{"gene":"TDRD6","run_date":"2026-04-28T21:42:58","timeline":{"discoveries":[{"year":2009,"finding":"TDRD6 directly physically interacts with the chromatoid body (CB) components MILI and MIWI (mouse PIWI proteins) in male germ cells, and this interaction is mediated by symmetrically dimethylated arginines (sDMAs) on MIWI N-terminal RG repeats recognized by Tudor domains.","method":"Co-immunoprecipitation of endogenous proteins; mass spectrometry identification of arginine methylation; mutagenesis of Tudor domain aromatic cage","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 — reciprocal Co-IP with MS-confirmed methylation, replicated across multiple studies","pmids":["19918066","19926723"],"is_preprint":false},{"year":2009,"finding":"TDRD6 is essential for spermiogenesis and chromatoid body (CB) architecture: Tdrd6-/- mice arrest at round spermatid stage, producing 'ghost' CBs with greatly disrupted architecture, and CB components MAEL, MIWI, and MVH fail to localize to CBs in the absence of TDRD6.","method":"Tdrd6 knockout mouse (loss-of-function), immunofluorescence, electron microscopy of CB ultrastructure","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype and multiple orthogonal methods","pmids":["19345099"],"is_preprint":false},{"year":2009,"finding":"Loss of TDRD6 leads to upregulation of more than 50 miRNAs, including precursor (pre-) and primary (pri-) miRNA forms, indicating TDRD6 is required for proper mature and precursor miRNA expression in testes.","method":"Tdrd6 knockout mouse, small RNA sequencing/microarray, qRT-PCR of pre- and pri-miRNAs","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with transcriptome-wide miRNA profiling and qRT-PCR validation","pmids":["19345099"],"is_preprint":false},{"year":2006,"finding":"TDRD6, TDRD1, and TDRD7 co-localize to nuage (chromatoid bodies) in mouse male germ cells and form a ribonucleoprotein complex together; this localization is downstream of MVH (mouse VASA homolog), as it is disrupted in Mvh mutants. A single Tudor domain is sufficient as a structural unit for nuage localization, but the repeated Tudor domain architecture is functionally essential for germ cell differentiation.","method":"Immunofluorescence co-localization, co-immunoprecipitation, analysis in Mvh mutant mice, overexpression of truncated dominant-negative forms","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including genetic epistasis (Mvh mutant), Co-IP, and domain truncation experiments","pmids":["17141210"],"is_preprint":false},{"year":2011,"finding":"TDRD6 and TDRD7 together orchestrate chromatoid body biogenesis in concert: single and double knockouts show that TDRD7 is required for initial CB establishment and fusion with processing bodies/GW bodies, while TDRD6 functions at a later stage of spermiogenesis when CBs exhibit aggresome-like properties. TDRD6 does not affect retrotransposons, distinguishing its pathway from TDRD1 and TDRD9.","method":"Single and double Tdrd7/Tdrd6 knockout mice, genetic epistasis, immunofluorescence, histology","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — double knockout genetic epistasis with defined phenotypic readouts","pmids":["21670278"],"is_preprint":false},{"year":2009,"finding":"MIWI binds to TDRD6 in an sDMA-dependent manner, demonstrating that sDMA modification of PIWI proteins is required for their interaction with Tudor-domain proteins including TDRD6, representing an evolutionarily conserved mechanism in germ cells.","method":"Co-immunoprecipitation in mouse, sDMA dependency tested biochemically","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with methylation-dependency test, cross-species validation","pmids":["19926723"],"is_preprint":false},{"year":2010,"finding":"Mouse VASA homolog (MVH) associates with TDRD6 (and TDRD1) in an arginine methylation-dependent manner, as symmetrically and asymmetrically dimethylated arginines are found on Vasa proteins and PRMT5 is required for Vasa sDMA production.","method":"Co-immunoprecipitation, mass spectrometry identification of dimethylarginines on Vasa, genetic perturbation of dPRMT5 in Drosophila","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with mass spectrometry, but TDRD6 interaction shown in single study","pmids":["20080973"],"is_preprint":false},{"year":2016,"finding":"TDRD6 is required for the long 3' UTR-triggered nonsense-mediated mRNA decay (NMD) pathway in chromatoid bodies: TDRD6 is essential for UPF1 localization to CBs, for UPF1-UPF2 and UPF1-MVH interactions, and for association of long 3' UTR mRNAs with UPF1/UPF2. Loss of TDRD6 increases stability and translational activity of long 3' UTR mRNAs but does not impair downstream exon-exon junction-triggered NMD.","method":"Tdrd6 knockout mice, proteome analysis of purified CBs, co-immunoprecipitation (UPF1-UPF2, UPF1-MVH), RNA-immunoprecipitation, polysome profiling","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods including CB proteomics, Co-IP, RNA-IP, and translational assays in KO mouse","pmids":["27149095"],"is_preprint":false},{"year":2017,"finding":"In meiotic prophase I spermatocytes, TDRD6 interacts with PRMT5 (protein arginine methyltransferase 5) and with spliceosomal core protein SmB in an arginine methylation-dependent and RNA-independent manner. Loss of TDRD6 reduces PRMT5-SmB association and SmB arginine dimethylation, impairs spliceosome assembly (resulting in 3.5-fold increased U5 snRNP levels), decreases SMN-positive bodies and Cajal bodies, and causes widespread splicing defects including aberrant intron/exon usage.","method":"Co-immunoprecipitation (TDRD6-PRMT5, TDRD6-SmB), RNA-independence confirmed, Tdrd6 KO spermatocytes, immunofluorescence of nuclear bodies, transcriptome analysis","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1-2 — KO mouse with multiple orthogonal methods: Co-IP, transcriptomics, snRNP quantification, nuclear body imaging","pmids":["28263986"],"is_preprint":false},{"year":2018,"finding":"In zebrafish, Tdrd6a interacts with Bucky ball (Buc), a prion-like protein required for Balbiani body formation, affecting Buc mobility and aggregation properties. Loss of Tdrd6a-Buc interaction causes defects in germ cell development, establishing Tdrd6a as a regulator of