxidant defense), PTEN (K63-linked, activating AKT/mTOR), RIP3 (K48-linked, inhibiting necroptosis), PPARγ (suppressing adipogenesis), and 14-3-3σ, and it cooperates with ZAP to restrict viral RNA translation through SPRY-mediated interaction and ligase-dependent ZAP activation [PMID:31953436, PMID:33931764, PMID:33953350, PMID:30323259, PMID:12075357, PMID:28060952]. TRIM25 also possesses ubiquitin-ligase-independent antiviral functions: it binds and destabilizes viral mRNAs directly, restricts influenza vRNP RNA chain elongation in the nucleus, and undergoes dsRNA-dependent liquid–liquid phase separation with G3BP1 at stress granules to enhance its catalytic output [PMID:35736141, PMID:29107643, PMID:38750080].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing TRIM25 as a RING-dependent E3 ubiquitin ligase resolved the question of whether this TRIM family member possessed intrinsic catalytic activity and identified 14-3-3σ as its first substrate linking it to cell proliferation.\",\n      \"evidence\": \"In vitro ubiquitination reconstitution with RING mutagenesis and mouse xenograft tumor model\",\n      \"pmids\": [\"12075357\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin chain linkage type on 14-3-3σ not determined\", \"E2 enzyme specificity not identified\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating that TRIM25 also functions as an ISG15 E3 ligase for 14-3-3σ revealed dual modifier specificity, connecting TRIM25 to interferon-stimulated pathways beyond canonical ubiquitination.\",\n      \"evidence\": \"siRNA knockdown in 293T and MCF-7 cells with interferon treatment and RING domain mutagenesis\",\n      \"pmids\": [\"16352599\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological contexts in which ISGylation vs. ubiquitination is favored were unclear\", \"Auto-ISGylation consequences not yet known\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Discovery that TRIM25 auto-ISGylates at K117 as a negative-feedback mechanism, and that it ubiquitinates ERα to paradoxically enhance transcription, expanded the substrate repertoire and revealed automodification as a regulatory switch.\",\n      \"evidence\": \"K117R mutagenesis with ISGylation assay; co-IP and ubiquitination assay with dominant-negative RING for ERα\",\n      \"pmids\": [\"17222803\", \"17418098\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Other auto-modification sites not mapped\", \"Structural basis for ERα recognition unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identification of TRIM25 as the E3 ligase that K63-polyubiquitinates RIG-I CARD at K172 to enable MAVS interaction established the central axis of TRIM25 in antiviral innate immunity.\",\n      \"evidence\": \"Reciprocal co-IP, K172R and T55I mutagenesis, IFN-β reporter assay\",\n      \"pmids\": [\"18948594\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether unanchored K63-Ub chains also contribute was unresolved\", \"Structural basis for CARD recognition not determined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Discovery that LUBAC targets TRIM25 for K48-linked degradation and that HOIL-1L competes for RIG-I binding revealed a dedicated negative regulatory circuit controlling TRIM25 protein levels and substrate access.\",\n      \"evidence\": \"Domain mapping, genetic deletion, IFN production assay\",\n      \"pmids\": [\"21292167\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative threshold of TRIM25 degradation needed to suppress IFN unknown\", \"Whether other E3 ligases compensate in LUBAC absence untested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"USP15 was identified as the deubiquitylase that counteracts LUBAC-mediated K48 ubiquitination of TRIM25, establishing a stabilizing DUB–E3 axis that sustains RIG-I signaling; separately, TRIM25 was found to act as an RNA-binding cofactor for Lin28a/TuT4-mediated pre-let-7 uridylation, revealing a non-immune RNA regulatory function.\",\n      \"evidence\": \"Endogenous interaction by mass spectrometry with catalytic-dead USP15 mutant; RNA pulldown with quantitative MS and in vitro uridylation reconstitution\",\n      \"pmids\": [\"24399297\", \"25457611\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether USP15 regulation is tissue-specific was unknown\", \"Full spectrum of TRIM25's RNA targets not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Dengue sfRNA was shown to bind TRIM25 directly and prevent its deubiquitylation, establishing the first viral RNA antagonist of TRIM25 and explaining sfRNA-mediated immune evasion.\",\n      \"evidence\": \"RNA-protein binding assay, TRIM25 deubiquitylation assay, IFN suppression, epidemiological validation\",\n      \"pmids\": [\"26138103\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact binding site on TRIM25 for sfRNA not mapped\", \"Whether other flavivirus sfRNAs use the same mechanism unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Crystal structure of the TRIM25 RING dimer demonstrated that dimerization is essential for E2 engagement and catalysis, and that SPRY domain binding to RIG-I allosterically promotes RING dimerization, providing the first structural framework for TRIM25 activation.\",\n      \"evidence\": \"X-ray crystallography of RING dimer, RING dimerization mutants in ubiquitination and IFN assays\",\n      \"pmids\": [\"27425606\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length TRIM25 structure not available\", \"How coiled-coil antiparallel architecture positions two SPRY domains relative to RING dimer unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A cluster of studies revealed that TRIM25 partners with ZAP via its SPRY domain to restrict viral RNA translation, that RNA binding by the PRY/SPRY domain is required for TRIM25 ligase activity, that influenza NS1 disrupts TRIM25 by binding its coiled-coil to misposition the SPRY domain, and that nuclear TRIM25 directly inhibits vRNP RNA elongation independently of ubiquitin ligase activity — collectively showing TRIM25 operates through both ligase-dependent and ligase-independent antiviral mechanisms in distinct subcellular compartments.