{"gene":"DNALI1","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2006,"finding":"Murine DNALI1 (Dnali1) protein localizes to sperm flagella and tracheal cilia, and its C-terminal region of cytoplasmic dynein heavy chain 1 was identified as a binding partner via yeast two-hybrid screening, confirmed by co-immunoprecipitation and co-localization experiments.","method":"Yeast two-hybrid screen with murine testicular cDNA library, co-immunoprecipitation, immunofluorescence co-localization","journal":"Molecular reproduction and development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and co-localization supporting yeast two-hybrid, single lab, two orthogonal methods","pmids":["16496424"],"is_preprint":false},{"year":2023,"finding":"DNALI1 is a light intermediate chain (LIC) component of a partial inner dynein arm (IDA) subspecies that includes DNAH1 and DNAH7 (but not DNAH10); loss of DNALI1 disrupts assembly and transport of fibrous sheath proteins AKAP3 and AKAP4, and DNALI1 interacts with cytoplasmic dynein complex proteins in the testis, suggesting a non-classical role in cytoplasmic dynein-mediated flagellar assembly.","method":"Bi-allelic patient mutation analysis, Dnali1-/- mouse model, immunofluorescence, immunoprecipitation, transmission electron microscopy","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal immunoprecipitation, knockout mouse model, and patient mutation converging on same mechanism across two species","pmids":["36792588"],"is_preprint":false},{"year":2023,"finding":"DNALI1 interacts with PACRG (stabilizes it) and is required for the localization of the MEIG1/PACRG complex within the manchette of elongating spermatids; DNALI1 deficiency in male germ cells disrupts manchette-based cargo transport (including SPAG16L) and impairs spermiogenesis without altering total testicular levels of MEIG1, PACRG, or SPAG16L.","method":"Co-immunoprecipitation, pull-down assays, conditional Dnali1 knockout mouse, immunofluorescence of spermatids, testis histology","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus pulldown plus in vivo KO with defined localization phenotype, single lab with multiple orthogonal methods","pmids":["37083624"],"is_preprint":false},{"year":2023,"finding":"Loss-of-function Dnali1 nonsense mutation in mice causes impaired sperm motility and male infertility with ultrastructural flagellar defects (asymmetrical distribution of longitudinal columns of the fibrous sheath), demonstrating DNALI1 is required for proper flagellar ultrastructure.","method":"Nonsense mutation knockin mouse model, sperm motility analysis, transmission electron microscopy, ICSI rescue","journal":"Basic and clinical andrology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined ultrastructural phenotype in KO mouse, single lab, TEM plus functional motility assay","pmids":["37993789"],"is_preprint":false},{"year":2024,"finding":"DNALI1 overexpression inhibits autophagosome-lysosome fusion and reduces autophagic flux under pathological (TBI) conditions, while DNALI1 silencing enhances autophagic flux and alleviates neurodegeneration in a CTE model; altered DNALI1 expression under normal conditions has no discernible effect on autophagy.","method":"Overexpression and siRNA knockdown in vitro and in vivo CTE model, autophagic flux assays, cell death assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function experiments with defined autophagic flux readout, single lab, two orthogonal perturbations","pmids":["38348540"],"is_preprint":false},{"year":2026,"finding":"DNAH3, an inner dynein arm heavy chain, physically interacts with DNALI1 and forms a complex required for flagellum assembly; absence of DNAH3 leads to loss of IDAs and disrupted DNALI1 localization.","method":"Co-immunoprecipitation, mass spectrometry, comparative proteomics, Dnah3 knockout mouse, immunofluorescence, transmission electron microscopy","journal":"Reproductive biology and endocrinology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with MS confirmation in KO mouse model, single lab, two orthogonal methods","pmids":["41731497"],"is_preprint":false},{"year":2024,"finding":"DNAH12 interacts with DNALI1 (and DNAH1) as part of the inner dynein arm complex; DNAH12 deficiency causes failed recruitment of DNALI1 (and DNAH1) to IDAs in sperm flagella, while having no effect on cilium organization, indicating a flagellum-specific assembly role for this complex.","method":"Co-immunoprecipitation, Dnah12-/- and Dnah12 mut/mut mouse models, immunofluorescence, transmission electron microscopy, whole-exome sequencing in patients","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP supported by KO mouse model and patient mutations, preprint, single lab","pmids":["bio_10.1101_2024.06.20.599934"],"is_preprint":true}],"current_model":"DNALI1 is an axonemal dynein light intermediate chain that localizes to sperm flagella and motile cilia, where it acts as a structural component of a partial inner dynein arm subspecies (with DNAH1, DNAH7, DNAH3, and DNAH12); it also localizes to the manchette of elongating spermatids and is required for MEIG1/PACRG complex formation there to enable cargo transport during flagellogenesis, interacts with cytoplasmic dynein heavy chain 1 to facilitate fibrous sheath protein (AKAP3/AKAP4) assembly, and under pathological conditions can inhibit autophagosome-lysosome fusion to impair autophagic flux."},"narrative":{"mechanistic_narrative":"DNALI1 is an axonemal inner dynein arm light intermediate chain that functions in the assembly of motile sperm flagella and, in elongating spermatids, in manchette-based cargo transport during spermiogenesis [PMID:36792588, PMID:37083624]. As a structural subunit of a partial inner dynein arm subspecies, it is recruited to flagellar IDAs together with the heavy chains DNAH1, DNAH7, DNAH3, and DNAH12, and its loss disrupts assembly and transport of the fibrous sheath proteins AKAP3 and AKAP4 [PMID:36792588, PMID:41731497]. Recruitment of DNALI1 to inner dynein arms depends on partner heavy chains: absence of DNAH3 or DNAH12 abolishes DNALI1 localization to flagellar IDAs, with DNAH12 acting in a flagellum-specific manner without affecting ciliary organization [PMID:41731497, PMID:bio_10.1101_2024.06.20.599934]. Beyond the axoneme, DNALI1 stabilizes PACRG and is required for localization of the MEIG1/PACRG complex within the spermatid manchette, where it supports transport of cargo such as SPAG16L without altering total cellular levels of these proteins [PMID:37083624]. Loss-of-function in mice causes impaired sperm motility, abnormal fibrous-sheath ultrastructure, and male infertility, and biallelic patient mutations link DNALI1 to human male infertility [PMID:36792588, PMID:37993789]. In a non-ciliary pathological context, DNALI1 overexpression inhibits autophagosome–lysosome fusion and reduces autophagic flux during traumatic brain injury, while its silencing enhances autophagic flux and alleviates neurodegeneration [PMID:38348540].","teleology":[{"year":2006,"claim":"Established the first molecular partner of DNALI1, placing it in physical association with cytoplasmic dynein heavy chain 1 in flagella and cilia, before any functional role was known.","evidence":"Yeast two-hybrid screen of murine testicular cDNA with reciprocal co-IP and immunofluorescence co-localization","pmids":["16496424"],"confidence":"Medium","gaps":["Did not define a functional consequence of the interaction","No knockout or phenotypic data","Interaction mapped only to the heavy chain C-terminus"]},{"year":2023,"claim":"Defined DNALI1 as a light intermediate chain of a partial inner dynein arm subspecies and showed it is required for fibrous sheath protein assembly, linking it to human male infertility.","evidence":"Biallelic patient mutation analysis, Dnali1-/- mouse, immunoprecipitation, immunofluorescence, and TEM","pmids":["36792588"],"confidence":"High","gaps":["Mechanism by which DNALI1 directs AKAP3/AKAP4 assembly unspecified","Stoichiometry within the IDA subspecies undefined","DNAH10 excluded but full heavy-chain composition incomplete"]},{"year":2023,"claim":"Identified a manchette-based role distinct from the axoneme, showing DNALI1 stabilizes PACRG and positions the MEIG1/PACRG complex for cargo transport during spermatid elongation.","evidence":"Reciprocal co-IP, pull-down, conditional Dnali1 knockout mouse, and spermatid immunofluorescence","pmids":["37083624"],"confidence":"High","gaps":["Direct vs indirect nature of the DNALI1-PACRG interaction not fully resolved","Transport mechanism of SPAG16L cargo not mechanistically dissected","Whether manchette and axonemal roles use the same DNALI1 pool unknown"]},{"year":2023,"claim":"Demonstrated that DNALI1 is required for normal flagellar ultrastructure, with loss causing fibrous-sheath disorganization and motility failure rescuable by ICSI.","evidence":"Nonsense-mutation knockin mouse, sperm motility analysis, TEM, and ICSI rescue","pmids":["37993789"],"confidence":"Medium","gaps":["Causal link between molecular defect and asymmetric column distribution not resolved","Single lab","No structural detail on the IDA defect"]},{"year":2024,"claim":"Revealed a context-dependent non-ciliary function in which DNALI1 