phase-separated germ plasm compartment assembly.","method":"Co-immunoprecipitation, live imaging (FRAP to assess mobility), genetic KO/knockdown in zebrafish, germ cell quantification","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, FRAP, and KO with defined developmental phenotype","pmids":["30086300"],"is_preprint":false},{"year":2024,"finding":"MIWI N-terminal arginines (NTRs) mediate interaction with TDRD6 that is necessary for chromatoid body compaction during spermiogenesis, as demonstrated by MIWI NTR mutant mice lacking this interaction.","method":"MIWI NTR knock-in mutant mice, immunofluorescence of CB compaction, Co-immunoprecipitation","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 — clean KI mutant mouse with defined CB phenotype and biochemical interaction mapping","pmids":["38520410"],"is_preprint":false},{"year":2024,"finding":"Bi-allelic loss-of-function TDRD6 variants in humans cause spermiogenesis defects including acrosomal hypoplasia, reduced sperm concentration, and impaired motility; in patient spermatids, chromatoid body components DDX4 (MVH) and UPF1 are mislocalized, and scRNA-seq reveals TDRD6 regulates mRNA metabolism processes involved in spermatid differentiation and cytoplasmic translation.","method":"Whole-exome sequencing, CRISPR-Cas9 Tdrd6 KO mice, immunofluorescence, immunoblotting, ultrastructural analysis, total RNA-seq, single-cell RNA-seq","journal":"Journal of medical genetics","confidence":"High","confidence_rationale":"Tier 2 — human genetics confirmed in KO mouse model with multiple orthogonal methods","pmids":["38341271"],"is_preprint":false}],"current_model":"TDRD6 is a multi-Tudor domain protein that localizes to chromatoid bodies in male germ cells downstream of MVH, where it acts as a scaffold that (1) recruits PIWI proteins (MIWI, MILI) via recognition of their symmetrically dimethylated arginine N-terminal repeats to maintain CB architecture and compaction, (2) enables the long 3' UTR-triggered NMD pathway by promoting UPF1 localization and UPF1-UPF2-MVH interactions within the CB, and (3) in meiotic spermatocytes, interacts with PRMT5 to promote arginine methylation of spliceosomal SmB and spliceosome maturation, thereby regulating mRNA splicing; collectively, loss of TDRD6 arrests spermiogenesis at the round spermatid stage, abolishes CB integrity, dysregulates miRNA expression, and causes male infertility in both mice and humans."},"narrative":{"teleology":[{"year":2006,"claim":"Establishing that TDRD6 localizes to nuage/chromatoid bodies in male germ cells as part of a TDRD1–TDRD6–TDRD7 ribonucleoprotein complex downstream of MVH resolved the cellular compartment and epistatic hierarchy in which TDRD6 operates.","evidence":"Immunofluorescence co-localization, co-immunoprecipitation, and Mvh mutant analysis in mouse testes","pmids":["17141210"],"confidence":"High","gaps":["Molecular function of TDRD6 within CBs unknown","Direct versus indirect dependence on MVH unresolved","Whether Tudor domain multiplicity has distinct partner specificity not tested"]},{"year":2009,"claim":"Demonstrating that TDRD6 binds MIWI and MILI via symmetrically dimethylated arginines, and that loss of TDRD6 disrupts CB architecture and arrests spermiogenesis at the round spermatid stage, established TDRD6 as a methylarginine-reading scaffold essential for CB integrity and male fertility.","evidence":"Tdrd6 knockout mice with electron microscopy, reciprocal co-immunoprecipitation, mass spectrometry of sDMA marks, and miRNA profiling","pmids":["19918066","19926723","19345099"],"confidence":"High","gaps":["How TDRD6 loss leads to miRNA dysregulation mechanistically unclear","Whether TDRD6 directly processes or merely stabilizes miRNA precursors unknown","Structural basis of multi-Tudor domain engagement with multiple PIWI partners unresolved"]},{"year":2010,"claim":"Showing that MVH/VASA associates with TDRD6 in an arginine methylation-dependent manner extended the sDMA-Tudor recognition paradigm beyond PIWI proteins to the core CB helicase.","evidence":"Co-immunoprecipitation and mass spectrometry of dimethylarginines on Vasa in mouse","pmids":["20080973"],"confidence":"Medium","gaps":["TDRD6–MVH interaction demonstrated in a single study without reciprocal validation","Which Tudor domains of TDRD6 engage MVH not mapped","Functional consequence of disrupting TDRD6–MVH interaction specifically not tested"]},{"year":2011,"claim":"Genetic epistasis using Tdrd6/Tdrd7 single and double knockouts delineated a sequential CB biogenesis program where TDRD7 acts early (CB establishment and P-body fusion) and TDRD6 acts later during CB maturation, separating TDRD6 function from retrotransposon silencing pathways.","evidence":"Single and double Tdrd6/Tdrd7 knockout mice with immunofluorescence and histology","pmids":["21670278"],"confidence":"High","gaps":["Molecular basis of temporal handoff from TDRD7 to TDRD6 unknown","What triggers the transition from P-body-like to aggresome-like CB properties is unresolved"]},{"year":2016,"claim":"Discovering that TDRD6 is required for UPF1 recruitment to CBs and for UPF1–UPF2–MVH complex formation revealed a previously unknown function: TDRD6 enables long 3′ UTR-triggered NMD within the chromatoid body, a pathway distinct from canonical exon-junction-triggered NMD.","evidence":"Tdrd6 knockout mice with CB proteomics, co-immunoprecipitation of UPF1–UPF2 and UPF1–MVH, RNA-immunoprecipitation, and polysome profiling","pmids":["27149095"],"confidence":"High","gaps":["Whether TDRD6 directly contacts UPF1 or acts through an intermediary not determined","How CB-localized NMD is coupled to translational repression mechanistically unclear","Whether this NMD function is conserved outside mouse germ cells unknown"]},{"year":2017,"claim":"Identification of TDRD6 interaction with PRMT5 and spliceosomal SmB in meiotic spermatocytes, and demonstration that TDRD6 loss impairs SmB arginine methylation, spliceosome assembly, and Cajal body formation, uncovered a nuclear function for TDRD6 in RNA splicing regulation distinct from its cytoplasmic CB role.","evidence":"Co-immunoprecipitation of TDRD6–PRMT5 and TDRD6–SmB (RNA-independent), Tdrd6 KO spermatocyte transcriptomics, snRNP quantification, and