{"gene":"DNAI4","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2026,"finding":"DNAI4 (dynein axonemal intermediate chain 4) is required for sperm flagellum assembly and male fertility in mice; Dnai4 knockout causes oligoasthenoteratospermia with MMAF, including disorganized mitochondrial sheaths, outer dense fibers, '9+2' axonemes, and missing inner dynein arms (IDA) and outer dynein arms. The IDA component DNAH10 was markedly reduced in testes and sperm tails of knockout mice.","method":"CRISPR/Cas9 knockout mice, electron microscopy, western blot, RT-PCR","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO mouse with defined male-specific infertility phenotype, ultrastructural analysis by electron microscopy, and molecular readout (DNAH10 reduction); single lab but multiple orthogonal methods","pmids":["42083518"],"is_preprint":false},{"year":2026,"finding":"DNAI4 physically interacts with the intraflagellar transport protein IFT144 (a retrograde IFT-A component) within mouse testes, and Dnai4 deletion leads to downregulation of other IFT-A members IFT140, IFT122, and IFT121 in sperm tails, placing DNAI4 upstream of retrograde intraflagellar transport.","method":"Co-immunoprecipitation from testes lysates; western blot of IFT subunits in Dnai4 KO sperm tails","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal Co-IP from testes and downstream IFT subunit loss confirmed by western blot, single lab, single study","pmids":["42083518"],"is_preprint":false},{"year":2019,"finding":"WDR78 (DNAI4) is the vertebrate orthologue of Chlamydomonas IC138 (an inner dynein arm intermediate chain). Wdr78 associates with Dynein-f subunits Dnah2 (a heavy chain) and Wdr63 (IC140 orthologue), and depletion of Wdr78 by RNAi causes all Dynein-f heavy chains and intermediate chains to fail to localize in mouse ependymal cilia, paralyzing ciliary beat. Zebrafish Wdr78 morphants display ciliopathy phenotypes (curved body, hydrocephalus, randomized left-right asymmetry, pronephric cysts) with paralyzed pronephric cilia.","method":"Co-immunoprecipitation, RNAi knockdown, high-speed video microscopy of cilia, zebrafish morpholino knockdown, immunofluorescence/localization","journal":"Journal of molecular cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP identifying Dynein-f complex partners, RNAi in two vertebrate model systems (mouse cells and zebrafish) with defined ciliary beat and localization phenotypes, multiple orthogonal methods","pmids":["30060180"],"is_preprint":false},{"year":2021,"finding":"WDR78 (DNAI4) interacts with WDR63 mainly via WD40-repeat domain interaction, and WDR63 requires WDR78 for proper inner dynein arm (IDA) assembly in sperm flagella. Loss of WDR63 causes absent inner dynein arms and disorganized '9+2' axonemes in spermatozoa.","method":"Co-immunoprecipitation (WDR63–WDR78 interaction), CRISPR-Cas9 Wdr63 knockout mice, transmission electron microscopy","journal":"Cell discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP mapping WD40-domain interaction plus KO mouse TEM evidence; WDR78 role inferred through its identified interaction partner WDR63, single lab","pmids":["34782613"],"is_preprint":false},{"year":2025,"finding":"WDR78 (DNAI4) interacts with TCTEX1D2 in mouse testes as a component of the inner dynein arm (axonemal dynein), establishing WDR78 as a binding partner of TCTEX1D2 within the inner dynein arm complex during sperm flagellum formation.","method":"Co-immunoprecipitation from mouse testes lysates","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP identifying WDR78 as IDA-associated binding partner of TCTEX1D2, replicated in both peer-reviewed paper and preprint from same lab","pmids":["39827215"],"is_preprint":false},{"year":2024,"finding":"WDR78 (DNAI4) interacts with TCTEX1D2 in mouse testes as a component of the inner dynein arm, confirmed independently in a preprint from the same laboratory group.","method":"Co-immunoprecipitation from mouse testes lysates","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP in preprint, same lab as peer-reviewed confirmation, no additional orthogonal method","pmids":["bio_10.1101_2024.06.27.600786"],"is_preprint":true},{"year":2013,"finding":"Overexpression of the splicing factor ZRANB2 in HeLa cells influences the alternative splicing of the WDR78 (DNAI4) primary transcript, indicating that WDR78 pre-mRNA is a regulated splicing target of ZRANB2.","method":"ZRANB2 overexpression in HeLa cells followed by Affymetrix Human Exon array transcriptome analysis","journal":"Molecular biology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single transcriptomic screen identifying WDR78 as one of many ZRANB2 splicing targets; no direct mechanistic validation for WDR78 specifically","pmids":["23666063"],"is_preprint":false}],"current_model":"DNAI4 (also known as WDR78) is an inner dynein arm intermediate chain (vertebrate orthologue of Chlamydomonas IC138) that localizes to motile cilia and sperm flagella, where it is essential for ciliary beat and sperm flagellum assembly: it physically associates with Dynein-f subunits (Dnah2, Wdr63/IC140 orthologue) and the IFT-A retrograde transport component IFT144, and its loss abrogates Dynein-f axonemal localization, disrupts inner and outer dynein arm assembly, causes MMAF and male infertility in mice, and produces ciliopathy phenotypes in zebrafish."