{"gene":"TDRD3","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2010,"finding":"TDRD3 Tudor domain functions as a 'reader' of asymmetric dimethylarginine (aDMA) marks on histones (H3R17me2a deposited by CARM1 and H4R3me2a deposited by PRMT1), identified by protein domain microarray. TDRD3 itself acts as a transcriptional coactivator, and this coactivator activity requires an intact Tudor domain. TDRD3 is recruited to an estrogen-responsive element in a CARM1-dependent manner, and ChIP-seq shows it localizes predominantly to transcriptional start sites.","method":"Protein domain microarray, co-immunoprecipitation, ChIP-seq, Tudor domain mutagenesis, estrogen-responsive element reporter assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (microarray, ChIP-seq, mutagenesis, reporter assay) in a focused study; widely replicated by subsequent structural work","pmids":["21172665"],"is_preprint":false},{"year":2008,"finding":"TDRD3 co-sediments with FMRP on actively translating polyribosomes and accumulates in cytoplasmic stress granules (SGs) in response to cellular stress. The Tudor domain is both required and sufficient for SG recruitment, and the methyl-binding surface of the Tudor domain is important for this process. Pull-down experiments identified five novel TDRD3-interacting partners, including SERPINE1 mRNA-binding protein 1 and DDX3 (DEAD/H box-3), which are also novel SG constituents.","method":"Polyribosome sedimentation, immunofluorescence, stress induction assays, Tudor domain deletion/mutation analysis, GST pull-down","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (sedimentation, localization, mutagenesis, pulldown) in a focused study; replicated in subsequent papers","pmids":["18632687"],"is_preprint":false},{"year":2008,"finding":"TDRD3 harbors an OB-fold domain and a ubiquitin-associated (UBA) domain capable of binding tetra-ubiquitin. TDRD3 directly interacts with FMRP and its autosomal homologs FXR1 and FXR2 via biochemical experiments. Overexpression of TDRD3 in cells induces SG formation and co-localization with endogenous FMRP. The disease-associated FMRP missense mutation I304N severely impairs interaction with TDRD3.","method":"Biochemical pull-down/co-immunoprecipitation, domain characterization, overexpression/immunofluorescence, UBA-tetra-ubiquitin binding assay","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction experiments, multiple domains characterized, single lab","pmids":["18664458"],"is_preprint":false},{"year":2012,"finding":"Crystal structures of the TDRD3 Tudor domain in complex with small molecules reveal that TDRD3 preferentially recognizes asymmetric dimethylarginine (aDMA) marks, in contrast to SMN which preferentially binds symmetric dimethylarginine. Quantitative binding characterization established distinct specificity profiles: TDRD3 selectively binds aDMA; SMN is promiscuous and prefers sDMA; SPF30 is the weakest binder, recognizing only GAR motif sequences.","method":"Crystal structure determination, quantitative binding assays (fluorescence polarization, ITC), peptide library screening","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with quantitative in vitro binding assays; replicated by independent NMR structural study","pmids":["22363433"],"is_preprint":false},{"year":2012,"finding":"NMR solution structure of the TDRD3 Tudor domain bound to asymmetrically dimethylated RNA Polymerase II CTD reveals that a unique aromatic cavity with tyrosine at position 566 acts as a selectivity filter for aDMA recognition, distinguishing it from other Tudor domain-containing proteins that bind symmetric dimethylarginine. Mutational analysis confirmed key residues required for aDMA selectivity.","method":"NMR structure determination, mutagenesis, binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with mutational validation; independently consistent with crystal structure data from PMID:22363433","pmids":["23066109"],"is_preprint":false},{"year":2017,"finding":"USP9X is identified as a TDRD3-interacting protein; the interaction is mediated through the Tudor domain of TDRD3 and arginine methylation of USP9X. USP9X stabilizes TDRD3 protein by preventing its ubiquitination (knockdown of USP9X increases TDRD3 ubiquitination). TDRD3 is essential for USP9X localization to stress granules. TDRD3 also regulates MCL1 (a USP9X deubiquitination target), suggesting TDRD3 modulates USP9X deubiquitinase activity.","method":"GST pull-down, co-immunoprecipitation, USP9X knockdown with ubiquitination assay, immunofluorescence in Tdrd3-null MEFs","journal":"Cell discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and pull-down plus null cell line experiments, single lab","pmids":["28101374"],"is_preprint":false},{"year":2017,"finding":"Crystal structures of TOP3B catalytic domain, TDRD3 DUF1767-OB-fold domains, and their complex reveal that the OB-fold domain of TDRD3 binds the toroidal-shaped catalytic domain of TOP3B. The TDRD3 OB-fold insertion loop and core region both contribute to the interaction; hydrophobic core surface and insertion loop termini are essential. Key structural elements Arg96, Val109, Phe139, and the short insertion loop of TDRD3 confer specificity for TOP3β over the non-cognate TOP3α.","method":"Crystal structure determination (3.44 Å complex, 1.62 Å TDRD3 domain, 3.6 Å complex), pull-down binding assays with mutagenesis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures at multiple resolutions with pull-down mutagenesis validation","pmids":["28176834"],"is_preprint":false},{"year":2021,"finding":"TDRD3 directly interacts with the DExH-box helicase DHX9 via its Tudor domain, recruiting DHX9 to target gene promoters. DHX9 resolves R-loops at promoters in a helicase-activity-dependent manner. Additionally, TDRD3 stimulates DHX9 helicase activity via its OB-fold domain, which likely binds single-stranded DNA in R-loop structures. Together DHX9 and TOP3B suppress promoter-associated R-loops downstream of TDRD3 recruitment.","method":"Co-immunoprecipitation, ChIP, R-loop detection assays (DRIP), helicase activity assays, domain deletion analysis, DHX9 helicase-dead mutant","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct interaction demonstrated by Co-IP, functional rescue by helicase-dead mutant, multiple orthogonal assays","pmids":["34329467"],"is_preprint":false},{"year":2022,"finding":"TDRD3 