nuclear body immunofluorescence","pmids":["28263986"],"confidence":"High","gaps":["Whether TDRD6 acts as a direct scaffold bridging PRMT5 to SmB or modulates PRMT5 catalytic activity is unresolved","Full catalog of splicing events affected and their functional consequences in spermatogenesis not mapped","How nuclear and cytoplasmic TDRD6 functions are coordinated during the meiosis-to-spermiogenesis transition unknown"]},{"year":2018,"claim":"In zebrafish, demonstration that Tdrd6a interacts with the prion-like protein Bucky ball and regulates its mobility within the Balbiani body established TDRD6 as a regulator of phase-separated germ plasm compartments beyond mammalian CBs.","evidence":"Co-immunoprecipitation, FRAP live imaging, and genetic knockout/knockdown in zebrafish with germ cell quantification","pmids":["30086300"],"confidence":"High","gaps":["Whether mammalian TDRD6 similarly regulates phase separation properties of CB components not tested","Structural basis of Tdrd6a–Buc interaction not resolved"]},{"year":2024,"claim":"MIWI knock-in mice lacking N-terminal arginine repeats confirmed that the MIWI–TDRD6 sDMA-dependent interaction is specifically required for CB compaction during spermiogenesis, moving beyond correlative knockout data to a defined interaction interface in vivo.","evidence":"MIWI NTR knock-in mutant mice with CB compaction assays and co-immunoprecipitation","pmids":["38520410"],"confidence":"High","gaps":["Whether other Tudor-domain proteins partially compensate for TDRD6 loss in CB compaction not addressed","Stoichiometry of MIWI–TDRD6 complexes within CBs unknown"]},{"year":2024,"claim":"Discovery that bi-allelic loss-of-function TDRD6 variants cause human male infertility with acrosomal hypoplasia, CB component mislocalization, and dysregulated mRNA metabolism confirmed the mouse phenotype translates to a human Mendelian disorder.","evidence":"Whole-exome sequencing in infertile men, CRISPR-Cas9 Tdrd6 KO mice, immunofluorescence, scRNA-seq","pmids":["38341271"],"confidence":"High","gaps":["Full allelic spectrum and genotype–phenotype correlations in humans not established","Whether partial loss of TDRD6 function causes subfertility rather than infertility unknown","Therapeutic rescue strategies not explored"]},{"year":null,"claim":"The structural basis for how TDRD6's multiple Tudor domains simultaneously engage distinct methylated partners (MIWI, MILI, MVH, SmB) and how this multivalent binding organizes CB and nuclear body architecture remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structure of any TDRD6 Tudor domain in complex with a methylated peptide","No reconstitution of TDRD6-dependent CB condensation in vitro","How TDRD6 coordinates its distinct splicing, NMD, and PIWI-pathway functions temporally during spermatogenesis remains unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,7,8,10]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,5,6]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3,7]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,7,8]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,4,9,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[7,8]}],"complexes":["chromatoid body"],"partners":["MIWI","MILI","MVH","UPF1","PRMT5","SMB","TDRD1","TDRD7"],"other_free_text":[]},"mechanistic_narrative":"TDRD6 is a multi-Tudor domain scaffold protein essential for male germ cell differentiation, functioning primarily within chromatoid bodies (CBs) to organize ribonucleoprotein complexes required for post-transcriptional gene regulation during spermiogenesis. TDRD6 recruits PIWI proteins (MIWI, MILI) through recognition of their symmetrically dimethylated arginine residues, and this interaction is necessary for CB compaction and proper localization of CB components including MAEL, MVH, and UPF1 [PMID:19918066, PMID:19345099, PMID:38520410]. Within CBs, TDRD6 enables a long 3′ UTR-triggered nonsense-mediated mRNA decay pathway by promoting UPF1–UPF2–MVH interactions, and separately, in meiotic spermatocytes it facilitates PRMT5-dependent arginine methylation of spliceosomal SmB to promote spliceosome maturation and correct mRNA splicing [PMID:27149095, PMID:28263986]. Bi-allelic loss-of-function TDRD6 variants in humans cause spermiogenesis failure with acrosomal hypoplasia, CB disassembly, and male infertility [PMID:38341271]."},"prefetch_data":{"uniprot":{"accession":"O60522","full_name":"Tudor domain-containing protein 6","aliases":["Antigen NY-CO-45","Cancer/testis antigen 41.2","CT41.2"],"length_aa":2096,"mass_kda":236.5,"function":"Tudor domain-containing protein involved in germ cell development, more specifically the formation of chromatoid body (during spermiogenesis), Balbiani body (during oogenesis), germ plasm (upon fertilization), and for proper miRNA expression and spliceosome maturation (By similarity). Essential for RNA-dependent helicase UPF1 localization to chromatoid body, for UPF1-UPF2 and UPF1-DDX4 interactions which are required for mRNA degradation, using the extended 3' UTR-triggered nonsense-mediated mRNA decay (NMD) pathway. Involved in spliceosome maturation and mRNA splicing in prophase I spermatocytes through interaction with arginine N-methyltransferase PRMT5 and symmetrically arginine dimethylated SNRPB (small nuclear ribonucleoprotein-associated protein) (By similarity)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O60522/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TDRD6","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/TDRD6","total_profiled":1310},"omim":[{"mim_id":"611200","title":"TUDOR DOMAIN-CONTAINING PROTEIN 6; TDRD6","url":"https://www.omim.org/entry/611200"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":25.9}],"url":"https://www.proteinatlas.org/search/TDRD6"},"hgnc":{"alias_symbol":["NY-CO-45","bA446F17.4","CT41.2","SPATA36"],"prev_symbol":[]},"alphafold":{"accession":"O60522","domains":[{"cath_id":"2.30.30.140","chopping":"13-57_68-138_149-217","consensus_level":"high","plddt":80.4043,"start":13,"end":217},{"cath_id":"2.30.30.140","chopping":"251-288_309-449","consensus_level":"high","plddt":80.0246,"start":251,"end":449},{"cath_id":"2.40.50.90","chopping":"488-518_535-668","consensus_level":"medium","plddt":85.5117,"start":488,"end":668},{"cath_id":"2.40.50.90","chopping":"1295-1344_1413-1477","consensus_level":"medium","plddt":82.1519,"start":1295,"end":1477},{"cath_id":"2.30.30.140","chopping":"1347-1405","consensus_level":"medium","plddt":85.2775,"start":1347,"end":1405},{"cath_id":"2.30.30.140","chopping":"1521-1697","consensus_level":"medium","plddt":79.2064,"start":1521,"end":1697},{"cath_id":"2.30.30,2.30.30","chopping":"2032-2076","consensus_level":"medium","plddt":79.3509,"start":2032,"end":2076}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O60522","model_url":"https://alphafold.ebi.ac.uk/files/AF-O60522-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O60522-F1-predicted_aligned_error_v6.png","plddt_mean":64.