},"narrative":{"mechanistic_narrative":"DNAI4 (also known as WDR78) is an axonemal inner dynein arm intermediate chain essential for the assembly and motility of motile cilia and sperm flagella [PMID:30060180, PMID:42083518]. It is the vertebrate orthologue of Chlamydomonas IC138 and functions as a core component of the Dynein-f inner dynein arm complex, physically associating with the heavy chain DNAH2 and the IC140 orthologue WDR63 through a WD40-repeat-mediated interaction; depletion of DNAI4 prevents Dynein-f heavy and intermediate chains from localizing to the axoneme and paralyzes ciliary beat [PMID:30060180, PMID:34782613]. Within the inner dynein arm it also binds TCTEX1D2 [PMID:39827215]. In sperm, loss of DNAI4 produces oligoasthenoteratospermia with multiple morphological abnormalities of the flagellum—disorganized mitochondrial sheaths, outer dense fibers, and '9+2' axonemes missing both inner and outer dynein arms—accompanied by marked reduction of the inner dynein arm component DNAH10 [PMID:42083518]. DNAI4 additionally interacts with the retrograde IFT-A component IFT144, and its loss downregulates other IFT-A subunits (IFT140, IFT122, IFT121) in sperm tails, linking it to intraflagellar transport [PMID:42083518]. Loss-of-function causes male infertility in mice and ciliopathy phenotypes including hydrocephalus, randomized left-right asymmetry, and pronephric cysts in zebrafish [PMID:42083518, PMID:30060180].","teleology":[{"year":2013,"claim":"Before its ciliary role was known, WDR78/DNAI4 was identified as a regulated transcript, establishing that its pre-mRNA is subject to alternative splicing control.","evidence":"ZRANB2 overexpression in HeLa cells with exon array transcriptome analysis","pmids":["23666063"],"confidence":"Low","gaps":["Single transcriptomic screen with no validation specific to WDR78","No connection to ciliary or flagellar function established","Functional consequence of splice regulation unknown"]},{"year":2019,"claim":"Established DNAI4/WDR78 as the vertebrate IC138 orthologue and a Dynein-f inner dynein arm intermediate chain required for axonemal dynein localization and ciliary motility, answering what protein family it belongs to and what it does.","evidence":"Co-IP identifying Dnah2 and Wdr63 partners, RNAi in mouse ependymal cilia, and zebrafish morpholino knockdown with ciliary beat and localization readouts","pmids":["30060180"],"confidence":"High","gaps":["Morpholino-based zebrafish phenotypes not confirmed by mutant","Mechanism by which it scaffolds Dynein-f heavy chains unresolved","Structural basis of complex assembly not defined"]},{"year":2021,"claim":"Mapped the DNAI4-WDR63 interaction to WD40-repeat domains and showed WDR63 requires DNAI4 for inner dynein arm assembly in sperm, defining the molecular interface for IDA construction.","evidence":"Co-IP domain mapping plus Wdr63 CRISPR knockout mouse TEM","pmids":["34782613"],"confidence":"Medium","gaps":["DNAI4 role inferred via its WDR63 partner rather than direct DNAI4 manipulation","Single lab","Stoichiometry of the IDA subcomplex not determined"]},{"year":2025,"claim":"Identified TCTEX1D2 as an additional inner dynein arm binding partner of DNAI4, expanding the roster of IDA subunits it associates with during flagellum formation.","evidence":"Co-immunoprecipitation from mouse testes lysates (with concordant preprint from same lab)","pmids":["39827215","bio_10.1101_2024.06.27.600786"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal or orthogonal validation","Same lab for both reports","Functional consequence of the interaction not tested"]},{"year":2026,"claim":"Direct DNAI4 knockout established its requirement for sperm flagellum assembly and male fertility and linked it to retrograde IFT, resolving its in vivo physiological role and a transport connection.","evidence":"CRISPR/Cas9 Dnai4 knockout mice with EM, western blot (DNAH10 loss), and Co-IP with IFT144 plus IFT-A subunit loss","pmids":["42083518"],"confidence":"High","gaps":["Whether the IFT144 interaction is direct versus complex-mediated not resolved","Human disease relevance not tested","How DNAI4 links IDA