modulates autophagy by inhibiting autophagosome-lysosome fusion under pathological stress.","evidence":"Overexpression and siRNA knockdown in vitro and in a CTE model with autophagic flux and cell death assays","pmids":["38348540"],"confidence":"Medium","gaps":["Molecular target controlling fusion not identified","No effect under normal conditions leaves physiological relevance unclear","Mechanistic link to its axonemal dynein role unexplored"]},{"year":2024,"claim":"Showed that DNAH12 recruits DNALI1 (and DNAH1) to inner dynein arms in a flagellum-specific manner, distinguishing flagellar from ciliary assembly requirements.","evidence":"Co-IP, Dnah12-/- and mutant mouse models, immunofluorescence, TEM, and patient whole-exome sequencing (preprint)","pmids":["bio_10.1101_2024.06.20.599934"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Basis of flagellum-specific (vs ciliary) requirement unexplained","Direct binding interface undefined"]},{"year":2026,"claim":"Identified DNAH3 as an additional heavy-chain partner whose loss disrupts DNALI1 localization, reinforcing that DNALI1 depends on multiple IDA heavy chains for proper assembly.","evidence":"Co-IP with mass spectrometry, comparative proteomics, Dnah3 knockout mouse, immunofluorescence, and TEM","pmids":["41731497"],"confidence":"Medium","gaps":["Whether DNAH3 and DNAH12 act in the same or distinct IDA subspecies unclear","Direct binding vs co-assembly dependence not separated","Single lab"]},{"year":null,"claim":"How DNALI1's axonemal/manchette transport functions mechanistically relate to its pathological autophagy-modulating activity, and what molecular determinant governs each, remains unresolved.","evidence":"No timeline discovery connects the two functional contexts","pmids":[],"confidence":"Low","gaps":["No shared molecular mechanism identified","No structural model of DNALI1 within any complex","Autophagy target of DNALI1 unidentified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,3]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,5,6]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[1,2,5]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,5,6]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4]}],"complexes":["inner dynein arm","MEIG1/PACRG complex"],"partners":["DYNC1H1","PACRG","MEIG1","DNAH1","DNAH7","DNAH3","DNAH12","SPAG16L"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O14645","full_name":"Axonemal dynein light intermediate polypeptide 1","aliases":["Inner dynein arm light chain, axonemal","hp28"],"length_aa":258,"mass_kda":29.7,"function":"Involved in sperm flagellum assembly","subcellular_location":"Cell projection, cilium; Cell projection, cilium, flagellum; Dynein axonemal particle; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O14645/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNALI1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DNALI1","total_profiled":1310},"omim":[{"mim_id":"621209","title":"SPERMATOGENIC FAILURE 100; SPGF100","url":"https://www.omim.org/entry/621209"},{"mim_id":"620354","title":"SPERMATOGENIC FAILURE 83; SPGF83","url":"https://www.omim.org/entry/620354"},{"mim_id":"618801","title":"CILIARY DYSKINESIA, PRIMARY, 45; CILD45","url":"https://www.omim.org/entry/618801"},{"mim_id":"618153","title":"SPERMATOGENIC FAILURE 34; SPGF34","url":"https://www.omim.org/entry/618153"},{"mim_id":"618063","title":"CILIARY DYSKINESIA, PRIMARY, 38; CILD38","url":"https://www.omim.org/entry/618063"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Primary cilium","reliability":"Supported"},{"location":"Mid piece","reliability":"Supported"},{"location":"Principal piece","reliability":"Supported"},{"location":"End piece","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Microtubules","reliability":"Additional"},{"location":"Cytokinetic bridge","reliability":"Additional"},{"location":"Mitotic spindle","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":75.0},{"tissue":"fallopian tube","ntpm":51.2}],"url":"https://www.proteinatlas.org/search/DNALI1"},"hgnc":{"alias_symbol":["P28","hp28","dJ423B22.5"],"prev_symbol":[]},"alphafold":{"accession":"O14645","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14645","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14645-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14645-F1-predicted_aligned_error_v6.png","plddt_mean":84.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNALI1","jax_strain_url":"https://www.jax.org/strain/search?query=DNALI1"},"sequence":{"accession":"O14645","fasta_url":"https://rest.uniprot.org/uniprotkb/O14645.