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TDRD6","jax_strain_url":"https://www.jax.org/strain/search?query=TDRD6"},"sequence":{"accession":"O60522","fasta_url":"https://rest.uniprot.org/uniprotkb/O60522.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O60522/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O60522"}},"corpus_meta":[{"pmid":"12124339","id":"PMC_12124339","title":"Cancer-related 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Part D, Genomics & proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/31125834","citation_count":10,"is_preprint":false},{"pmid":"29731491","id":"PMC_29731491","title":"Oocyte-specific gene Oog1 suppresses the expression of spermatogenesis-specific genes in oocytes.","date":"2018","source":"The Journal of reproduction and development","url":"https://pubmed.ncbi.nlm.nih.gov/29731491","citation_count":9,"is_preprint":false},{"pmid":"35399512","id":"PMC_35399512","title":"Integrative Analysis of RNA Expression and Regulatory Networks in Mice Liver Infected by Echinococcus multilocularis.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35399512","citation_count":9,"is_preprint":false},{"pmid":"33711033","id":"PMC_33711033","title":"Integrated analysis of RNA-binding proteins in thyroid cancer.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/33711033","citation_count":8,"is_preprint":false},{"pmid":"29109362","id":"PMC_29109362","title":"PAPOLB/TPAP regulates spermiogenesis independently of chromatoid body-associated factors.","date":"2017","source":"The Journal of reproduction and development","url":"https://pubmed.ncbi.nlm.nih.gov/29109362","citation_count":8,"is_preprint":false},{"pmid":"37073353","id":"PMC_37073353","title":"Evolutionary dynamics and conserved function of the Tudor domain-containing (TDRD) proteins in teleost fish.","date":"2021","source":"Marine life science & technology","url":"https://pubmed.ncbi.nlm.nih.gov/37073353","citation_count":7,"is_preprint":false},{"pmid":"32728493","id":"PMC_32728493","title":"Cellular heterogeneity map of diverse immune and stromal phenotypes within breast tumor microenvironment.","date":"2020","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/32728493","citation_count":7,"is_preprint":false},{"pmid":"40311511","id":"PMC_40311511","title":"Comprehensive transcriptome analysis and lncRNA-miRNA-mRNA establishment of schizophrenia based on induced pluripotent stem cells.","date":"2025","source":"Schizophrenia research","url":"https://pubmed.ncbi.nlm.nih.gov/40311511","citation_count":3,"is_preprint":false},{"pmid":"28660752","id":"PMC_28660752","title":"Biased Duplications and Loss of Members in Tdrd Family in Teleost Fish.","date":"2017","source":"Journal of experimental zoology. Part B, Molecular and developmental evolution","url":"https://pubmed.ncbi.nlm.nih.gov/28660752","citation_count":3,"is_preprint":false},{"pmid":"37385406","id":"PMC_37385406","title":"Paternal source of germ plasm determinants in the viviparous teleost, Gambusia holbrooki; dads do matter.","date":"2023","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/37385406","citation_count":1,"is_preprint":false},{"pmid":"38260298","id":"PMC_38260298","title":"MIWI arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38260298","citation_count":0,"is_preprint":false},{"pmid":"40894159","id":"PMC_40894159","title":"Interpretable machine learning coupled to spatial transcriptomics unveils mechanisms of macrophage-driven fibroblast activation in ischemic cardiomyopathy.","date":"2025","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40894159","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17797,"output_tokens":3097,"usd":0.049923},"stage2":{"model":"claude-opus-4-6","input_tokens":6442,"output_tokens":5628,"usd":0.259365},"total_usd":0.309288,"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\": 2009,\n      \"finding\": \"TDRD6 directly physically interacts with the chromatoid body (CB) components MILI and MIWI (mouse PIWI proteins) in male germ cells, and this interaction is mediated by symmetrically dimethylated arginines (sDMAs) on MIWI N-terminal RG repeats recognized by Tudor domains.\",\n      \"method\": \"Co-immunoprecipitation of endogenous proteins; mass spectrometry identification of arginine methylation; mutagenesis of Tudor domain aromatic cage\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — reciprocal Co-IP with MS-confirmed methylation, replicated across multiple studies\",\n      \"pmids\": [\"19918066\", \"19926723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TDRD6 is essential for spermiogenesis and chromatoid body (CB) architecture: Tdrd6-/- mice arrest at round spermatid stage, producing 'ghost' CBs with greatly disrupted architecture, and CB components MAEL, MIWI, and MVH fail to localize to CBs in the absence of TDRD6.\",\n      \"method\": \"Tdrd6 knockout mouse (loss-of-function), immunofluorescence, electron microscopy of CB ultrastructure\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype and multiple orthogonal methods\",\n      \"pmids\": [\"19345099\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Loss of TDRD6 leads to upregulation of more than 50 miRNAs, including precursor (pre-) and primary (pri-) miRNA forms, indicating TDRD6 is required for proper mature and precursor miRNA expression in testes.