assembly to retrograde IFT mechanistically unknown"]},{"year":null,"claim":"How DNAI4 mechanistically coordinates inner dynein arm assembly with intraflagellar transport, and whether DNAI4 variants cause human ciliopathy or infertility, remain open.","evidence":"","pmids":[],"confidence":"High","gaps":["No human patient mutation evidence in the corpus","No structural model of the DNAI4-containing IDA complex","Mechanism coupling IFT-A retrograde transport to dynein arm docking undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[2,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,0]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[2,0]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[2,0]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0]}],"complexes":["inner dynein arm (Dynein-f)","axoneme"],"partners":["DNAH2","WDR63","TCTEX1D2","IFT144","DNAH10"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5VTH9","full_name":"Dynein axonemal intermediate chain 4","aliases":["WD repeat-containing protein 78"],"length_aa":848,"mass_kda":94.6,"function":"Plays a critical role in the assembly of axonemal dynein complex, thereby playing a role in ciliary motility","subcellular_location":"Cytoplasm, cytoskeleton, flagellum axoneme; Cytoplasm, cytoskeleton, cilium axoneme; Dynein axonemal particle","url":"https://www.uniprot.org/uniprotkb/Q5VTH9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAI4","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DNAI4","total_profiled":1310},"omim":[{"mim_id":"619156","title":"DYNEIN, AXONEMAL, INTERMEDIATE CHAIN 4; DNAI4","url":"https://www.omim.org/entry/619156"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Flagellar centriole","reliability":"Approved"},{"location":"Mid piece","reliability":"Additional"},{"location":"Principal piece","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":19.4},{"tissue":"fallopian tube","ntpm":26.1},{"tissue":"testis","ntpm":32.9}],"url":"https://www.proteinatlas.org/search/DNAI4"},"hgnc":{"alias_symbol":["DIC4","FLJ23129"],"prev_symbol":["WDR78"]},"alphafold":{"accession":"Q5VTH9","domains":[{"cath_id":"2.130.10.10","chopping":"479-639_659-841","consensus_level":"medium","plddt":90.242,"start":479,"end":841}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VTH9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VTH9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VTH9-F1-predicted_aligned_error_v6.png","plddt_mean":67.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAI4","jax_strain_url":"https://www.jax.org/strain/search?query=DNAI4"},"sequence":{"accession":"Q5VTH9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5VTH9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5VTH9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VTH9"}},"corpus_meta":[{"pmid":"10593888","id":"PMC_10593888","title":"Distinct specificities of inwardly rectifying K(+) channels for phosphoinositides.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10593888","citation_count":177,"is_preprint":false},{"pmid":"18562499","id":"PMC_18562499","title":"Direct regulation of BK channels by phosphatidylinositol 4,5-bisphosphate as a novel signaling pathway.","date":"2008","source":"The Journal of general physiology","url":"https://pubmed.ncbi.nlm.nih.gov/18562499","citation_count":85,"is_preprint":false},{"pmid":"1170169","id":"PMC_1170169","title":"Lipid specificity of beta-hydroxybutyrate dehydrogenase activation.","date":"1975","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1170169","citation_count":73,"is_preprint":false},{"pmid":"25105564","id":"PMC_25105564","title":"Structural basis of nSH2 regulation and lipid binding in 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cancer","url":"https://pubmed.ncbi.nlm.nih.gov/2335395","citation_count":37,"is_preprint":false},{"pmid":"30060180","id":"PMC_30060180","title":"Vertebrate Dynein-f depends on Wdr78 for axonemal localization and is essential for ciliary beat.","date":"2019","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/30060180","citation_count":34,"is_preprint":false},{"pmid":"1756493","id":"PMC_1756493","title":"Chromosomal abnormalities in giant cell tumors of bone.","date":"1991","source":"Cancer genetics and cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/1756493","citation_count":32,"is_preprint":false},{"pmid":"23666063","id":"PMC_23666063","title":"ZRANB2 localizes to supraspliceosomes and influences the alternative splicing of multiple genes in the transcriptome.","date":"2013","source":"Molecular biology 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Report of a case and review of the literature.","date":"1999","source":"Cancer genetics and cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/10432932","citation_count":16,"is_preprint":false},{"pmid":"33378017","id":"PMC_33378017","title":"Molecular insights into the development of hepatic metastases in colorectal cancer: a metastasis prediction study.","date":"2020","source":"European review for medical and pharmacological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33378017","citation_count":9,"is_preprint":false},{"pmid":"24641677","id":"PMC_24641677","title":"1,3-disubstituted-4-aminopyrazolo [3, 4-d] pyrimidines, a new class of potent inhibitors for phospholipase D.","date":"2014","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/24641677","citation_count":9,"is_preprint":false},{"pmid":"38247231","id":"PMC_38247231","title":"Tanreqing suppresses the proliferation and migration of non-small cell lung cancer cells by mediating the inactivation of the HIF1α signaling pathway via exosomal circ-WDR78.","date":"2024","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/38247231","citation_count":8,"is_preprint":false},{"pmid":"37371464","id":"PMC_37371464","title":"Multiple Inositol Polyphosphate Phosphatase Compartmentalization Separates Inositol Phosphate Metabolism from Inositol Lipid Signaling.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37371464","citation_count":7,"is_preprint":false},{"pmid":"39827215","id":"PMC_39827215","title":"TCTEX1D2 is essential for sperm flagellum formation in mice.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39827215","citation_count":5,"is_preprint":false},{"pmid":"22340903","id":"PMC_22340903","title":"Establishment and characterization of a new human acute myelomonocytic leukemia cell line JIH-3.","date":"2012","source":"Leukemia research","url":"https://pubmed.ncbi.nlm.nih.gov/22340903","citation_count":3,"is_preprint":false},{"pmid":"32721119","id":"PMC_32721119","title":"Tumorigenic effects of TLX overexpression in HEK 293T cells.","date":"2019","source":"Cancer reports (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/32721119","citation_count":2,"is_preprint":false},{"pmid":"26691755","id":"PMC_26691755","title":"Identifying New Drug Targets for Potent Phospholipase D Inhibitors: Combining Sequence Alignment, Molecular Docking, and Enzyme Activity/Binding Assays.","date":"2016","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/26691755","citation_count":2,"is_preprint":false},{"pmid":"36674645","id":"PMC_36674645","title":"Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36674645","citation_count":1,"is_preprint":false},{"pmid":"42083518","id":"PMC_42083518","title":"DNAI4 is required for flagellum assembly and male fertility in mice.","date":"2026","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/42083518","citation_count":0,"is_preprint":false},{"pmid":"41566712","id":"PMC_41566712","title":"Comparative genomics reveals evolutionary signatures of genes associated with jumping in beetles.","date":"2026","source":"Zoological research","url":"https://pubmed.ncbi.nlm.nih.gov/41566712","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.27.600786","title":"TCTEX1D2 has two distinct functions in sperm flagellum formation in mice; cytoplasmic dynein 2 and inner dynein arm","date":"2024-06-27","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.27.600786","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15078,"output_tokens":1933,"usd":0.037115,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8795,"output_tokens":2345,"usd":0.0513,"stage2_stop_reason":"end_turn"},"total_usd":0.088415,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2026,\n      \"finding\": \"DNAI4 (dynein axonemal intermediate chain 4) is required for sperm flagellum assembly and male fertility in mice; Dnai4 knockout causes oligoasthenoteratospermia with MMAF, including disorganized mitochondrial sheaths, outer dense fibers, '9+2' axonemes, and missing inner dynein arms (IDA) and outer dynein arms. The IDA component DNAH10 was markedly reduced in testes and sperm tails of knockout mice.\",\n      \"method\": \"CRISPR/Cas9 knockout mice, electron microscopy, western blot, RT-PCR\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO mouse with defined male-specific infertility phenotype, ultrastructural analysis by electron microscopy, and molecular readout (DNAH10 reduction); single lab but multiple orthogonal methods\",\n      \"pmids\": [\"42083518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"DNAI4 physically interacts with the intraflagellar transport protein IFT144 (a retrograde IFT-A component) within mouse testes, and Dnai4 deletion leads to downregulation of other IFT-A members IFT140, IFT122, and IFT121 in sperm tails, placing DNAI4 upstream of retrograde intraflagellar transport.