{"gene":"TDRD1","run_date":"2026-04-28T21:42:58","timeline":{"discoveries":[{"year":2006,"finding":"TDRD1/MTR-1 localizes to nuage/germinal granules (specifically intermitochondrial cement) in mouse male germ cells, and its intracellular localization is downstream of MVH/DDX4 (mouse vasa homologue). Loss of TDRD1 abolishes intermitochondrial cement formation but chromatoid bodies persist, while MVH mutants show strong reduction of intermitochondrial cement.","method":"Targeted gene knockout in mice, subcellular localization by immunofluorescence, genetic epistasis with Mvh/Ddx4 mutants","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with loss-of-function mouse model and defined cellular phenotype, replicated across labs","pmids":["17038506"],"is_preprint":false},{"year":2006,"finding":"TDRD1/MTR-1, TDRD6, and TDRD7/TRAP co-localize to nuage and form a ribonucleoprotein complex together; their co-localization is disrupted in Mvh/Ddx4 mutants. A single Tudor domain is a structural unit sufficient for nuage localization, but truncated dominant-negative forms are detrimental to meiotic spermatocytes.","method":"Co-immunoprecipitation, in vivo overexpression of truncated forms, genetic epistasis with Mvh mutants, immunofluorescence localization","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP establishing complex, epistasis, and functional domain mapping with overexpression","pmids":["17141210"],"is_preprint":false},{"year":2009,"finding":"TDRD1/MTR-1 physically interacts with both MILI and MIWI (mouse Piwi family proteins) in adult mouse testes, forming a complex whose integrity is required for proper subcellular localization of MILI and TDRD1, and for chromatoid body formation in round spermatids.","method":"Co-immunoprecipitation from mouse testis lysates, immunofluorescence localization in Miwi-null spermatids","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with defined cellular phenotype (chromatoid body disruption) in knockout background","pmids":["19735482"],"is_preprint":false},{"year":2011,"finding":"Zebrafish Tdrd1 acts as a molecular scaffold binding both Piwi proteins (Ziwi and Zili) through specific tudor domain–symmetrically dimethylated arginine (sDMA) interactions, and its complexes contain piRNAs and longer transcripts (Tdrd1-associated transcripts, TATs) representing likely cleaved Piwi pathway targets and piRNA biogenesis intermediates. Tdrd1 is required for efficient Piwi-pathway activity and nuage formation.","method":"Co-immunoprecipitation, sequence specificity analysis of tudor domain–sDMA interactions, RNA sequencing of Tdrd1 complexes, loss-of-function in zebrafish","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, RNA biochemistry, loss-of-function) in zebrafish ortholog","pmids":["21743441"],"is_preprint":false},{"year":2012,"finding":"The four extended Tudor domains (TDs) of murine TDRD1 bind symmetrically dimethylated arginine (sDMA)-containing peptides from MILI with differential affinity: TD2 and TD3 show preference for consecutive MILI peptides, TD4 has lower affinity, and TD1 has very weak affinity due to a non-consensus aromatic cage that can be restored by a single point mutation. Crystal structure of TD3 bound to a methylated MILI peptide reveals an unexpected peptide orientation with contacts outside the aromatic cage.","method":"Binding affinity measurements (ITC/fluorescence), pull-down with endogenous Piwi proteins, crystal structure of TD3–sDMA peptide complex, solution NMR titration, small-angle X-ray scattering (SAXS) of tandem Tudor domains, active-site mutagenesis","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 — crystal structure + mutagenesis + in vitro binding assays + NMR, multiple orthogonal methods in single study","pmids":["22996915"],"is_preprint":false},{"year":2013,"finding":"ERG transcription factor directly activates TDRD1 transcription in prostate cancer by binding a functional ERG-binding site in the TDRD1 promoter; ERG shRNA knockdown reduces TDRD1 expression and decreases TDRD1 promoter activity.","method":"shRNA knockdown of ERG, promoter reporter assay, mutation analysis of ERG binding site in TDRD1 promoter","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 — promoter mutation analysis and shRNA with reporter assay, single lab","pmids":["23319146"],"is_preprint":false},{"year":2013,"finding":"ERG governs loss of DNA methylation at the TDRD1 promoter-associated CpG island, leading to TDRD1 overexpression; demethylation of the TDRD1 promoter by DNA methyltransferase inhibitors induces TDRD1 in ERG-negative prostate cancer cells.","method":"MeDIP-Seq, bisulfite sequencing, ERG siRNA knockdown and