localizes to stress granules partly based on the methylation status of G3BP1. TDRD3 overexpression forms granules containing translation components independently of G3BP. TDRD3 is cleaved by enteroviral 2A proteinase. TDRD3 knockdown alters transcriptional regulation of numerous IFN effectors (including recruitment of IRF3, IRF7, TBK1, STING to SGs), establishing TDRD3 as an antiviral restriction factor.","method":"Immunofluorescence, knockdown/knockout experiments, viral infection assays, transcriptional analysis, co-localization studies","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods in single lab, KO/KD with defined phenotypic readouts","pmids":["35085371"],"is_preprint":false},{"year":2023,"finding":"TDRD3 stabilizes TOP3B by recruiting the deubiquitinase USP9X to form a TDRD3-USP9X complex; inactivation of USP9X destabilizes TOP3B. MIB1 E3 ligase independently mediates TOP3B ubiquitylation and proteasomal degradation by directly interacting with TOP3B independently of TDRD3. The TDRD3-USP9X complex works downstream of MIB1. Loss of TDRD3 increases TOP3B cleavage complexes (TOP3Bccs) in DNA and RNA, induces R-loops, γH2AX, and growth defects. TDRD3 biochemically increases the turnover rate of TOP3B.","method":"Co-immunoprecipitation, ubiquitylation assays, TOP3Bcc measurement, γH2AX assays, knockdown/double-knockdown epistasis, DRIP-seq for R-loops, growth assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal biochemical and genetic epistasis approaches in a single focused study","pmids":["37980342"],"is_preprint":false},{"year":2024,"finding":"In Tdrd3-null mice, the TOP3B-TDRD3 complex is essential for normal brain function; loss of TDRD3 causes defects in cognitive behaviors, synaptic plasticity, adult neurogenesis, and neuronal activity-dependent transcription. Multiple neurodevelopmentally critical genes show reduced levels in mature but not nascent transcripts in Tdrd3-null mice, indicating a post-transcriptional (not transcriptional) regulatory role of the complex.","method":"Tdrd3-null mouse generation, behavioral assays, electrophysiology (synaptic plasticity), neurogenesis assays, RNA-seq comparing nascent vs. mature transcripts","journal":"Progress in neurobiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — null mouse model with multiple phenotypic readouts, single lab","pmids":["38216113"],"is_preprint":false},{"year":2024,"finding":"PRMT1 methylates stress granule constituent RNA-binding proteins on their RGG motifs, and TDRD3 as an aDMA reader enhances RNA binding to recruit additional RNAs and RBPs, thereby lowering the percolation threshold and promoting stress granule assembly.","method":"Methylation assays, stress granule formation assays, RNA-binding assays, deletion/mutation analysis","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional SG assembly assays with mechanistic dissection, single lab","pmids":["39097054"],"is_preprint":false},{"year":2024,"finding":"TDRD3 contains UBA and LC3-interacting region (LIR) motifs similar to selective autophagy receptor p62/SQSTM1. KO of TDRD3 reduces starvation-induced autophagy; reintroduction restores it dose-dependently. TDRD3 levels decrease during autophagy (consistent with receptor turnover). The LIR3 motif of TDRD3 mediates interaction with LC3B (shown by Co-IP and colocalization). TDRD3 LIR motifs also regulate SG condensation, SG decay rate upon stress release, and SG formation kinetics.","method":"TDRD3 KO/rescue experiments, autophagy flux assays, co-immunoprecipitation (LIR3-LC3B), immunofluorescence/super-resolution microscopy, deletion mutant analysis","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, not yet peer-reviewed; mechanistic claims based on single Co-IP and deletion mutants","pmids":["39345463"],"is_preprint":true},{"year":2018,"finding":"NMR fragment screening identified 14 small molecule hits against the TDRD3 Tudor domain aromatic cage. Crystal structure of the TDRD3 Tudor domain with hit 1 reveals it protrudes into the aromatic cage, inducing a distinct binding mode with aromatic residues tilting to accommodate π-π stacking and N596 side chain rotating 3.1 Å to form a hydrogen bond. This structural plasticity distinguishes TDRD3 from SMN, 53BP1, and SND1 Tudor domains.","method":"NMR fragment-based screening, competitive fluorescence polarization, ITC, crystal structure determination (PDB: 5YJ8)","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with cross-validated binding assays (FP and ITC), single lab","pmids":["29645362"],"is_preprint":false},{"year":2026,"finding":"In Treg-specific Tdrd3-knockout mice, TDRD3 is required for iTreg (but not thymic Treg) differentiation. Mechanistically, TDRD3 is recruited by transcription factor FOXO1 (presumably in a methylation-dependent manner) to activate Klf2 expression, which is essential for Treg differentiation. Enforced Klf2 expression in Tdrd3-deficient CD4+ T cells rescues both iTreg development and suppressive function.","method":"Treg-specific conditional Tdrd3 knockout mouse, adoptive transfer colitis model, Klf2 rescue by enforced expression, ChIP/transcriptional analysis","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis (Klf2 rescue), conditional KO with defined cellular phenotype, single lab","pmids":["41576154"],"is_preprint":false}],"current_model":"TDRD3 is a multifunctional scaffold protein whose Tudor domain selectively reads asymmetric dimethylarginine (aDMA) marks on histones and RNA Polymerase II CTD to recruit transcriptional coactivators and resolve R-loops at gene promoters by recruiting TOP3B (via its OB-fold) and DHX9 (via the Tudor domain); in the cytoplasm, it co-sediments with FMRP on polyribosomes, assembles into stress granules through Tudor-domain-dependent recognition of methylated RBPs (promoted by PRMT1-mediated methylation), acts as an antiviral restriction factor by facilitating IFN signaling, and stabilizes TOP3B by recruiting the deubiquitinase USP9X while preventing accumulation of toxic TOP3B cleavage complexes."