\",\n      \"method\": \"Co-immunoprecipitation from testes lysates; western blot of IFT subunits in Dnai4 KO sperm tails\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal Co-IP from testes and downstream IFT subunit loss confirmed by western blot, single lab, single study\",\n      \"pmids\": [\"42083518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WDR78 (DNAI4) is the vertebrate orthologue of Chlamydomonas IC138 (an inner dynein arm intermediate chain). Wdr78 associates with Dynein-f subunits Dnah2 (a heavy chain) and Wdr63 (IC140 orthologue), and depletion of Wdr78 by RNAi causes all Dynein-f heavy chains and intermediate chains to fail to localize in mouse ependymal cilia, paralyzing ciliary beat. Zebrafish Wdr78 morphants display ciliopathy phenotypes (curved body, hydrocephalus, randomized left-right asymmetry, pronephric cysts) with paralyzed pronephric cilia.\",\n      \"method\": \"Co-immunoprecipitation, RNAi knockdown, high-speed video microscopy of cilia, zebrafish morpholino knockdown, immunofluorescence/localization\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP identifying Dynein-f complex partners, RNAi in two vertebrate model systems (mouse cells and zebrafish) with defined ciliary beat and localization phenotypes, multiple orthogonal methods\",\n      \"pmids\": [\"30060180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"WDR78 (DNAI4) interacts with WDR63 mainly via WD40-repeat domain interaction, and WDR63 requires WDR78 for proper inner dynein arm (IDA) assembly in sperm flagella. Loss of WDR63 causes absent inner dynein arms and disorganized '9+2' axonemes in spermatozoa.\",\n      \"method\": \"Co-immunoprecipitation (WDR63–WDR78 interaction), CRISPR-Cas9 Wdr63 knockout mice, transmission electron microscopy\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP mapping WD40-domain interaction plus KO mouse TEM evidence; WDR78 role inferred through its identified interaction partner WDR63, single lab\",\n      \"pmids\": [\"34782613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WDR78 (DNAI4) interacts with TCTEX1D2 in mouse testes as a component of the inner dynein arm (axonemal dynein), establishing WDR78 as a binding partner of TCTEX1D2 within the inner dynein arm complex during sperm flagellum formation.\",\n      \"method\": \"Co-immunoprecipitation from mouse testes lysates\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP identifying WDR78 as IDA-associated binding partner of TCTEX1D2, replicated in both peer-reviewed paper and preprint from same lab\",\n      \"pmids\": [\"39827215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"WDR78 (DNAI4) interacts with TCTEX1D2 in mouse testes as a component of the inner dynein arm, confirmed independently in a preprint from the same laboratory group.\",\n      \"method\": \"Co-immunoprecipitation from mouse testes lysates\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP in preprint, same lab as peer-reviewed confirmation, no additional orthogonal method\",\n      \"pmids\": [\"bio_10.1101_2024.06.27.600786\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Overexpression of the splicing factor ZRANB2 in HeLa cells influences the alternative splicing of the WDR78 (DNAI4) primary transcript, indicating that WDR78 pre-mRNA is a regulated splicing target of ZRANB2.\",\n      \"method\": \"ZRANB2 overexpression in HeLa cells followed by Affymetrix Human Exon array transcriptome analysis\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single transcriptomic screen identifying WDR78 as one of many ZRANB2 splicing targets; no direct mechanistic validation for WDR78 specifically\",\n      \"pmids\": [\"23666063\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAI4 (also known as WDR78) is an inner dynein arm intermediate chain (vertebrate orthologue of Chlamydomonas IC138) that localizes to motile cilia and sperm flagella, where it is essential for ciliary beat and sperm flagellum assembly: it physically associates with Dynein-f subunits (Dnah2, Wdr63/IC140 orthologue) and the IFT-A retrograde transport component IFT144, and its loss abrogates Dynein-f axonemal localization, disrupts inner and outer dynein arm assembly, causes MMAF and male infertility in mice, and produces ciliopathy phenotypes in zebrafish.