forced overexpression, treatment with DNA methyltransferase inhibitors","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — multiple epigenetic methods with gain- and loss-of-function manipulation, single lab","pmids":["23555854"],"is_preprint":false},{"year":2023,"finding":"In prostate cancer cells, TDRD1 interacts with methylated Sm proteins (in a PRMT5-dependent manner) in the cytoplasm and with Coilin (scaffold of Cajal bodies) in the nucleus. TDRD1 ablation disrupts Cajal body integrity, impairs snRNP biogenesis, and reduces prostate cancer cell proliferation, defining a PRMT5-TDRD1 signaling axis.","method":"Mass spectrometry interactome, co-immunoprecipitation of methylated Sm proteins and Coilin, TDRD1 knockdown/ablation with Cajal body immunofluorescence and proliferation assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — MS interactome + Co-IP + KO with defined cellular phenotype, single lab","pmids":["37041411"],"is_preprint":false},{"year":2024,"finding":"TDRD1 triggers intermitochondrial cement (IMC) assembly via phase separation, driven by cooperation of its tetramerized coiled-coil domain and dimethylarginine-binding Tudor domains (but independent of its intrinsically disordered region). TDRD1 is recruited to mitochondria by MILI, then enhances mitochondrial clustering and triggers IMC assembly to promote piRNA processing. Phase separation-deficient TDRD1 in mice disrupts IMC assembly, impairs piRNA biogenesis, causes transposon de-repression, and leads to spermatogenic arrest. This phase separation mechanism is conserved in vertebrates but not invertebrates.","method":"In vitro phase separation assays, domain deletion and mutation analysis, mouse knock-in models with phase separation-deficient TDRD1, piRNA sequencing, transposon expression analysis, immunofluorescence of mitochondria and IMC, co-immunoprecipitation with MILI","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution of phase separation + domain mutagenesis + mouse knock-in models with defined molecular and cellular phenotypes","pmids":["39029469"],"is_preprint":false}],"current_model":"TDRD1 is a multi-Tudor domain scaffold protein that localizes to nuage/intermitochondrial cement (IMC) downstream of MVH/DDX4 in germ cells; its extended Tudor domains (particularly TD2 and TD3) bind symmetrically dimethylated arginine (sDMA) motifs on Piwi proteins (MILI, MIWI) to nucleate piRNA pathway complexes containing piRNAs and target transcripts, while its coiled-coil domain drives liquid-liquid phase separation to assemble the IMC among mitochondria and promote piRNA biogenesis, and in prostate cancer cells TDRD1 is ectopically expressed downstream of ERG and functions in snRNP biogenesis by bridging PRMT5-methylated Sm proteins and Cajal body scaffold Coilin."},"narrative":{"teleology":[{"year":2006,"claim":"Establishing TDRD1 as a nuage/IMC component whose localization depends on MVH/DDX4 resolved where in the germ cell TDRD1 operates and placed it in a genetic hierarchy downstream of the RNA helicase Vasa.","evidence":"Gene knockout in mice with immunofluorescence and genetic epistasis with Mvh/Ddx4 mutants","pmids":["17038506","17141210"],"confidence":"High","gaps":["Direct binding targets of TDRD1 were unknown","No structural information on Tudor domain recognition","Mechanism by which TDRD1 promotes IMC assembly was unresolved"]},{"year":2009,"claim":"Demonstration that TDRD1 physically interacts with both MILI and MIWI identified the Piwi proteins as direct partners and showed that complex integrity is required for chromatoid body formation, linking TDRD1 to the piRNA pathway.","evidence":"Reciprocal co-immunoprecipitation from mouse testis lysates; immunofluorescence in Miwi-null spermatids","pmids":["19735482"],"confidence":"High","gaps":["Whether interaction depends on arginine methylation was untested","RNA content of TDRD1 complexes was unknown"]},{"year":2011,"claim":"Work in zebrafish showed that TDRD1 Tudor domains specifically recognize sDMA modifications on Piwi proteins and that TDRD1 complexes contain piRNAs and longer target transcripts (TATs), establishing TDRD1 as a scaffold coupling Piwi recognition to piRNA biogenesis intermediates.","evidence":"Co-IP with sDMA specificity analysis, RNA-seq of TDRD1 complexes, loss-of-function in zebrafish","pmids":["21743441"],"confidence":"High","gaps":["Structural basis of sDMA recognition by individual Tudor domains was unknown","Relative contributions of the four Tudor domains were unresolved"]},{"year":2012,"claim":"Crystal structure of the TD3–sDMA-MILI peptide complex and systematic binding measurements across all four Tudor domains revealed that