},"narrative":{"mechanistic_narrative":"TDRD3 is a multifunctional scaffold protein whose Tudor domain reads asymmetric dimethylarginine (aDMA) marks to couple methylarginine signaling to transcriptional regulation, genome stability, and cytoplasmic stress responses [PMID:21172665, PMID:22363433]. Its Tudor domain selectively recognizes aDMA marks on histones (H3R17me2a, H4R3me2a) and the RNA Polymerase II CTD, a specificity conferred by a unique aromatic cavity that distinguishes it from sDMA-binding Tudor proteins, and it acts as a transcriptional coactivator recruited to gene start sites in a CARM1-dependent manner [PMID:21172665, PMID:23066109]. At promoters, TDRD3 nucleates an R-loop-resolving complex, recruiting the helicase DHX9 through its Tudor domain and the topoisomerase TOP3B through its OB-fold; TDRD3 stimulates DHX9 helicase activity and the two enzymes together suppress promoter-associated R-loops [PMID:28176834, PMID:34329467]. TDRD3 also governs TOP3B abundance by recruiting the deubiquitinase USP9X to form a TDRD3-USP9X complex that stabilizes TOP3B and limits accumulation of toxic TOP3B cleavage complexes; loss of TDRD3 induces R-loops, γH2AX, and growth defects [PMID:28101374, PMID:37980342]. In the cytoplasm, TDRD3 co-sediments with FMRP on polyribosomes and assembles into stress granules through Tudor-domain-dependent, methylation-sensitive recognition of RGG-methylated RNA-binding proteins, a process promoted by PRMT1 [PMID:18632687, PMID:18664458, PMID:39097054]. The TOP3B-TDRD3 complex post-transcriptionally supports neurodevelopmental gene expression and is required for normal cognition and synaptic plasticity in mice [PMID:38216113], and TDRD3 is additionally required for FOXO1-driven Klf2 activation during inducible Treg differentiation [PMID:41576154] and functions as an antiviral restriction factor facilitating interferon signaling [PMID:35085371].","teleology":[{"year":2008,"claim":"Established that TDRD3 is a cytoplasmic RNA-regulatory protein, linking it physically to the FMRP family and to stress granule biology before its nuclear role was known.","evidence":"Polyribosome sedimentation, GST pull-down, and Tudor-domain mutagenesis showing co-sedimentation with FMRP, direct binding to FMRP/FXR1/FXR2, and Tudor-dependent stress granule recruitment","pmids":["18632687","18664458"],"confidence":"High","gaps":["Did not define the methylated ligand recognized by the Tudor domain in stress granules","Functional consequence of FMRP-TDRD3 association on translation not resolved","OB-fold and UBA domain functions only described biochemically"]},{"year":2010,"claim":"Defined TDRD3 as a transcriptional coactivator that reads aDMA histone marks, establishing its nuclear chromatin function and Tudor-domain dependence.","evidence":"Protein domain microarray, ChIP-seq, Tudor mutagenesis, and estrogen-responsive element reporter assays in cells","pmids":["21172665"],"confidence":"High","gaps":["Structural basis of aDMA selectivity not yet resolved","Coactivator partners recruited downstream of TDRD3 not identified"]},{"year":2012,"claim":"Resolved the structural basis for TDRD3's aDMA preference, explaining how it distinguishes asymmetric from symmetric dimethylarginine and binds the RNA Pol II CTD.","evidence":"Crystal structures with quantitative binding (FP, ITC) and an NMR structure of the Tudor domain bound to aDMA Pol II CTD, with Y566 identified as a selectivity filter","pmids":["22363433","23066109"],"confidence":"High","gaps":["In vivo consequences of CTD reading on transcription elongation not addressed","Did not connect reader activity to a specific downstream effector complex"]},{"year":2017,"claim":"Connected TDRD3 to two distinct partners that explain its dual roles in protein stability and genome maintenance: USP9X-mediated stabilization and OB-fold-mediated TOP3B binding.","evidence":"GST pull-down, reciprocal Co-IP, ubiquitination assays in USP9X-knockdown and Tdrd3-null MEFs, plus multi-resolution crystal structures of the TDRD3 OB-fold-TOP3B complex with mutagenesis","pmids":["28101374","28176834"],"confidence":"Medium","gaps":["Functional integration of USP9X stabilization with TOP3B recruitment not yet unified","TOP3B catalytic output downstream of TDRD3 binding not measured in these studies"]},{"year":2021,"claim":"Showed that TDRD3 acts as a promoter scaffold coordinating R-loop resolution by recruiting and stimulating DHX9 alongside TOP3B.","evidence":"Co-IP, ChIP, DRIP R-loop detection, helicase activity assays, and a DHX9 helicase-dead rescue with TDRD3 domain deletions","pmids":["34329467"],"confidence":"High","gaps":["Order of recruitment of DHX9 versus TOP3B at promoters not defined","Genome-wide rules selecting which promoters require TDRD3 unknown"]},{"year":2022,"claim":"Extended TDRD3 stress-granule biology to innate immunity, identifying it as an antiviral restriction factor that shapes interferon-effector transcription and is targeted by viral proteases.","evidence":"Immunofluorescence, knockdown/knockout, viral infection assays, and transcriptional profiling showing IRF3/IRF7/TBK1/STING recruitment to stress granules","pmids":["35085371"],"confidence":"Medium","gaps":["Direct molecular link between TDRD3 granule scaffolding and IFN signaling not established","Whether antiviral function requires Tudor-domain methyl reading not tested"]},{"year":2023,"claim":"Defined the ubiquitin-regulatory circuit controlling TOP3B levels and the pathological consequences of TDRD3 loss, placing the TDRD3-USP9X complex downstream of the MIB1 E3 ligase.","evidence":"Co-IP, ubiquitylation assays, TOP3Bcc measurement, γH2AX assays, double-knockdown epistasis, and DRIP-seq","pmids":["37980342"],"confidence":"High","gaps":["What activates MIB1-mediated TOP3B degradation is unknown","Whether TOP3Bcc accumulation drives the genome-instability phenotype causally not fully separated"]},{"year":2024,"claim":"Established physiological roles for the TOP3B-TDRD3 complex in brain function and for PRMT1-driven methylation in promoting stress granule assembly.","evidence":"Tdrd3-null mice with behavioral, electrophysiological, neurogenesis, and nascent-versus-mature RNA-seq assays; plus methylation and stress-granule assembly assays dissecting PRMT1-aDMA-reader logic","pmids":["38216113","39097054"],"confidence":"Medium","gaps":["Mechanism by which mature but not nascent transcripts are reduced not pinpointed","Which RBP substrates of PRMT1 are read by TDRD3 in vivo not enumerated"]},{"year":2024,"claim":"Implicated TDRD3 in selective autophagy via p62-like UBA and LIR motifs that also tune stress-granule dynamics.","evidence":"TDRD3 KO/rescue autophagy