\",\n      \"method\": \"Tdrd6 knockout mouse, small RNA sequencing/microarray, qRT-PCR of pre- and pri-miRNAs\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with transcriptome-wide miRNA profiling and qRT-PCR validation\",\n      \"pmids\": [\"19345099\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TDRD6, TDRD1, and TDRD7 co-localize to nuage (chromatoid bodies) in mouse male germ cells and form a ribonucleoprotein complex together; this localization is downstream of MVH (mouse VASA homolog), as it is disrupted in Mvh mutants. A single Tudor domain is sufficient as a structural unit for nuage localization, but the repeated Tudor domain architecture is functionally essential for germ cell differentiation.\",\n      \"method\": \"Immunofluorescence co-localization, co-immunoprecipitation, analysis in Mvh mutant mice, overexpression of truncated dominant-negative forms\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including genetic epistasis (Mvh mutant), Co-IP, and domain truncation experiments\",\n      \"pmids\": [\"17141210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"TDRD6 and TDRD7 together orchestrate chromatoid body biogenesis in concert: single and double knockouts show that TDRD7 is required for initial CB establishment and fusion with processing bodies/GW bodies, while TDRD6 functions at a later stage of spermiogenesis when CBs exhibit aggresome-like properties. TDRD6 does not affect retrotransposons, distinguishing its pathway from TDRD1 and TDRD9.\",\n      \"method\": \"Single and double Tdrd7/Tdrd6 knockout mice, genetic epistasis, immunofluorescence, histology\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — double knockout genetic epistasis with defined phenotypic readouts\",\n      \"pmids\": [\"21670278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MIWI binds to TDRD6 in an sDMA-dependent manner, demonstrating that sDMA modification of PIWI proteins is required for their interaction with Tudor-domain proteins including TDRD6, representing an evolutionarily conserved mechanism in germ cells.\",\n      \"method\": \"Co-immunoprecipitation in mouse, sDMA dependency tested biochemically\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with methylation-dependency test, cross-species validation\",\n      \"pmids\": [\"19926723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mouse VASA homolog (MVH) associates with TDRD6 (and TDRD1) in an arginine methylation-dependent manner, as symmetrically and asymmetrically dimethylated arginines are found on Vasa proteins and PRMT5 is required for Vasa sDMA production.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry identification of dimethylarginines on Vasa, genetic perturbation of dPRMT5 in Drosophila\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with mass spectrometry, but TDRD6 interaction shown in single study\",\n      \"pmids\": [\"20080973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TDRD6 is required for the long 3' UTR-triggered nonsense-mediated mRNA decay (NMD) pathway in chromatoid bodies: TDRD6 is essential for UPF1 localization to CBs, for UPF1-UPF2 and UPF1-MVH interactions, and for association of long 3' UTR mRNAs with UPF1/UPF2. Loss of TDRD6 increases stability and translational activity of long 3' UTR mRNAs but does not impair downstream exon-exon junction-triggered NMD.\",\n      \"method\": \"Tdrd6 knockout mice, proteome analysis of purified CBs, co-immunoprecipitation (UPF1-UPF2, UPF1-MVH), RNA-immunoprecipitation, polysome profiling\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods including CB proteomics, Co-IP, RNA-IP, and translational assays in KO mouse\",\n      \"pmids\": [\"27149095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In meiotic prophase I spermatocytes, TDRD6 interacts with PRMT5 (protein arginine methyltransferase 5) and with spliceosomal core protein SmB in an arginine methylation-dependent and RNA-independent manner. Loss of TDRD6 reduces PRMT5-SmB association and SmB arginine dimethylation, impairs spliceosome assembly (resulting in 3.5-fold increased U5 snRNP levels), decreases SMN-positive bodies and Cajal bodies, and causes widespread splicing defects including aberrant intron/exon usage.\",\n      \"method\": \"Co-immunoprecipitation (TDRD6-PRMT5, TDRD6-SmB), RNA-independence confirmed, Tdrd6 KO spermatocytes, immunofluorescence of nuclear bodies, transcriptome analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — KO mouse with multiple orthogonal methods: Co-IP, transcriptomics, snRNP quantification, nuclear body imaging\",\n      \"pmids\": [\"28263986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In zebrafish, Tdrd6a interacts with Bucky ball (Buc), a prion-like protein required for Balbiani body formation, affecting Buc mobility and aggregation properties. Loss of Tdrd6a-Buc interaction causes defects in germ cell development, establishing Tdrd6a as a regulator of phase-separated germ plasm compartment assembly.\",\n      \"method\": \"Co-immunoprecipitation, live imaging (FRAP to assess mobility), genetic KO/knockdown in zebrafish, germ cell quantification\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, FRAP, and KO with defined developmental phenotype\",\n      \"pmids\": [\"30086300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"MIWI N-terminal arginines (NTRs) mediate interaction with TDRD6 that is necessary for chromatoid body compaction during spermiogenesis, as demonstrated by MIWI NTR mutant mice lacking this interaction.\",\n      \"method\": \"MIWI NTR knock-in mutant mice, immunofluorescence of CB compaction, Co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KI mutant mouse with defined CB phenotype and biochemical interaction mapping\",\n      \"pmids\": [\"38520410\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Bi-allelic loss-of-function TDRD6 variants in humans cause spermiogenesis defects including acrosomal hypoplasia, reduced sperm concentration, and impaired motility; in patient spermatids, chromatoid body components DDX4 (MVH) and UPF1 are mislocalized, and scRNA-seq reveals TDRD6 regulates mRNA metabolism processes involved in spermatid differentiation and cytoplasmic translation.