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14645/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14645"}},"corpus_meta":[{"pmid":"16496424","id":"PMC_16496424","title":"The murine Dnali1 gene encodes a flagellar protein that interacts with the cytoplasmic dynein heavy chain 1.","date":"2006","source":"Molecular reproduction and development","url":"https://pubmed.ncbi.nlm.nih.gov/16496424","citation_count":46,"is_preprint":false},{"pmid":"36792588","id":"PMC_36792588","title":"DNALI1 deficiency causes male infertility with severe asthenozoospermia in humans and mice by disrupting the assembly of the flagellar inner dynein arms and fibrous sheath.","date":"2023","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/36792588","citation_count":44,"is_preprint":false},{"pmid":"38348540","id":"PMC_38348540","title":"DNALI1 Promotes Neurodegeneration after Traumatic Brain Injury via Inhibition of Autophagosome-Lysosome Fusion.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/38348540","citation_count":15,"is_preprint":false},{"pmid":"37083624","id":"PMC_37083624","title":"DNALI1 interacts with the MEIG1/PACRG complex within the manchette and is required for proper sperm flagellum assembly in mice.","date":"2023","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/37083624","citation_count":13,"is_preprint":false},{"pmid":"36726469","id":"PMC_36726469","title":"Homozygous mutation in DNALI1 leads to asthenoteratozoospermia by affecting the inner dynein arms.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/36726469","citation_count":9,"is_preprint":false},{"pmid":"2254013","id":"PMC_2254013","title":"Purification and characterization of an outer membrane protein adhesin from Haemophilus parainfluenzae HP-28.","date":"1990","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/2254013","citation_count":9,"is_preprint":false},{"pmid":"37993789","id":"PMC_37993789","title":"Dnali1 is required for sperm motility and male fertility in mice.","date":"2023","source":"Basic and clinical andrology","url":"https://pubmed.ncbi.nlm.nih.gov/37993789","citation_count":8,"is_preprint":false},{"pmid":"38212584","id":"PMC_38212584","title":"Splicing Mutation in DNALI1 Causes Male Infertility with Severe Oligoasthenoteratozoospermia in Humans.","date":"2024","source":"Reproductive sciences (Thousand Oaks, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/38212584","citation_count":3,"is_preprint":false},{"pmid":"33877529","id":"PMC_33877529","title":"Sexually dimorphic expression and regulatory sequence of dnali1 in the olive flounder Paralichthys olivaceus.","date":"2021","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/33877529","citation_count":1,"is_preprint":false},{"pmid":"41731497","id":"PMC_41731497","title":"DNAH3 interacts with DNALI1 and is required for sperm flagellum function and male fertility.","date":"2026","source":"Reproductive biology and endocrinology : RB&E","url":"https://pubmed.ncbi.nlm.nih.gov/41731497","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.20.599934","title":"Deficiency in DNAH12 causes male infertility by impairing DNAH1 and DNALI1 recruitment in humans and mice","date":"2024-06-23","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.20.599934","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7674,"output_tokens":1829,"usd":0.025229,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8695,"output_tokens":2888,"usd":0.057838,"stage2_stop_reason":"end_turn"},"total_usd":0.083067,"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\": 2006,\n      \"finding\": \"Murine DNALI1 (Dnali1) protein localizes to sperm flagella and tracheal cilia, and its C-terminal region of cytoplasmic dynein heavy chain 1 was identified as a binding partner via yeast two-hybrid screening, confirmed by co-immunoprecipitation and co-localization experiments.\",\n      \"method\": \"Yeast two-hybrid screen with murine testicular cDNA library, co-immunoprecipitation, immunofluorescence co-localization\",\n      \"journal\": \"Molecular reproduction and development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and co-localization supporting yeast two-hybrid, single lab, two orthogonal methods\",\n      \"pmids\": [\"16496424\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNALI1 is a light intermediate chain (LIC) component of a partial inner dynein arm (IDA) subspecies that includes DNAH1 and DNAH7 (but not DNAH10); loss of DNALI1 disrupts assembly and transport of fibrous sheath proteins AKAP3 and AKAP4, and DNALI1 interacts with cytoplasmic dynein complex proteins in the testis, suggesting a non-classical role in cytoplasmic dynein-mediated flagellar assembly.