flux assays, LIR3-LC3B Co-IP, super-resolution microscopy, and deletion mutants (preprint)","pmids":["39345463"],"confidence":"Low","gaps":["Preprint, not yet peer-reviewed; LC3B interaction based on single Co-IP and deletion mutants","Cargo selected by TDRD3 as an autophagy receptor not identified"]},{"year":2026,"claim":"Identified a transcription-factor-directed role for TDRD3 in immune cell differentiation, recruited by FOXO1 to activate Klf2 during iTreg development.","evidence":"Treg-specific conditional Tdrd3-knockout mice, adoptive transfer colitis model, ChIP/transcriptional analysis, and Klf2 enforced-expression rescue","pmids":["41576154"],"confidence":"Medium","gaps":["Methylation dependence of FOXO1-TDRD3 recruitment assumed but not directly shown","Whether this uses the same aDMA-reading mechanism as histone/CTD reading untested"]},{"year":null,"claim":"How TDRD3's distinct activities — nuclear aDMA reading/R-loop resolution, TOP3B stabilization, cytoplasmic stress-granule and autophagy functions, and antiviral/immune roles — are partitioned and regulated within a cell remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model of how methylation signals route TDRD3 between nuclear and cytoplasmic functions","Signals controlling switching between coactivator, R-loop, and granule roles unknown","No human disease link established by direct genetic evidence in the timeline"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,14]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,3,4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[6,7,9]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,11]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,7,9]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,7]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,2,11]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,14]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[7,9]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5,9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[8,14]}],"complexes":["TDRD3-TOP3B complex","TDRD3-USP9X complex","stress granule"],"partners":["TOP3B","DHX9","USP9X","FMRP","FXR1","FXR2","G3BP1","DDX3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H7E2","full_name":"Tudor domain-containing protein 3","aliases":[],"length_aa":651,"mass_kda":73.2,"function":"Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins (PubMed:15955813). Plays a role in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci (PubMed:21172665). In cytoplasm, acts as an antiviral factor that participates in the assembly of stress granules together with G3BP1 (PubMed:35085371)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H7E2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TDRD3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"NPM1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TDRD3","total_profiled":1310},"omim":[{"mim_id":"614392","title":"TUDOR DOMAIN-CONTAINING PROTEIN 3; TDRD3","url":"https://www.omim.org/entry/614392"},{"mim_id":"603582","title":"TOPOISOMERASE, DNA, III, BETA; TOP3B","url":"https://www.omim.org/entry/603582"},{"mim_id":"309550","title":"FRAGILE X MESSENGER RIBONUCLEOPROTEIN 1; FMR1","url":"https://www.omim.org/entry/309550"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Golgi apparatus","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TDRD3"},"hgnc":{"alias_symbol":["FLJ21007"],"prev_symbol":[]},"alphafold":{"accession":"Q9H7E2","domains":[{"cath_id":"2.40.50.770","chopping":"2-76","consensus_level":"high","plddt":92.8977,"start":2,"end":76},{"cath_id":"-","chopping":"195-225","consensus_level":"high","plddt":92.5855,"start":195,"end":225},{"cath_id":"2.30.30.140","chopping":"559-606","consensus_level":"high","plddt":94.1923,"start":559,"end":606}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7E2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7E2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H7E2-F1-predicted_aligned_error_v6.png","plddt_mean":58.66},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TDRD3","jax_strain_url":"https://www.jax.org/strain/search?query=TDRD3"},"sequence":{"accession":"Q9H7E2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H7E2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H7E2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H7E2"}},"corpus_meta":[{"pmid":"21172665","id":"PMC_21172665","title":"TDRD3 is an effector molecule for arginine-methylated histone marks.","date":"2010","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/21172665","citation_count":182,"is_preprint":false},{"pmid":"18632687","id":"PMC_18632687","title":"TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules.","date":"2008","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18632687","citation_count":99,"is_preprint":false},{"pmid":"22363433","id":"PMC_22363433","title":"Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22363433","citation_count":72,"is_preprint":false},{"pmid":"18664458","id":"PMC_18664458","title":"Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP.","date":"2008","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18664458","citation_count":68,"is_preprint":false},{"pmid":"34329467","id":"PMC_34329467","title":"TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34329467","citation_count":52,"is_preprint":false},{"pmid":"23066109","id":"PMC_23066109","title":"Recognition of asymmetrically dimethylated arginine by TDRD3.