\",\n      \"method\": \"Whole-exome sequencing, CRISPR-Cas9 Tdrd6 KO mice, immunofluorescence, immunoblotting, ultrastructural analysis, total RNA-seq, single-cell RNA-seq\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — human genetics confirmed in KO mouse model with multiple orthogonal methods\",\n      \"pmids\": [\"38341271\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TDRD6 is a multi-Tudor domain protein that localizes to chromatoid bodies in male germ cells downstream of MVH, where it acts as a scaffold that (1) recruits PIWI proteins (MIWI, MILI) via recognition of their symmetrically dimethylated arginine N-terminal repeats to maintain CB architecture and compaction, (2) enables the long 3' UTR-triggered NMD pathway by promoting UPF1 localization and UPF1-UPF2-MVH interactions within the CB, and (3) in meiotic spermatocytes, interacts with PRMT5 to promote arginine methylation of spliceosomal SmB and spliceosome maturation, thereby regulating mRNA splicing; collectively, loss of TDRD6 arrests spermiogenesis at the round spermatid stage, abolishes CB integrity, dysregulates miRNA expression, and causes male infertility in both mice and humans.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TDRD6 is a multi-Tudor domain scaffold protein essential for male germ cell differentiation, functioning primarily within chromatoid bodies (CBs) to organize ribonucleoprotein complexes required for post-transcriptional gene regulation during spermiogenesis. TDRD6 recruits PIWI proteins (MIWI, MILI) through recognition of their symmetrically dimethylated arginine residues, and this interaction is necessary for CB compaction and proper localization of CB components including MAEL, MVH, and UPF1 [PMID:19918066, PMID:19345099, PMID:38520410]. Within CBs, TDRD6 enables a long 3′ UTR-triggered nonsense-mediated mRNA decay pathway by promoting UPF1–UPF2–MVH interactions, and separately, in meiotic spermatocytes it facilitates PRMT5-dependent arginine methylation of spliceosomal SmB to promote spliceosome maturation and correct mRNA splicing [PMID:27149095, PMID:28263986]. Bi-allelic loss-of-function TDRD6 variants in humans cause spermiogenesis failure with acrosomal hypoplasia, CB disassembly, and male infertility [PMID:38341271].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing that TDRD6 localizes to nuage/chromatoid bodies in male germ cells as part of a TDRD1–TDRD6–TDRD7 ribonucleoprotein complex downstream of MVH resolved the cellular compartment and epistatic hierarchy in which TDRD6 operates.\",\n      \"evidence\": \"Immunofluorescence co-localization, co-immunoprecipitation, and Mvh mutant analysis in mouse testes\",\n      \"pmids\": [\"17141210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular function of TDRD6 within CBs unknown\", \"Direct versus indirect dependence on MVH unresolved\", \"Whether Tudor domain multiplicity has distinct partner specificity not tested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrating that TDRD6 binds MIWI and MILI via symmetrically dimethylated arginines, and that loss of TDRD6 disrupts CB architecture and arrests spermiogenesis at the round spermatid stage, established TDRD6 as a methylarginine-reading scaffold essential for CB integrity and male fertility.\",\n      \"evidence\": \"Tdrd6 knockout mice with electron microscopy, reciprocal co-immunoprecipitation, mass spectrometry of sDMA marks, and miRNA profiling\",\n      \"pmids\": [\"19918066\", \"19926723\", \"19345099\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TDRD6 loss leads to miRNA dysregulation mechanistically unclear\", \"Whether TDRD6 directly processes or merely stabilizes miRNA precursors unknown\", \"Structural basis of multi-Tudor domain engagement with multiple PIWI partners unresolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showing that MVH/VASA associates with TDRD6 in an arginine methylation-dependent manner extended the sDMA-Tudor recognition paradigm beyond PIWI proteins to the core CB helicase.\",\n      \"evidence\": \"Co-immunoprecipitation and mass spectrometry of dimethylarginines on Vasa in mouse\",\n      \"pmids\": [\"20080973\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TDRD6–MVH interaction demonstrated in a single study without reciprocal validation\", \"Which Tudor domains of TDRD6 engage MVH not mapped\", \"Functional consequence of disrupting TDRD6–MVH interaction specifically not tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Genetic epistasis using Tdrd6/Tdrd7 single and double knockouts delineated a sequential CB biogenesis program where TDRD7 acts early (CB establishment and P-body fusion) and TDRD6 acts later during CB maturation, separating TDRD6 function from retrotransposon silencing pathways.\",\n      \"evidence\": \"Single and double Tdrd6/Tdrd7 knockout mice with immunofluorescence and histology\",\n      \"pmids\": [\"21670278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of temporal handoff from TDRD7 to TDRD6 unknown\", \"What triggers the transition from P-body-like to aggresome-like CB properties is unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Discovering that TDRD6 is required for UPF1 recruitment to CBs and for UPF1–UPF2–MVH complex formation revealed a previously unknown function: TDRD6 enables long 3′ UTR-triggered NMD within the chromatoid body, a pathway distinct from canonical exon-junction-triggered NMD.\",\n      \"evidence\": \"Tdrd6 knockout mice with CB proteomics, co-immunoprecipitation of UPF1–UPF2 and UPF1–MVH, RNA-immunoprecipitation, and polysome profiling\",\n      \"pmids\": [\"27149095\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TDRD6 directly contacts UPF1 or acts through an intermediary not determined\", \"How CB-localized NMD is coupled to translational repression mechanistically unclear\", \"Whether this NMD function is conserved outside mouse germ cells unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identification of TDRD6 interaction with PRMT5 and spliceosomal SmB in meiotic spermatocytes, and demonstration that TDRD6 loss impairs SmB arginine methylation, spliceosome assembly, and Cajal body formation, uncovered a nuclear function for TDRD6 in RNA splicing regulation distinct from its cytoplasmic CB role.