\",\n      \"method\": \"Bi-allelic patient mutation analysis, Dnali1-/- mouse model, immunofluorescence, immunoprecipitation, transmission electron microscopy\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal immunoprecipitation, knockout mouse model, and patient mutation converging on same mechanism across two species\",\n      \"pmids\": [\"36792588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNALI1 interacts with PACRG (stabilizes it) and is required for the localization of the MEIG1/PACRG complex within the manchette of elongating spermatids; DNALI1 deficiency in male germ cells disrupts manchette-based cargo transport (including SPAG16L) and impairs spermiogenesis without altering total testicular levels of MEIG1, PACRG, or SPAG16L.\",\n      \"method\": \"Co-immunoprecipitation, pull-down assays, conditional Dnali1 knockout mouse, immunofluorescence of spermatids, testis histology\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus pulldown plus in vivo KO with defined localization phenotype, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37083624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Loss-of-function Dnali1 nonsense mutation in mice causes impaired sperm motility and male infertility with ultrastructural flagellar defects (asymmetrical distribution of longitudinal columns of the fibrous sheath), demonstrating DNALI1 is required for proper flagellar ultrastructure.\",\n      \"method\": \"Nonsense mutation knockin mouse model, sperm motility analysis, transmission electron microscopy, ICSI rescue\",\n      \"journal\": \"Basic and clinical andrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined ultrastructural phenotype in KO mouse, single lab, TEM plus functional motility assay\",\n      \"pmids\": [\"37993789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DNALI1 overexpression inhibits autophagosome-lysosome fusion and reduces autophagic flux under pathological (TBI) conditions, while DNALI1 silencing enhances autophagic flux and alleviates neurodegeneration in a CTE model; altered DNALI1 expression under normal conditions has no discernible effect on autophagy.\",\n      \"method\": \"Overexpression and siRNA knockdown in vitro and in vivo CTE model, autophagic flux assays, cell death assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function experiments with defined autophagic flux readout, single lab, two orthogonal perturbations\",\n      \"pmids\": [\"38348540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"DNAH3, an inner dynein arm heavy chain, physically interacts with DNALI1 and forms a complex required for flagellum assembly; absence of DNAH3 leads to loss of IDAs and disrupted DNALI1 localization.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, comparative proteomics, Dnah3 knockout mouse, immunofluorescence, transmission electron microscopy\",\n      \"journal\": \"Reproductive biology and endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with MS confirmation in KO mouse model, single lab, two orthogonal methods\",\n      \"pmids\": [\"41731497\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DNAH12 interacts with DNALI1 (and DNAH1) as part of the inner dynein arm complex; DNAH12 deficiency causes failed recruitment of DNALI1 (and DNAH1) to IDAs in sperm flagella, while having no effect on cilium organization, indicating a flagellum-specific assembly role for this complex.\",\n      \"method\": \"Co-immunoprecipitation, Dnah12-/- and Dnah12 mut/mut mouse models, immunofluorescence, transmission electron microscopy, whole-exome sequencing in patients\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP supported by KO mouse model and patient mutations, preprint, single lab\",\n      \"pmids\": [\"bio_10.1101_2024.06.20.599934\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DNALI1 is an axonemal dynein light intermediate chain that localizes to sperm flagella and motile cilia, where it acts as a structural component of a partial inner dynein arm subspecies (with DNAH1, DNAH7, DNAH3, and DNAH12); it also localizes to the manchette of elongating spermatids and is required for MEIG1/PACRG complex formation there to enable cargo transport during flagellogenesis, interacts with cytoplasmic dynein heavy chain 1 to facilitate fibrous sheath protein (AKAP3/AKAP4) assembly, and under pathological conditions can inhibit autophagosome-lysosome fusion to impair autophagic flux.