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/23066109","citation_count":36,"is_preprint":false},{"pmid":"28101374","id":"PMC_28101374","title":"Arginine methylation of USP9X promotes its interaction with TDRD3 and its anti-apoptotic activities in breast cancer cells.","date":"2017","source":"Cell discovery","url":"https://pubmed.ncbi.nlm.nih.gov/28101374","citation_count":31,"is_preprint":false},{"pmid":"28176834","id":"PMC_28176834","title":"Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28176834","citation_count":29,"is_preprint":false},{"pmid":"35085371","id":"PMC_35085371","title":"TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/35085371","citation_count":26,"is_preprint":false},{"pmid":"29645362","id":"PMC_29645362","title":"Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.","date":"2018","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/29645362","citation_count":19,"is_preprint":false},{"pmid":"37980342","id":"PMC_37980342","title":"The TDRD3-USP9X complex and MIB1 regulate TOP3B homeostasis and prevent deleterious TOP3B cleavage complexes.","date":"2023","source":"Nature 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square","url":"https://pubmed.ncbi.nlm.nih.gov/36909584","citation_count":4,"is_preprint":false},{"pmid":"37499935","id":"PMC_37499935","title":"Crystal structure of Tudor domain of TDRD3 in complex with a small molecule antagonist.","date":"2023","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/37499935","citation_count":4,"is_preprint":false},{"pmid":"37417852","id":"PMC_37417852","title":"Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study.","date":"2023","source":"JBRA assisted reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/37417852","citation_count":2,"is_preprint":false},{"pmid":"39345463","id":"PMC_39345463","title":"TDRD3 functions as a selective autophagy receptor with dual roles in autophagy and modulation of stress granule stability.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39345463","citation_count":2,"is_preprint":false},{"pmid":"41576154","id":"PMC_41576154","title":"TDRD3, a Tudor domain-containing protein, regulates Klf2-dependent Treg differentiation and function to modulate immune tolerance.","date":"2026","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/41576154","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10755,"output_tokens":4233,"usd":0.04788,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12212,"output_tokens":4469,"usd":0.086392,"stage2_stop_reason":"end_turn"},"total_usd":0.134272,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"TDRD3 Tudor domain functions as a 'reader' of asymmetric dimethylarginine (aDMA) marks on histones (H3R17me2a deposited by CARM1 and H4R3me2a deposited by PRMT1), identified by protein domain microarray. TDRD3 itself acts as a transcriptional coactivator, and this coactivator activity requires an intact Tudor domain. TDRD3 is recruited to an estrogen-responsive element in a CARM1-dependent manner, and ChIP-seq shows it localizes predominantly to transcriptional start sites.\",\n      \"method\": \"Protein domain microarray, co-immunoprecipitation, ChIP-seq, Tudor domain mutagenesis, estrogen-responsive element reporter assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (microarray, ChIP-seq, mutagenesis, reporter assay) in a focused study; widely replicated by subsequent structural work\",\n      \"pmids\": [\"21172665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TDRD3 co-sediments with FMRP on actively translating polyribosomes and accumulates in cytoplasmic stress granules (SGs) in response to cellular stress. The Tudor domain is both required and sufficient for SG recruitment, and the methyl-binding surface of the Tudor domain is important for this process. Pull-down experiments identified five novel TDRD3-interacting partners, including SERPINE1 mRNA-binding protein 1 and DDX3 (DEAD/H box-3), which are also novel SG constituents.\",\n      \"method\": \"Polyribosome sedimentation, immunofluorescence, stress induction assays, Tudor domain deletion/mutation analysis, GST pull-down\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (sedimentation, localization, mutagenesis, pulldown) in a focused study; replicated in subsequent papers\",\n      \"pmids\": [\"18632687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TDRD3 harbors an OB-fold domain and a ubiquitin-associated (UBA) domain capable of binding tetra-ubiquitin. TDRD3 directly interacts with FMRP and its autosomal homologs FXR1 and FXR2 via biochemical experiments. Overexpression of TDRD3 in cells induces SG formation and co-localization with endogenous FMRP. The disease-associated FMRP missense mutation I304N severely impairs interaction with TDRD3.\",\n      \"method\": \"Biochemical pull-down/co-immunoprecipitation, domain characterization, overexpression/immunofluorescence, UBA-tetra-ubiquitin binding assay\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction experiments, multiple domains characterized, single lab\",\n      \"pmids\": [\"18664458\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structures of the TDRD3 Tudor domain in complex with small molecules reveal that TDRD3 preferentially recognizes asymmetric dimethylarginine (aDMA) marks, in contrast to SMN which preferentially binds symmetric dimethylarginine. Quantitative binding characterization established distinct specificity profiles: TDRD3 selectively binds aDMA; SMN is promiscuous and prefers sDMA; SPF30 is the weakest binder, recognizing only GAR motif sequences.\",\n      \"method\": \"Crystal structure determination, quantitative binding assays (fluorescence polarization, ITC), peptide library screening\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with quantitative in vitro binding assays; replicated by independent NMR structural study\",\n      \"pmids\": [\"22363433\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"NMR solution structure of the TDRD3 Tudor domain bound to asymmetrically dimethylated RNA Polymerase II CTD reveals that a unique aromatic cavity with tyrosine at position 566 acts as a selectivity filter for aDMA recognition, distinguishing it from other Tudor domain-containing proteins that bind symmetric dimethylarginine. Mutational analysis confirmed key residues required for aDMA selectivity.\",\n      \"method\": \"NMR structure determination, mutagenesis, binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with mutational validation; independently consistent with crystal structure data from PMID:22363433\",\n      \"pmids\": [\"23066109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"USP9X is identified as a TDRD3-interacting protein; the interaction is mediated through the Tudor domain of TDRD3 and arginine methylation of USP9X. USP9X stabilizes TDRD3 protein by preventing its ubiquitination (knockdown of USP9X increases TDRD3 ubiquitination). TDRD3 is essential for USP9X localization to stress granules. TDRD3 also regulates MCL1 (a USP9X deubiquitination target), suggesting TDRD3 modulates USP9X deubiquitinase activity.