\",\n      \"evidence\": \"Co-immunoprecipitation of TDRD6–PRMT5 and TDRD6–SmB (RNA-independent), Tdrd6 KO spermatocyte transcriptomics, snRNP quantification, and nuclear body immunofluorescence\",\n      \"pmids\": [\"28263986\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TDRD6 acts as a direct scaffold bridging PRMT5 to SmB or modulates PRMT5 catalytic activity is unresolved\", \"Full catalog of splicing events affected and their functional consequences in spermatogenesis not mapped\", \"How nuclear and cytoplasmic TDRD6 functions are coordinated during the meiosis-to-spermiogenesis transition unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"In zebrafish, demonstration that Tdrd6a interacts with the prion-like protein Bucky ball and regulates its mobility within the Balbiani body established TDRD6 as a regulator of phase-separated germ plasm compartments beyond mammalian CBs.\",\n      \"evidence\": \"Co-immunoprecipitation, FRAP live imaging, and genetic knockout/knockdown in zebrafish with germ cell quantification\",\n      \"pmids\": [\"30086300\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether mammalian TDRD6 similarly regulates phase separation properties of CB components not tested\", \"Structural basis of Tdrd6a–Buc interaction not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"MIWI knock-in mice lacking N-terminal arginine repeats confirmed that the MIWI–TDRD6 sDMA-dependent interaction is specifically required for CB compaction during spermiogenesis, moving beyond correlative knockout data to a defined interaction interface in vivo.\",\n      \"evidence\": \"MIWI NTR knock-in mutant mice with CB compaction assays and co-immunoprecipitation\",\n      \"pmids\": [\"38520410\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other Tudor-domain proteins partially compensate for TDRD6 loss in CB compaction not addressed\", \"Stoichiometry of MIWI–TDRD6 complexes within CBs unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Discovery that bi-allelic loss-of-function TDRD6 variants cause human male infertility with acrosomal hypoplasia, CB component mislocalization, and dysregulated mRNA metabolism confirmed the mouse phenotype translates to a human Mendelian disorder.\",\n      \"evidence\": \"Whole-exome sequencing in infertile men, CRISPR-Cas9 Tdrd6 KO mice, immunofluorescence, scRNA-seq\",\n      \"pmids\": [\"38341271\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full allelic spectrum and genotype–phenotype correlations in humans not established\", \"Whether partial loss of TDRD6 function causes subfertility rather than infertility unknown\", \"Therapeutic rescue strategies not explored\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis for how TDRD6's multiple Tudor domains simultaneously engage distinct methylated partners (MIWI, MILI, MVH, SmB) and how this multivalent binding organizes CB and nuclear body architecture remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of any TDRD6 Tudor domain in complex with a methylated peptide\", \"No reconstitution of TDRD6-dependent CB condensation in vitro\", \"How TDRD6 coordinates its distinct splicing, NMD, and PIWI-pathway functions temporally during spermatogenesis remains unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 7, 8, 10]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3, 7]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008953854\", \"supporting_discovery_ids\": [2, 7, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 7, 8]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 4, 9, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"complexes\": [\n      \"chromatoid body\"\n    ],\n    \"partners\": [\n      \"MIWI\",\n      \"MILI\",\n      \"MVH\",\n      \"UPF1\",\n      \"PRMT5\",\n      \"SmB\",\n      \"TDRD1\",\n      \"TDRD7\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\nWait, I need to fix the pathway entries. I accidentally included a malformed GO term. Let me correct:\n\n```json\n{\n  \"mechanistic_narrative\": \"TDRD6 is a multi-Tudor domain scaffold protein essential for male germ cell differentiation, functioning primarily within chromatoid bodies (CBs) to organize ribonucleoprotein complexes required for post-transcriptional gene regulation during spermiogenesis. TDRD6 recruits PIWI proteins (MIWI, MILI) through recognition of their symmetrically dimethylated arginine residues, and this interaction is necessary for CB compaction and proper localization of CB components including MAEL, MVH, and UPF1 [PMID:19918066, PMID:19345099, PMID:38520410]. Within CBs, TDRD6 enables a long 3′ UTR-triggered nonsense-mediated mRNA decay pathway by promoting UPF1–UPF2–MVH interactions, and separately, in meiotic spermatocytes it facilitates PRMT5-dependent arginine methylation of spliceosomal SmB to promote spliceosome maturation and correct mRNA splicing [PMID:27149095, PMID:28263986]. Bi-allelic loss-of-function TDRD6 variants in humans cause spermiogenesis failure with acrosomal hypoplasia, CB disassembly, and male infertility [PMID:38341271].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing that TDRD6 localizes to nuage/chromatoid bodies in male germ cells as part of a TDRD1–TDRD6–TDRD7 ribonucleoprotein complex downstream of MVH resolved the cellular compartment and epistatic hierarchy in which TDRD6 operates.\",\n      \"evidence\": \"Immunofluorescence co-localization, co-immunoprecipitation, and Mvh mutant analysis in mouse testes\",\n      \"pmids\": [\"17141210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular function of TDRD6 within CBs unknown\", \"Direct versus indirect dependence on MVH unresolved\", \"Whether Tudor domain multiplicity has distinct partner specificity not tested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrating that TDRD6 binds MIWI and MILI via symmetrically dimethylated arginines, and that loss of TDRD6 disrupts CB architecture and arrests spermiogenesis at the round spermatid stage, established TDRD6 as a methylarginine-reading scaffold essential for CB integrity and male fertility.