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAI4 (also known as WDR78) is an axonemal inner dynein arm intermediate chain essential for the assembly and motility of motile cilia and sperm flagella [#2, #0]. It is the vertebrate orthologue of Chlamydomonas IC138 and functions as a core component of the Dynein-f inner dynein arm complex, physically associating with the heavy chain DNAH2 and the IC140 orthologue WDR63 through a WD40-repeat-mediated interaction; depletion of DNAI4 prevents Dynein-f heavy and intermediate chains from localizing to the axoneme and paralyzes ciliary beat [#2, #3]. Within the inner dynein arm it also binds TCTEX1D2 [#4]. In sperm, loss of DNAI4 produces oligoasthenoteratospermia with multiple morphological abnormalities of the flagellum—disorganized mitochondrial sheaths, outer dense fibers, and '9+2' axonemes missing both inner and outer dynein arms—accompanied by marked reduction of the inner dynein arm component DNAH10 [#0]. DNAI4 additionally interacts with the retrograde IFT-A component IFT144, and its loss downregulates other IFT-A subunits (IFT140, IFT122, IFT121) in sperm tails, linking it to intraflagellar transport [#1]. Loss-of-function causes male infertility in mice and ciliopathy phenotypes including hydrocephalus, randomized left-right asymmetry, and pronephric cysts in zebrafish [#0, #2].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Before its ciliary role was known, WDR78/DNAI4 was identified as a regulated transcript, establishing that its pre-mRNA is subject to alternative splicing control.\",\n      \"evidence\": \"ZRANB2 overexpression in HeLa cells with exon array transcriptome analysis\",\n      \"pmids\": [\"23666063\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single transcriptomic screen with no validation specific to WDR78\", \"No connection to ciliary or flagellar function established\", \"Functional consequence of splice regulation unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established DNAI4/WDR78 as the vertebrate IC138 orthologue and a Dynein-f inner dynein arm intermediate chain required for axonemal dynein localization and ciliary motility, answering what protein family it belongs to and what it does.\",\n      \"evidence\": \"Co-IP identifying Dnah2 and Wdr63 partners, RNAi in mouse ependymal cilia, and zebrafish morpholino knockdown with ciliary beat and localization readouts\",\n      \"pmids\": [\"30060180\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Morpholino-based zebrafish phenotypes not confirmed by mutant\", \"Mechanism by which it scaffolds Dynein-f heavy chains unresolved\", \"Structural basis of complex assembly not defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Mapped the DNAI4-WDR63 interaction to WD40-repeat domains and showed WDR63 requires DNAI4 for inner dynein arm assembly in sperm, defining the molecular interface for IDA construction.\",\n      \"evidence\": \"Co-IP domain mapping plus Wdr63 CRISPR knockout mouse TEM\",\n      \"pmids\": [\"34782613\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DNAI4 role inferred via its WDR63 partner rather than direct DNAI4 manipulation\", \"Single lab\", \"Stoichiometry of the IDA subcomplex not determined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified TCTEX1D2 as an additional inner dynein arm binding partner of DNAI4, expanding the roster of IDA subunits it associates with during flagellum formation.\",\n      \"evidence\": \"Co-immunoprecipitation from mouse testes lysates (with concordant preprint from same lab)\",\n      \"pmids\": [\"39827215\", \"bio_10.1101_2024.06.27.600786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP without reciprocal or orthogonal validation\", \"Same lab for both reports\", \"Functional consequence of the interaction not tested\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Direct DNAI4 knockout established its requirement for sperm flagellum assembly and male fertility and linked it to retrograde IFT, resolving its in vivo physiological role and a transport connection.\",\n      \"evidence\": \"CRISPR/Cas9 Dnai4 knockout mice with EM, western blot (DNAH10 loss), and Co-IP with IFT144 plus IFT-A subunit loss\",\n      \"pmids\": [\"42083518\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the IFT144 interaction is direct versus complex-mediated not resolved\", \"Human disease relevance not tested\", \"How DNAI4 links IDA assembly to retrograde IFT mechanistically unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNAI4 mechanistically coordinates inner dynein arm assembly with intraflagellar transport, and whether DNAI4 variants cause human ciliopathy or infertility, remain open.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No human patient mutation evidence in the corpus\", \"No structural model of the DNAI4-containing IDA complex\", \"Mechanism coupling IFT-A retrograde transport to dynein arm docking undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [2, 0]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [2, 0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"inner dynein arm (Dynein-f)\", \"axoneme\"],\n    \"partners\": [\"DNAH2\", \"WDR63\", \"TCTEX1D2\", \"IFT144\", \"DNAH10\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}