\",\n      \"method\": \"GST pull-down, co-immunoprecipitation, USP9X knockdown with ubiquitination assay, immunofluorescence in Tdrd3-null MEFs\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and pull-down plus null cell line experiments, single lab\",\n      \"pmids\": [\"28101374\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structures of TOP3B catalytic domain, TDRD3 DUF1767-OB-fold domains, and their complex reveal that the OB-fold domain of TDRD3 binds the toroidal-shaped catalytic domain of TOP3B. The TDRD3 OB-fold insertion loop and core region both contribute to the interaction; hydrophobic core surface and insertion loop termini are essential. Key structural elements Arg96, Val109, Phe139, and the short insertion loop of TDRD3 confer specificity for TOP3β over the non-cognate TOP3α.\",\n      \"method\": \"Crystal structure determination (3.44 Å complex, 1.62 Å TDRD3 domain, 3.6 Å complex), pull-down binding assays with mutagenesis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures at multiple resolutions with pull-down mutagenesis validation\",\n      \"pmids\": [\"28176834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TDRD3 directly interacts with the DExH-box helicase DHX9 via its Tudor domain, recruiting DHX9 to target gene promoters. DHX9 resolves R-loops at promoters in a helicase-activity-dependent manner. Additionally, TDRD3 stimulates DHX9 helicase activity via its OB-fold domain, which likely binds single-stranded DNA in R-loop structures. Together DHX9 and TOP3B suppress promoter-associated R-loops downstream of TDRD3 recruitment.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, R-loop detection assays (DRIP), helicase activity assays, domain deletion analysis, DHX9 helicase-dead mutant\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct interaction demonstrated by Co-IP, functional rescue by helicase-dead mutant, multiple orthogonal assays\",\n      \"pmids\": [\"34329467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TDRD3 localizes to stress granules partly based on the methylation status of G3BP1. TDRD3 overexpression forms granules containing translation components independently of G3BP. TDRD3 is cleaved by enteroviral 2A proteinase. TDRD3 knockdown alters transcriptional regulation of numerous IFN effectors (including recruitment of IRF3, IRF7, TBK1, STING to SGs), establishing TDRD3 as an antiviral restriction factor.\",\n      \"method\": \"Immunofluorescence, knockdown/knockout experiments, viral infection assays, transcriptional analysis, co-localization studies\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods in single lab, KO/KD with defined phenotypic readouts\",\n      \"pmids\": [\"35085371\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TDRD3 stabilizes TOP3B by recruiting the deubiquitinase USP9X to form a TDRD3-USP9X complex; inactivation of USP9X destabilizes TOP3B. MIB1 E3 ligase independently mediates TOP3B ubiquitylation and proteasomal degradation by directly interacting with TOP3B independently of TDRD3. The TDRD3-USP9X complex works downstream of MIB1. Loss of TDRD3 increases TOP3B cleavage complexes (TOP3Bccs) in DNA and RNA, induces R-loops, γH2AX, and growth defects. TDRD3 biochemically increases the turnover rate of TOP3B.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitylation assays, TOP3Bcc measurement, γH2AX assays, knockdown/double-knockdown epistasis, DRIP-seq for R-loops, growth assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal biochemical and genetic epistasis approaches in a single focused study\",\n      \"pmids\": [\"37980342\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Tdrd3-null mice, the TOP3B-TDRD3 complex is essential for normal brain function; loss of TDRD3 causes defects in cognitive behaviors, synaptic plasticity, adult neurogenesis, and neuronal activity-dependent transcription. Multiple neurodevelopmentally critical genes show reduced levels in mature but not nascent transcripts in Tdrd3-null mice, indicating a post-transcriptional (not transcriptional) regulatory role of the complex.\",\n      \"method\": \"Tdrd3-null mouse generation, behavioral assays, electrophysiology (synaptic plasticity), neurogenesis assays, RNA-seq comparing nascent vs. mature transcripts\",\n      \"journal\": \"Progress in neurobiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — null mouse model with multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"38216113\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PRMT1 methylates stress granule constituent RNA-binding proteins on their RGG motifs, and TDRD3 as an aDMA reader enhances RNA binding to recruit additional RNAs and RBPs, thereby lowering the percolation threshold and promoting stress granule assembly.\",\n      \"method\": \"Methylation assays, stress granule formation assays, RNA-binding assays, deletion/mutation analysis\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional SG assembly assays with mechanistic dissection, single lab\",\n      \"pmids\": [\"39097054\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TDRD3 contains UBA and LC3-interacting region (LIR) motifs similar to selective autophagy receptor p62/SQSTM1. KO of TDRD3 reduces starvation-induced autophagy; reintroduction restores it dose-dependently. TDRD3 levels decrease during autophagy (consistent with receptor turnover). The LIR3 motif of TDRD3 mediates interaction with LC3B (shown by Co-IP and colocalization). TDRD3 LIR motifs also regulate SG condensation, SG decay rate upon stress release, and SG formation kinetics.\",\n      \"method\": \"TDRD3 KO/rescue experiments, autophagy flux assays, co-immunoprecipitation (LIR3-LC3B), immunofluorescence/super-resolution microscopy, deletion mutant analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, not yet peer-reviewed; mechanistic claims based on single Co-IP and deletion mutants\",\n      \"pmids\": [\"39345463\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NMR fragment screening identified 14 small molecule hits against the TDRD3 Tudor domain aromatic cage. Crystal structure of the TDRD3 Tudor domain with hit 1 reveals it protrudes into the aromatic cage, inducing a distinct binding mode with aromatic residues tilting to accommodate π-π stacking and N596 side chain rotating 3.1 Å to form a hydrogen bond. This structural plasticity distinguishes TDRD3 from SMN, 53BP1, and SND1 Tudor domains.