\",\n      \"evidence\": \"Crystal structures of TRIM25 CC-SPRY and CC-NS1 complex; CLIP-seq; genome-wide RNAi screen; vRNP binding with ligase-dead mutant; BiFC and super-resolution imaging in infected cells\",\n      \"pmids\": [\"28060952\", \"29117863\", \"29739942\", \"29107643\", \"27807226\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How nuclear vs. cytoplasmic TRIM25 pools are regulated remained unclear\", \"Whether TRIM25 RNA binding activates ligase by an allosteric or proximity mechanism was unresolved\", \"Full repertoire of ZAP-targeted viral RNAs requiring TRIM25 not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Multiple viral antagonists were shown to converge on TRIM25: HPV16 E6 promotes K48-linked TRIM25 degradation through a complex with USP15, while TRIM25 was also demonstrated to ubiquitinate PPARγ for proteasomal degradation, expanding its non-immune substrate repertoire to adipocyte differentiation.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, CRISPR KO; in vitro ubiquitination with TRIM25-KO MEFs and adipocyte differentiation assay\",\n      \"pmids\": [\"29263274\", \"30323259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether E6-mediated TRIM25 suppression contributes to HPV-driven oncogenesis in vivo untested\", \"Ubiquitin chain type on PPARγ not determined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"New regulatory layers were uncovered: NLRP12 blocks TRIM25-mediated RIG-I ubiquitination, MAP3K13 phosphorylates TRIM25 at S12 to stabilize it and enable FBXW7α ubiquitination (increasing Myc), EBV BPLF1 uses 14-3-3 proteins to sequester TRIM25 into inactive aggregates, and lncRNA Lnczc3h7a scaffolds the RIG-I–TRIM25 complex.\",\n      \"evidence\": \"KO mice with viral infection; phosphorylation site mutagenesis and xenograft; BPLF1 catalytic mutants with p62 colocalization; RNA pulldown and in vivo knockdown\",\n      \"pmids\": [\"30902577\", \"31186535\", \"31710640\", \"31036902\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interplay between these multiple regulators under physiological infection conditions not modeled\", \"Whether MAP3K13-S12 phosphorylation affects antiviral functions of TRIM25 unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"TRIM25's substrate repertoire was further expanded to include RIP3 (K48-linked ubiquitination at K501 inhibiting necroptosis), PTEN (K63-linked at K266 activating AKT/mTOR), and IBDV VP3 (K27-linked at K854), while viral antagonism was extended to SARS-CoV-2 N protein and JCV small t antigen targeting TRIM25 RNA-binding activity.\",\n      \"evidence\": \"In vitro ubiquitination with site-directed mutagenesis and KO cells; co-IP and domain mapping with IFN readout\",\n      \"pmids\": [\"33953350\", \"33931764\", \"34516573\", \"34452305\", \"33849980\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"K27-linked ubiquitination mechanism by TRIM25 is unusual and structural basis unknown\", \"Whether PTEN ubiquitination is relevant outside NSCLC not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Substrate-trapping (R54P mutant) combined with mass spectrometry identified G3BP1/2, UPF1, NME1, and PABPC4 as direct TRIM25 substrates mediating IFN-independent antiviral activity against alphaviruses, and separate work showed TRIM25 destabilizes IAV mRNAs through a mechanism independent of both its ligase and canonical RNA-binding domain.\",\n      \"evidence\": \"Catalytic trap mutant interactome by MS with siRNA validation; RNA tethering assay with ΔRING and ΔRBD mutants\",\n      \"pmids\": [\"36067236\", \"35736141\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin chain type and sites on G3BP1/2 and UPF1 not mapped\", \"Molecular mechanism of ligase-independent RNA destabilization unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"TRIM25 was shown to undergo dsRNA-dependent liquid–liquid phase separation and co-condense with G3BP1 in antiviral stress granules, with phase separation significantly enhancing its ubiquitination activity, providing a biophysical mechanism for spatiotemporal activation of TRIM25 during infection.\",\n      \"evidence\": \"Live-cell imaging, in vitro LLPS reconstitution with dsRNA titration, ubiquitination assay in condensates\",\n      \"pmids\": [\"38750080\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which TRIM25 domains drive phase separation not fully mapped\", \"Whether LLPS is required for all TRIM25 antiviral functions or only RIG-I signaling is unknown\", \"Post-translational modifications regulating LLPS not identified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A full-length structural model of TRIM25 showing how the B-box, coiled-coil, and SPRY domains coordinate RING dimerization, RNA binding, substrate engagement, and phase separation remains unresolved, as does the in vivo hierarchy among its many substrates and the tissue-specific regulation of its immune versus non-immune functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No full-length structure available\", \"In vivo substrate hierarchy and competition not determined\", \"Tissue-specific regulation of immune vs. metabolic TRIM25 functions not characterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 3, 4, 10, 18, 23, 26, 27, 30]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1, 10]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8, 12, 25, 32]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [11, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [15, 20, 33]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [4, 5, 7, 9, 10, 14, 17, 19, 21, 28, 29]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 3, 18, 23, 26, 27, 30]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [27, 23]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [8, 32]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [26]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RIG-I\", \"ZAP\", \"USP15\", \"G3BP1\", \"MAVS\", \"NS1\", \"NLRP12\", \"14-3-3\"],\n    \"other_free_text\": []\n  }\n}\n```"}