TD2 and TD3 are the principal sDMA readers, while TD1 has a degenerate aromatic cage, defining the molecular logic of multivalent Piwi recognition.","evidence":"X-ray crystallography, ITC/fluorescence binding, NMR titration, SAXS, active-site mutagenesis","pmids":["22996915"],"confidence":"High","gaps":["How multivalent Tudor–Piwi interactions organize higher-order assemblies was unclear","Role of non-Tudor domains (coiled-coil, IDR) was uncharacterized"]},{"year":2013,"claim":"Identification of ERG-driven transcriptional activation and promoter demethylation as the mechanism of ectopic TDRD1 expression in prostate cancer connected a germline piRNA factor to oncogenesis.","evidence":"ERG shRNA/overexpression, promoter reporter and mutant analysis, MeDIP-Seq, bisulfite sequencing, DNMT inhibitor treatment","pmids":["23319146","23555854"],"confidence":"Medium","gaps":["Functional consequences of TDRD1 expression in cancer cells were not yet defined","Whether TDRD1 uses sDMA-reading activity in somatic cells was unknown"]},{"year":2023,"claim":"Discovery that TDRD1 in prostate cancer cells bridges PRMT5-methylated Sm proteins and Cajal body scaffold Coilin to promote snRNP biogenesis revealed a non-piRNA function for TDRD1's sDMA-reading activity in somatic cancer cells.","evidence":"Mass spectrometry interactome, co-IP of methylated Sm and Coilin, TDRD1 ablation with Cajal body and proliferation assays","pmids":["37041411"],"confidence":"Medium","gaps":["Whether this snRNP function occurs in normal germ cells is untested","The specific Tudor domain(s) engaging Sm proteins vs. Coilin are unidentified","Single-lab finding awaits independent replication"]},{"year":2024,"claim":"Reconstitution of TDRD1-driven phase separation showed that the coiled-coil domain (via tetramerization) cooperates with Tudor-domain multivalency to drive IMC assembly among mitochondria, with phase separation–deficient knock-in mice failing to assemble IMC and arresting spermatogenesis, establishing phase separation as the biophysical mechanism underlying nuage organization.","evidence":"In vitro phase separation assays, domain deletion/mutation, mouse knock-in models, piRNA sequencing, transposon expression analysis","pmids":["39029469"],"confidence":"High","gaps":["How TDRD1 condensates are regulated (post-translational modifications, client stoichiometry) is unknown","Whether phase separation contributes to TDRD1's somatic cancer functions has not been tested","The invertebrate mechanisms that substitute for TDRD1-driven phase separation remain uncharacterized"]},{"year":null,"claim":"Key open questions include the full piRNA precursor processing steps occurring within TDRD1 condensates, how the four Tudor domains coordinate simultaneous engagement of multiple methylated clients in vivo, and whether TDRD1's phase separation and snRNP biogenesis functions intersect in cancer.","evidence":"","pmids":[],"confidence":"Low","gaps":["No reconstituted piRNA processing assay with TDRD1 condensates exists","Stoichiometry and dynamics of Tudor–Piwi engagement in condensates are unresolved","Relationship between phase separation capacity and oncogenic function is untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,4,7]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[4]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,8]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3,7,8]}],"complexes":["piRNA pathway nuage/IMC granule","TDRD1-MILI-piRNA complex"],"partners":["MILI","MIWI","MVH","TDRD6","TDRD7","PRMT5","COIL"],"other_free_text":[]},"mechanistic_narrative":"TDRD1 is a germline-enriched scaffold protein whose extended Tudor domains recognize symmetrically dimethylated arginine (sDMA) motifs on Piwi-family proteins to nucleate piRNA pathway complexes essential for transposon silencing and spermatogenesis. Its four tandem Tudor domains bind sDMA-modified MILI peptides with differential affinity—TD2 and TD3 being the principal readers—while its coiled-coil domain drives liquid-liquid phase separation to assemble intermitochondrial cement (IMC), the perinuclear granule compartment required for piRNA biogenesis; phase separation–deficient TDRD1 in mice abolishes IMC, derepresses transposons, and causes spermatogenic arrest [PMID:22996915, PMID:39029469]. TDRD1 localization to nuage depends on MVH/DDX4 and on recruitment to mitochondria by MILI, and its complexes contain piRNAs and target transcripts that represent piRNA biogenesis intermediates [PMID:17038506, PMID:21743441]. In prostate cancer, TDRD1 is ectopically activated by the ERG transcription factor and functions in snRNP biogenesis by bridging PRMT5-methylated Sm proteins and the Cajal body scaffold Coilin, with TDRD1 loss disrupting Cajal body integrity and reducing proliferation [PMID:23319146, PMID:37041411]."