\",\n      \"method\": \"NMR fragment-based screening, competitive fluorescence polarization, ITC, crystal structure determination (PDB: 5YJ8)\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with cross-validated binding assays (FP and ITC), single lab\",\n      \"pmids\": [\"29645362\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In Treg-specific Tdrd3-knockout mice, TDRD3 is required for iTreg (but not thymic Treg) differentiation. Mechanistically, TDRD3 is recruited by transcription factor FOXO1 (presumably in a methylation-dependent manner) to activate Klf2 expression, which is essential for Treg differentiation. Enforced Klf2 expression in Tdrd3-deficient CD4+ T cells rescues both iTreg development and suppressive function.\",\n      \"method\": \"Treg-specific conditional Tdrd3 knockout mouse, adoptive transfer colitis model, Klf2 rescue by enforced expression, ChIP/transcriptional analysis\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis (Klf2 rescue), conditional KO with defined cellular phenotype, single lab\",\n      \"pmids\": [\"41576154\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TDRD3 is a multifunctional scaffold protein whose Tudor domain selectively reads asymmetric dimethylarginine (aDMA) marks on histones and RNA Polymerase II CTD to recruit transcriptional coactivators and resolve R-loops at gene promoters by recruiting TOP3B (via its OB-fold) and DHX9 (via the Tudor domain); in the cytoplasm, it co-sediments with FMRP on polyribosomes, assembles into stress granules through Tudor-domain-dependent recognition of methylated RBPs (promoted by PRMT1-mediated methylation), acts as an antiviral restriction factor by facilitating IFN signaling, and stabilizes TOP3B by recruiting the deubiquitinase USP9X while preventing accumulation of toxic TOP3B cleavage complexes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TDRD3 is a multifunctional scaffold protein whose Tudor domain reads asymmetric dimethylarginine (aDMA) marks to couple methylarginine signaling to transcriptional regulation, genome stability, and cytoplasmic stress responses [#0, #3]. Its Tudor domain selectively recognizes aDMA marks on histones (H3R17me2a, H4R3me2a) and the RNA Polymerase II CTD, a specificity conferred by a unique aromatic cavity that distinguishes it from sDMA-binding Tudor proteins, and it acts as a transcriptional coactivator recruited to gene start sites in a CARM1-dependent manner [#0, #4]. At promoters, TDRD3 nucleates an R-loop-resolving complex, recruiting the helicase DHX9 through its Tudor domain and the topoisomerase TOP3B through its OB-fold; TDRD3 stimulates DHX9 helicase activity and the two enzymes together suppress promoter-associated R-loops [#6, #7]. TDRD3 also governs TOP3B abundance by recruiting the deubiquitinase USP9X to form a TDRD3-USP9X complex that stabilizes TOP3B and limits accumulation of toxic TOP3B cleavage complexes; loss of TDRD3 induces R-loops, \\u03b3H2AX, and growth defects [#5, #9]. In the cytoplasm, TDRD3 co-sediments with FMRP on polyribosomes and assembles into stress granules through Tudor-domain-dependent, methylation-sensitive recognition of RGG-methylated RNA-binding proteins, a process promoted by PRMT1 [#1, #2, #11]. The TOP3B-TDRD3 complex post-transcriptionally supports neurodevelopmental gene expression and is required for normal cognition and synaptic plasticity in mice [#10], and TDRD3 is additionally required for FOXO1-driven Klf2 activation during inducible Treg differentiation [#14] and functions as an antiviral restriction factor facilitating interferon signaling [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established that TDRD3 is a cytoplasmic RNA-regulatory protein, linking it physically to the FMRP family and to stress granule biology before its nuclear role was known.\",\n      \"evidence\": \"Polyribosome sedimentation, GST pull-down, and Tudor-domain mutagenesis showing co-sedimentation with FMRP, direct binding to FMRP/FXR1/FXR2, and Tudor-dependent stress granule recruitment\",\n      \"pmids\": [\n        \"18632687\",\n        \"18664458\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not define the methylated ligand recognized by the Tudor domain in stress granules\",\n        \"Functional consequence of FMRP-TDRD3 association on translation not resolved\",\n        \"OB-fold and UBA domain functions only described biochemically\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined TDRD3 as a transcriptional coactivator that reads aDMA histone marks, establishing its nuclear chromatin function and Tudor-domain dependence.\",\n      \"evidence\": \"Protein domain microarray, ChIP-seq, Tudor mutagenesis, and estrogen-responsive element reporter assays in cells\",\n      \"pmids\": [\n        \"21172665\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of aDMA selectivity not yet resolved\",\n        \"Coactivator partners recruited downstream of TDRD3 not identified\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved the structural basis for TDRD3's aDMA preference, explaining how it distinguishes asymmetric from symmetric dimethylarginine and binds the RNA Pol II CTD.\",\n      \"evidence\": \"Crystal structures with quantitative binding (FP, ITC) and an NMR structure of the Tudor domain bound to aDMA Pol II CTD, with Y566 identified as a selectivity filter\",\n      \"pmids\": [\n        \"22363433\",\n        \"23066109\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"In vivo consequences of CTD reading on transcription elongation not addressed\",\n        \"Did not connect reader activity to a specific downstream effector complex\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected TDRD3 to two distinct partners that explain its dual roles in protein stability and genome maintenance: USP9X-mediated stabilization and OB-fold-mediated TOP3B binding.\",\n      \"evidence\": \"GST pull-down, reciprocal Co-IP, ubiquitination assays in USP9X-knockdown and Tdrd3-null MEFs, plus multi-resolution crystal structures of the TDRD3 OB-fold-TOP3B complex with mutagenesis\",\n      \"pmids\": [\n        \"28101374\",\n        \"28176834\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional integration of USP9X stabilization with TOP3B recruitment not yet unified\",\n        \"TOP3B catalytic output downstream of TDRD3 binding not measured in these studies\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed that TDRD3 acts as a promoter scaffold coordinating R-loop resolution by recruiting and stimulating DHX9 alongside TOP3B.