\",\n      \"evidence\": \"Tdrd6 knockout mice with electron microscopy, reciprocal co-immunoprecipitation, mass spectrometry of sDMA marks, and miRNA profiling\",\n      \"pmids\": [\"19918066\", \"19926723\", \"19345099\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TDRD6 loss leads to miRNA dysregulation mechanistically unclear\", \"Whether TDRD6 directly processes or merely stabilizes miRNA precursors unknown\", \"Structural basis of multi-Tudor domain engagement with multiple PIWI partners unresolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showing that MVH/VASA associates with TDRD6 in an arginine methylation-dependent manner extended the sDMA-Tudor recognition paradigm beyond PIWI proteins to the core CB helicase.\",\n      \"evidence\": \"Co-immunoprecipitation and mass spectrometry of dimethylarginines on Vasa in mouse\",\n      \"pmids\": [\"20080973\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TDRD6–MVH interaction demonstrated in a single study without reciprocal validation\", \"Which Tudor domains of TDRD6 engage MVH not mapped\", \"Functional consequence of disrupting TDRD6–MVH interaction specifically not tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Genetic epistasis using Tdrd6/Tdrd7 single and double knockouts delineated a sequential CB biogenesis program where TDRD7 acts early and TDRD6 acts later during CB maturation, separating TDRD6 function from retrotransposon silencing pathways.\",\n      \"evidence\": \"Single and double Tdrd6/Tdrd7 knockout mice with immunofluorescence and histology\",\n      \"pmids\": [\"21670278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of temporal handoff from TDRD7 to TDRD6 unknown\", \"What triggers the transition from P-body-like to aggresome-like CB properties is unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Discovering that TDRD6 is required for UPF1 recruitment to CBs and for UPF1–UPF2–MVH complex formation revealed a function in long 3′ UTR-triggered NMD within the chromatoid body, distinct from canonical exon-junction-triggered NMD.\",\n      \"evidence\": \"Tdrd6 knockout mice with CB proteomics, co-immunoprecipitation of UPF1–UPF2 and UPF1–MVH, RNA-immunoprecipitation, and polysome profiling\",\n      \"pmids\": [\"27149095\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TDRD6 directly contacts UPF1 or acts through an intermediary not determined\", \"How CB-localized NMD is coupled to translational repression mechanistically unclear\", \"Whether this NMD function is conserved outside mouse germ cells unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identification of TDRD6 interaction with PRMT5 and spliceosomal SmB in meiotic spermatocytes, and demonstration that TDRD6 loss impairs SmB arginine methylation, spliceosome assembly, and Cajal body formation, uncovered a nuclear function for TDRD6 in RNA splicing regulation.\",\n      \"evidence\": \"Co-immunoprecipitation of TDRD6–PRMT5 and TDRD6–SmB (RNA-independent), Tdrd6 KO spermatocyte transcriptomics, snRNP quantification, and nuclear body immunofluorescence\",\n      \"pmids\": [\"28263986\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TDRD6 acts as a direct scaffold bridging PRMT5 to SmB or modulates PRMT5 catalytic activity is unresolved\", \"Full catalog of affected splicing events not mapped\", \"How nuclear and cytoplasmic TDRD6 functions are coordinated during spermatogenesis unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"In zebrafish, demonstration that Tdrd6a interacts with the prion-like protein Bucky ball and regulates its mobility within the Balbiani body established TDRD6 as a regulator of phase-separated germ plasm compartments beyond mammalian CBs.\",\n      \"evidence\": \"Co-immunoprecipitation, FRAP live imaging, and genetic knockout/knockdown in zebrafish with germ cell quantification\",\n      \"pmids\": [\"30086300\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether mammalian TDRD6 similarly regulates phase separation properties of CB components not tested\", \"Structural basis of Tdrd6a–Buc interaction not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"MIWI knock-in mice lacking N-terminal arginine repeats confirmed that the MIWI–TDRD6 sDMA-dependent interaction is specifically required for CB compaction during spermiogenesis, moving beyond correlative knockout data to a defined interaction interface.\",\n      \"evidence\": \"MIWI NTR knock-in mutant mice with CB compaction assays and co-immunoprecipitation\",\n      \"pmids\": [\"38520410\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other Tudor-domain proteins partially compensate for TDRD6 loss in CB compaction not addressed\", \"Stoichiometry of MIWI–TDRD6 complexes within CBs unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Discovery that bi-allelic loss-of-function TDRD6 variants cause human male infertility with acrosomal hypoplasia and CB component mislocalization confirmed the mouse phenotype translates to a human Mendelian disorder.\",\n      \"evidence\": \"Whole-exome sequencing in infertile men, CRISPR-Cas9 Tdrd6 KO mice, immunofluorescence, scRNA-seq\",\n      \"pmids\": [\"38341271\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full allelic spectrum and genotype–phenotype correlations in humans not established\", \"Whether partial loss of TDRD6 function causes subfertility rather than infertility unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis for how TDRD6's multiple Tudor domains simultaneously engage distinct methylated partners and how this multivalent binding organizes CB and nuclear body architecture remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution structure of any TDRD6 Tudor domain in complex with a methylated peptide\", \"No reconstitution of TDRD6-dependent CB condensation in vitro\", \"How TDRD6 coordinates its distinct splicing, NMD, and PIWI-pathway functions temporally during spermatogenesis remains unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 7, 8, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3, 7]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 7, 8]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 4, 9, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7, 8]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [1, 4, 11]}\n    ],\n    \"complexes\": [\n      \"chromatoid body\"\n    ],\n    \"partners\": [\n      \"MIWI\",\n      \"MILI\",\n      \"MVH\",\n      \"UPF1\",\n      \"PRMT5\",\n      \"SmB\",\n      \"TDRD1\",\n      \"TDRD7\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}