},"prefetch_data":{"uniprot":{"accession":"Q9BXT4","full_name":"Tudor domain-containing protein 1","aliases":["Cancer/testis antigen 41.1","CT41.1"],"length_aa":1180,"mass_kda":132.0,"function":"Plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Required for the localization of Piwi proteins to the meiotic nuage. Involved in the piRNA metabolic process by ensuring the entry of correct transcripts into the normal piRNA pool and limiting the entry of cellular transcripts into the piRNA pathway. May act by allowing the recruitment of piRNA biogenesis or loading factors that ensure the correct entry of transcripts and piRNAs into Piwi proteins (By similarity)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9BXT4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TDRD1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TDRD1","total_profiled":1310},"omim":[{"mim_id":"617963","title":"TUDOR DOMAIN-CONTAINING PROTEIN 9; TDRD9","url":"https://www.omim.org/entry/617963"},{"mim_id":"617748","title":"TUDOR DOMAIN-CONTAINING PROTEIN 5; TDRD5","url":"https://www.omim.org/entry/617748"},{"mim_id":"614960","title":"PHOSPHOLIPASE D FAMILY, MEMBER 6; PLD6","url":"https://www.omim.org/entry/614960"},{"mim_id":"605796","title":"TUDOR DOMAIN-CONTAINING PROTEIN 1; TDRD1","url":"https://www.omim.org/entry/605796"},{"mim_id":"605794","title":"MOV10-LIKE RISC COMPLEX RNA HELICASE 1; MOV10L1","url":"https://www.omim.org/entry/605794"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":14.7}],"url":"https://www.proteinatlas.org/search/TDRD1"},"hgnc":{"alias_symbol":["CT41.1"],"prev_symbol":[]},"alphafold":{"accession":"Q9BXT4","domains":[{"cath_id":"-","chopping":"170-199","consensus_level":"high","plddt":81.4123,"start":170,"end":199},{"cath_id":"2.30.30.140","chopping":"252-448","consensus_level":"high","plddt":87.4979,"start":252,"end":448},{"cath_id":"2.30.30.140","chopping":"487-676","consensus_level":"medium","plddt":88.4904,"start":487,"end":676},{"cath_id":"2.40.50.90","chopping":"715-897","consensus_level":"high","plddt":88.2602,"start":715,"end":897},{"cath_id":"2.30.30.140","chopping":"931-982_991-1125","consensus_level":"medium","plddt":83.8889,"start":931,"end":1125},{"cath_id":"1.10.287","chopping":"1144-1179","consensus_level":"high","plddt":59.3608,"start":1144,"end":1179}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BXT4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BXT4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BXT4-F1-predicted_aligned_error_v6.png","plddt_mean":71.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TDRD1","jax_strain_url":"https://www.jax.org/strain/search?query=TDRD1"},"sequence":{"accession":"Q9BXT4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BXT4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BXT4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BXT4"}},"corpus_meta":[{"pmid":"17038506","id":"PMC_17038506","title":"Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/17038506","citation_count":204,"is_preprint":false},{"pmid":"17141210","id":"PMC_17141210","title":"Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice.","date":"2006","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/17141210","citation_count":127,"is_preprint":false},{"pmid":"21743441","id":"PMC_21743441","title":"Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.","date":"2011","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/21743441","citation_count":67,"is_preprint":false},{"pmid":"19735482","id":"PMC_19735482","title":"Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells.","date":"2009","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/19735482","citation_count":57,"is_preprint":false},{"pmid":"23319146","id":"PMC_23319146","title":"Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer.","date":"2013","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/23319146","citation_count":56,"is_preprint":false},{"pmid":"22996915","id":"PMC_22996915","title":"The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.","date":"2012","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/22996915","citation_count":47,"is_preprint":false},{"pmid":"24938434","id":"PMC_24938434","title":"Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk prostate cancer.","date":"2014","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/24938434","citation_count":25,"is_preprint":false},{"pmid":"23555854","id":"PMC_23555854","title":"ERG induces epigenetic activation of Tudor domain-containing protein 1 (TDRD1) in ERG rearrangement-positive prostate cancer.