\",\n      \"evidence\": \"Co-IP, ChIP, DRIP R-loop detection, helicase activity assays, and a DHX9 helicase-dead rescue with TDRD3 domain deletions\",\n      \"pmids\": [\n        \"34329467\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Order of recruitment of DHX9 versus TOP3B at promoters not defined\",\n        \"Genome-wide rules selecting which promoters require TDRD3 unknown\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended TDRD3 stress-granule biology to innate immunity, identifying it as an antiviral restriction factor that shapes interferon-effector transcription and is targeted by viral proteases.\",\n      \"evidence\": \"Immunofluorescence, knockdown/knockout, viral infection assays, and transcriptional profiling showing IRF3/IRF7/TBK1/STING recruitment to stress granules\",\n      \"pmids\": [\n        \"35085371\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct molecular link between TDRD3 granule scaffolding and IFN signaling not established\",\n        \"Whether antiviral function requires Tudor-domain methyl reading not tested\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the ubiquitin-regulatory circuit controlling TOP3B levels and the pathological consequences of TDRD3 loss, placing the TDRD3-USP9X complex downstream of the MIB1 E3 ligase.\",\n      \"evidence\": \"Co-IP, ubiquitylation assays, TOP3Bcc measurement, \\u03b3H2AX assays, double-knockdown epistasis, and DRIP-seq\",\n      \"pmids\": [\n        \"37980342\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"What activates MIB1-mediated TOP3B degradation is unknown\",\n        \"Whether TOP3Bcc accumulation drives the genome-instability phenotype causally not fully separated\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established physiological roles for the TOP3B-TDRD3 complex in brain function and for PRMT1-driven methylation in promoting stress granule assembly.\",\n      \"evidence\": \"Tdrd3-null mice with behavioral, electrophysiological, neurogenesis, and nascent-versus-mature RNA-seq assays; plus methylation and stress-granule assembly assays dissecting PRMT1-aDMA-reader logic\",\n      \"pmids\": [\n        \"38216113\",\n        \"39097054\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which mature but not nascent transcripts are reduced not pinpointed\",\n        \"Which RBP substrates of PRMT1 are read by TDRD3 in vivo not enumerated\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated TDRD3 in selective autophagy via p62-like UBA and LIR motifs that also tune stress-granule dynamics.\",\n      \"evidence\": \"TDRD3 KO/rescue autophagy flux assays, LIR3-LC3B Co-IP, super-resolution microscopy, and deletion mutants (preprint)\",\n      \"pmids\": [\n        \"39345463\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Preprint, not yet peer-reviewed; LC3B interaction based on single Co-IP and deletion mutants\",\n        \"Cargo selected by TDRD3 as an autophagy receptor not identified\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified a transcription-factor-directed role for TDRD3 in immune cell differentiation, recruited by FOXO1 to activate Klf2 during iTreg development.\",\n      \"evidence\": \"Treg-specific conditional Tdrd3-knockout mice, adoptive transfer colitis model, ChIP/transcriptional analysis, and Klf2 enforced-expression rescue\",\n      \"pmids\": [\n        \"41576154\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Methylation dependence of FOXO1-TDRD3 recruitment assumed but not directly shown\",\n        \"Whether this uses the same aDMA-reading mechanism as histone/CTD reading untested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TDRD3's distinct activities — nuclear aDMA reading/R-loop resolution, TOP3B stabilization, cytoplasmic stress-granule and autophagy functions, and antiviral/immune roles — are partitioned and regulated within a cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No unified model of how methylation signals route TDRD3 between nuclear and cytoplasmic functions\",\n        \"Signals controlling switching between coactivator, R-loop, and granule roles unknown\",\n        \"No human disease link established by direct genetic evidence in the timeline\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0140110\",\n        \"supporting_discovery_ids\": [\n          0,\n          14\n        ]\n      },\n      {\n        \"term_id\": \"GO:0042393\",\n        \"supporting_discovery_ids\": [\n          0,\n          3,\n          4\n        ]\n      },\n      {\n        \"term_id\": \"GO:0060090\",\n        \"supporting_discovery_ids\": [\n          6,\n          7,\n          9\n        ]\n      },\n      {\n        \"term_id\": \"GO:0003723\",\n        \"supporting_discovery_ids\": [\n          1,\n          11\n        ]\n      },\n      {\n        \"term_id\": \"GO:0098772\",\n        \"supporting_discovery_ids\": [\n          5,\n          7,\n          9\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005634\",\n        \"supporting_discovery_ids\": [\n          0,\n          7\n        ]\n      },\n      {\n        \"term_id\": \"GO:0005829\",\n        \"supporting_discovery_ids\": [\n          1,\n          2,\n          11\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"R-HSA-74160\",\n        \"supporting_discovery_ids\": [\n          0,\n          14\n        ]\n      },\n      {\n        \"term_id\": \"R-HSA-73894\",\n        \"supporting_discovery_ids\": [\n          7,\n          9\n        ]\n      },\n      {\n        \"term_id\": \"R-HSA-8953854\",\n        \"supporting_discovery_ids\": [\n          1,\n          11\n        ]\n      },\n      {\n        \"term_id\": \"R-HSA-392499\",\n        \"supporting_discovery_ids\": [\n          5,\n          9\n        ]\n      },\n      {\n        \"term_id\": \"R-HSA-168256\",\n        \"supporting_discovery_ids\": [\n          8,\n          14\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"TDRD3-TOP3B complex\",\n      \"TDRD3-USP9X complex\",\n      \"stress granule\"\n    ],\n    \"partners\": [\n      \"TOP3B\",\n      \"DHX9\",\n      \"USP9X\",\n      \"FMRP\",\n      \"FXR1\",\n      \"FXR2\",\n      \"G3BP1\",\n      \"DDX3\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}