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23555854","citation_count":24,"is_preprint":false},{"pmid":"32059713","id":"PMC_32059713","title":"Testicular expression of TDRD1, TDRD5, TDRD9 and TDRD12 in azoospermia.","date":"2020","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32059713","citation_count":23,"is_preprint":false},{"pmid":"25668702","id":"PMC_25668702","title":"Gonad specific genes in Atlantic salmon (Salmon salar L.): characterization of tdrd7-2, dazl-2, piwil1 and tdrd1 genes.","date":"2015","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/25668702","citation_count":17,"is_preprint":false},{"pmid":"27272765","id":"PMC_27272765","title":"The Germ Cell Gene TDRD1 as an ERG Target Gene and a Novel Prostate Cancer Biomarker.","date":"2016","source":"The Prostate","url":"https://pubmed.ncbi.nlm.nih.gov/27272765","citation_count":16,"is_preprint":false},{"pmid":"39029469","id":"PMC_39029469","title":"TDRD1 phase separation drives intermitochondrial cement assembly to promote piRNA biogenesis and fertility.","date":"2024","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/39029469","citation_count":15,"is_preprint":false},{"pmid":"29920365","id":"PMC_29920365","title":"tdrd1 is a germline-specific and sexually dimorphically expressed gene in Paralichthys olivaceus.","date":"2018","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/29920365","citation_count":14,"is_preprint":false},{"pmid":"27233649","id":"PMC_27233649","title":"Association of a TDRD1 variant with spermatogenic failure susceptibility in the Han Chinese.","date":"2016","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/27233649","citation_count":11,"is_preprint":false},{"pmid":"37041411","id":"PMC_37041411","title":"The cancer testis antigen TDRD1 regulates prostate cancer proliferation by associating with the snRNP biogenesis machinery.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37041411","citation_count":7,"is_preprint":false},{"pmid":"35790000","id":"PMC_35790000","title":"DNA hypomethylation activation Wnt/TCF7L2/TDRD1 pathway promotes spermatogonial stem cell formation.","date":"2022","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/35790000","citation_count":4,"is_preprint":false},{"pmid":"32286072","id":"PMC_32286072","title":"Upregulation of TDRD1 Promotes the Sexual Maturation in Allotetraploids Hybridized from Red Crucian Carp (Carassius auratus Red var) (♀) and Common Carp (Cyprinus carpio L) (♂).","date":"2020","source":"Journal of proteome research","url":"https://pubmed.ncbi.nlm.nih.gov/32286072","citation_count":3,"is_preprint":false},{"pmid":"35347417","id":"PMC_35347417","title":"Characteristics of the TDRD1 gene promoter in chickens.","date":"2022","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/35347417","citation_count":2,"is_preprint":false},{"pmid":"36921513","id":"PMC_36921513","title":"H3K4me2 cooperates with Wnt/TCF7L2 to regulate TDRD1 and promote chicken spermatogonia stem cell formation.","date":"2023","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/36921513","citation_count":2,"is_preprint":false},{"pmid":"36865141","id":"PMC_36865141","title":"The cancer testis antigen TDRD1 regulates prostate cancer proliferation by associating with snRNP biogenesis machinery.","date":"2023","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/36865141","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11861,"output_tokens":2494,"usd":0.036497},"stage2":{"model":"claude-opus-4-6","input_tokens":5792,"output_tokens":2303,"usd":0.129802},"total_usd":0.166299,"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\": 2006,\n      \"finding\": \"TDRD1/MTR-1 localizes to nuage/germinal granules (specifically intermitochondrial cement) in mouse male germ cells, and its intracellular localization is downstream of MVH/DDX4 (mouse vasa homologue). Loss of TDRD1 abolishes intermitochondrial cement formation but chromatoid bodies persist, while MVH mutants show strong reduction of intermitochondrial cement.\",\n      \"method\": \"Targeted gene knockout in mice, subcellular localization by immunofluorescence, genetic epistasis with Mvh/Ddx4 mutants\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with loss-of-function mouse model and defined cellular phenotype, replicated across labs\",\n      \"pmids\": [\"17038506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TDRD1/MTR-1, TDRD6, and TDRD7/TRAP co-localize to nuage and form a ribonucleoprotein complex together; their co-localization is disrupted in Mvh/Ddx4 mutants. A single Tudor domain is a structural unit sufficient for nuage localization, but truncated dominant-negative forms are detrimental to meiotic spermatocytes.\",\n      \"method\": \"Co-immunoprecipitation, in vivo overexpression of truncated forms, genetic epistasis with Mvh mutants, immunofluorescence localization\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP establishing complex, epistasis, and functional domain mapping with overexpression\",\n      \"pmids\": [\"17141210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TDRD1/MTR-1 physically interacts with both MILI and MIWI (mouse Piwi family proteins) in adult mouse testes, forming a complex whose integrity is required for proper subcellular localization of MILI and TDRD1, and for chromatoid body formation in round spermatids.\",\n      \"method\": \"Co-immunoprecipitation from mouse testis lysates, immunofluorescence localization in Miwi-null spermatids\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with defined cellular phenotype (chromatoid body disruption) in knockout background\",\n      \"pmids\": [\"19735482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Zebrafish Tdrd1 acts as a molecular scaffold binding both Piwi proteins (Ziwi and Zili) through specific tudor domain–symmetrically dimethylated arginine (sDMA) interactions, and its complexes contain piRNAs and longer transcripts (Tdrd1-associated transcripts, TATs) representing likely cleaved Piwi pathway targets and piRNA biogenesis intermediates. Tdrd1 is required for efficient Piwi-pathway activity and nuage formation.\",\n      \"method\": \"Co-immunoprecipitation, sequence specificity analysis of tudor domain–sDMA interactions, RNA sequencing of Tdrd1 complexes, loss-of-function in zebrafish\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, RNA biochemistry, loss-of-function) in zebrafish ortholog\",\n      \"pmids\": [\"21743441\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The four extended Tudor domains (TDs) of murine TDRD1 bind symmetrically dimethylated arginine (sDMA)-containing peptides from MILI with differential affinity: TD2 and TD3 show preference for consecutive MILI peptides, TD4 has lower affinity, and TD1 has very weak affinity due to a non-consensus aromatic cage that can be restored by a single point mutation. Crystal structure of TD3 bound to a methylated MILI peptide reveals an unexpected peptide orientation with contacts outside the aromatic cage.\",\n      \"method\": \"Binding affinity measurements (ITC/fluorescence), pull-down with endogenous Piwi proteins, crystal structure of TD3–sDMA peptide complex, solution NMR titration, small-angle X-ray scattering (SAXS) of tandem Tudor domains, active-site mutagenesis\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure + mutagenesis + in vitro binding assays + NMR, multiple orthogonal methods in single study\",\n      \"pmids\": [\"22996915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ERG transcription factor directly activates TDRD1 transcription in prostate cancer by binding a functional ERG-binding site in the TDRD1 promoter; ERG shRNA knockdown reduces TDRD1 expression and decreases TDRD1 promoter activity.\",\n      \"method\": \"shRNA knockdown of ERG, promoter reporter assay, mutation analysis of ERG binding site in TDRD1 promoter\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — promoter mutation analysis and shRNA with reporter assay, single lab\",\n      \"pmids\": [\"23319146\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ERG governs loss of DNA methylation at the TDRD1 promoter-associated CpG island, leading to TDRD1 overexpression; demethylation of the TDRD1 promoter by DNA methyltransferase inhibitors induces TDRD1 in ERG-negative prostate cancer cells.\",\n      \"method\": \"MeDIP-Seq, bisulfite sequencing, ERG siRNA knockdown and forced overexpression, treatment with DNA methyltransferase inhibitors\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple epigenetic methods with gain- and loss-of-function manipulation, single lab\",\n      \"pmids\": [\"23555854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In prostate cancer cells, TDRD1 interacts with methylated Sm proteins (in a PRMT5-dependent manner) in the cytoplasm and with Coilin (scaffold of Cajal bodies) in the nucleus. TDRD1 ablation disrupts Cajal body integrity, impairs snRNP biogenesis, and reduces prostate cancer cell proliferation, defining a PRMT5-TDRD1 signaling axis.\",\n      \"method\": \"Mass spectrometry interactome, co-immunoprecipitation of methylated Sm proteins and Coilin, TDRD1 knockdown/ablation with Cajal body immunofluorescence and proliferation assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — MS interactome + Co-IP + KO with defined cellular phenotype, single lab\",\n      \"pmids\": [\"37041411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TDRD1 triggers intermitochondrial cement (IMC) assembly via phase separation, driven by cooperation of its tetramerized coiled-coil domain and dimethylarginine-binding Tudor domains (but independent of its intrinsically disordered region). TDRD1 is recruited to mitochondria by MILI, then enhances mitochondrial clustering and triggers IMC assembly to promote piRNA processing. Phase separation-deficient TDRD1 in mice disrupts IMC assembly, impairs piRNA biogenesis, causes transposon de-repression, and leads to spermatogenic arrest. This phase separation mechanism is conserved in vertebrates but not invertebrates.\",\n      \"method\": \"In vitro phase separation assays, domain deletion and mutation analysis, mouse knock-in models with phase separation-deficient TDRD1, piRNA sequencing, transposon expression analysis, immunofluorescence of mitochondria and IMC, co-immunoprecipitation with MILI\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution of phase separation + domain mutagenesis + mouse knock-in models with defined molecular and cellular phenotypes\",\n      \"pmids\": [\"39029469\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TDRD1 is a multi-Tudor domain scaffold protein that localizes to nuage/intermitochondrial cement (IMC) downstream of MVH/DDX4 in germ cells; its extended Tudor domains (particularly TD2 and TD3) bind symmetrically dimethylated arginine (sDMA) motifs on Piwi proteins (MILI, MIWI) to nucleate piRNA pathway complexes containing piRNAs and target transcripts, while its coiled-coil domain drives liquid-liquid phase separation to assemble the IMC among mitochondria and promote piRNA biogenesis, and in prostate cancer cells TDRD1 is ectopically expressed downstream of ERG and functions in snRNP biogenesis by bridging PRMT5-methylated Sm proteins and Cajal body scaffold Coilin.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TDRD1 is a germline-enriched scaffold protein whose extended Tudor domains recognize symmetrically dimethylated arginine (sDMA) motifs on Piwi-family proteins to nucleate piRNA pathway complexes essential for transposon silencing and spermatogenesis. Its four tandem Tudor domains bind sDMA-modified MILI peptides with differential affinity—TD2 and TD3 being the principal readers—while its coiled-coil domain drives liquid-liquid phase separation to assemble intermitochondrial cement (IMC), the perinuclear granule compartment required for piRNA biogenesis; phase separation–deficient TDRD1 in mice abolishes IMC, derepresses transposons, and causes spermatogenic arrest [PMID:22996915, PMID:39029469]. TDRD1 localization to nuage depends on MVH/DDX4 and on recruitment to mitochondria by MILI, and its complexes contain piRNAs and target transcripts that represent piRNA biogenesis intermediates [PMID:17038506, PMID:21743441]. In prostate cancer, TDRD1 is ectopically activated by the ERG transcription factor and functions in snRNP biogenesis by bridging PRMT5-methylated Sm proteins and the Cajal body scaffold Coilin, with TDRD1 loss disrupting Cajal body integrity and reducing proliferation [PMID:23319146, PMID:37041411].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing TDRD1 as a nuage/IMC component whose localization depends on MVH/DDX4 resolved where in the germ cell TDRD1 operates and placed it in a genetic hierarchy downstream of the RNA helicase Vasa.\",\n      \"evidence\": \"Gene knockout in mice with immunofluorescence and genetic epistasis with Mvh/Ddx4 mutants\",\n      \"pmids\": [\"17038506\", \"17141210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct binding targets of TDRD1 were unknown\",\n        \"No structural information on Tudor domain recognition\",\n        \"Mechanism by which TDRD1 promotes IMC assembly was unresolved\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstration that TDRD1 physically interacts with both MILI and MIWI identified the Piwi proteins as direct partners and showed that complex integrity is required for chromatoid body formation, linking TDRD1 to the piRNA pathway.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation from mouse testis lysates; immunofluorescence in Miwi-null spermatids\",\n      \"pmids\": [\"19735482\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether interaction depends on arginine methylation was untested\",\n        \"RNA content of TDRD1 complexes was unknown\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Work in zebrafish showed that TDRD1 Tudor domains specifically recognize sDMA modifications on Piwi proteins and that TDRD1 complexes contain piRNAs and longer target transcripts (TATs), establishing TDRD1 as a scaffold coupling Piwi recognition to piRNA biogenesis intermediates.\",\n      \"evidence\": \"Co-IP with sDMA specificity analysis, RNA-seq of TDRD1 complexes, loss-of-function in zebrafish\",\n      \"pmids\": [\"21743441\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of sDMA recognition by individual Tudor domains was unknown\",\n        \"Relative contributions of the four Tudor domains were unresolved\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Crystal structure of the TD3–sDMA-MILI peptide complex and systematic binding measurements across all four Tudor domains revealed that TD2 and TD3 are the principal sDMA readers, while TD1 has a degenerate aromatic cage, defining the molecular logic of multivalent Piwi recognition.\",\n      \"evidence\": \"X-ray crystallography, ITC/fluorescence binding, NMR titration, SAXS, active-site mutagenesis\",\n      \"pmids\": [\"22996915\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How multivalent Tudor–Piwi interactions organize higher-order assemblies was unclear\",\n        \"Role of non-Tudor domains (coiled-coil, IDR) was uncharacterized\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identification of ERG-driven transcriptional activation and promoter demethylation as the mechanism of ectopic TDRD1 expression in prostate cancer connected a germline piRNA factor to oncogenesis.\",\n      \"evidence\": \"ERG shRNA/overexpression, promoter reporter and mutant analysis, MeDIP-Seq, bisulfite sequencing, DNMT inhibitor treatment\",\n      \"pmids\": [\"23319146\", \"23555854\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequences of TDRD1 expression in cancer cells were not yet defined\",\n        \"Whether TDRD1 uses sDMA-reading activity in somatic cells was unknown\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Discovery that TDRD1 in prostate cancer cells bridges PRMT5-methylated Sm proteins and Cajal body scaffold Coilin to promote snRNP biogenesis revealed a non-piRNA function for TDRD1's sDMA-reading activity in somatic cancer cells.\",\n      \"evidence\": \"Mass spectrometry interactome, co-IP of methylated Sm and Coilin, TDRD1 ablation with Cajal body and proliferation assays\",\n      \"pmids\": [\"37041411\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether this snRNP function occurs in normal germ cells is untested\",\n        \"The specific Tudor domain(s) engaging Sm proteins vs. Coilin are unidentified\",\n        \"Single-lab finding awaits independent replication\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Reconstitution of TDRD1-driven phase separation showed that the coiled-coil domain (via tetramerization) cooperates with Tudor-domain multivalency to drive IMC assembly among mitochondria, with phase separation–deficient knock-in mice failing to assemble IMC and arresting spermatogenesis, establishing phase separation as the biophysical mechanism underlying nuage organization.\",\n      \"evidence\": \"In vitro phase separation assays, domain deletion/mutation, mouse knock-in models, piRNA sequencing, transposon expression analysis\",\n      \"pmids\": [\"39029469\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TDRD1 condensates are regulated (post-translational modifications, client stoichiometry) is unknown\",\n        \"Whether phase separation contributes to TDRD1's somatic cancer functions has not been tested\",\n        \"The invertebrate mechanisms that substitute for TDRD1-driven phase separation remain uncharacterized\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the full piRNA precursor processing steps occurring within TDRD1 condensates, how the four Tudor domains coordinate simultaneous engagement of multiple methylated clients in vivo, and whether TDRD1's phase separation and snRNP biogenesis functions intersect in cancer.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No reconstituted piRNA processing assay with TDRD1 condensates exists\",\n        \"Stoichiometry and dynamics of Tudor–Piwi engagement in condensates are unresolved\",\n        \"Relationship between phase separation capacity and oncogenic function is untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 4, 7]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3, 7, 8]}\n    ],\n    \"complexes\": [\n      \"piRNA pathway nuage/IMC granule\",\n      \"TDRD1-MILI-piRNA complex\"\n    ],\n    \"partners\": [\n      \"MILI\",\n      \"MIWI\",\n      \"MVH\",\n      \"TDRD6\",\n      \"TDRD7\",\n      \"PRMT5\",\n      \"COIL\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}