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNALI1 is an axonemal inner dynein arm light intermediate chain that functions in the assembly of motile sperm flagella and, in elongating spermatids, in manchette-based cargo transport during spermiogenesis [#1, #2]. As a structural subunit of a partial inner dynein arm subspecies, it is recruited to flagellar IDAs together with the heavy chains DNAH1, DNAH7, DNAH3, and DNAH12, and its loss disrupts assembly and transport of the fibrous sheath proteins AKAP3 and AKAP4 [#1, #5]. Recruitment of DNALI1 to inner dynein arms depends on partner heavy chains: absence of DNAH3 or DNAH12 abolishes DNALI1 localization to flagellar IDAs, with DNAH12 acting in a flagellum-specific manner without affecting ciliary organization [#5, #6]. Beyond the axoneme, DNALI1 stabilizes PACRG and is required for localization of the MEIG1/PACRG complex within the spermatid manchette, where it supports transport of cargo such as SPAG16L without altering total cellular levels of these proteins [#2]. Loss-of-function in mice causes impaired sperm motility, abnormal fibrous-sheath ultrastructure, and male infertility, and biallelic patient mutations link DNALI1 to human male infertility [#1, #3]. In a non-ciliary pathological context, DNALI1 overexpression inhibits autophagosome–lysosome fusion and reduces autophagic flux during traumatic brain injury, while its silencing enhances autophagic flux and alleviates neurodegeneration [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established the first molecular partner of DNALI1, placing it in physical association with cytoplasmic dynein heavy chain 1 in flagella and cilia, before any functional role was known.\",\n      \"evidence\": \"Yeast two-hybrid screen of murine testicular cDNA with reciprocal co-IP and immunofluorescence co-localization\",\n      \"pmids\": [\"16496424\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define a functional consequence of the interaction\", \"No knockout or phenotypic data\", \"Interaction mapped only to the heavy chain C-terminus\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined DNALI1 as a light intermediate chain of a partial inner dynein arm subspecies and showed it is required for fibrous sheath protein assembly, linking it to human male infertility.\",\n      \"evidence\": \"Biallelic patient mutation analysis, Dnali1-/- mouse, immunoprecipitation, immunofluorescence, and TEM\",\n      \"pmids\": [\"36792588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which DNALI1 directs AKAP3/AKAP4 assembly unspecified\", \"Stoichiometry within the IDA subspecies undefined\", \"DNAH10 excluded but full heavy-chain composition incomplete\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified a manchette-based role distinct from the axoneme, showing DNALI1 stabilizes PACRG and positions the MEIG1/PACRG complex for cargo transport during spermatid elongation.\",\n      \"evidence\": \"Reciprocal co-IP, pull-down, conditional Dnali1 knockout mouse, and spermatid immunofluorescence\",\n      \"pmids\": [\"37083624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs indirect nature of the DNALI1-PACRG interaction not fully resolved\", \"Transport mechanism of SPAG16L cargo not mechanistically dissected\", \"Whether manchette and axonemal roles use the same DNALI1 pool unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated that DNALI1 is required for normal flagellar ultrastructure, with loss causing fibrous-sheath disorganization and motility failure rescuable by ICSI.\",\n      \"evidence\": \"Nonsense-mutation knockin mouse, sperm motility analysis, TEM, and ICSI rescue\",\n      \"pmids\": [\"37993789\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal link between molecular defect and asymmetric column distribution not resolved\", \"Single lab\", \"No structural detail on the IDA defect\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed a context-dependent non-ciliary function in which DNALI1 modulates autophagy by inhibiting autophagosome-lysosome fusion under pathological stress.\",\n      \"evidence\": \"Overexpression and siRNA knockdown in vitro and in a CTE model with autophagic flux and cell death assays\",\n      \"pmids\": [\"38348540\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular target controlling fusion not identified\", \"No effect under normal conditions leaves physiological relevance unclear\", \"Mechanistic link to its axonemal dynein role unexplored\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed that DNAH12 recruits DNALI1 (and DNAH1) to inner dynein arms in a flagellum-specific manner, distinguishing flagellar from ciliary assembly requirements.\",\n      \"evidence\": \"Co-IP, Dnah12-/- and mutant mouse models, immunofluorescence, TEM, and patient whole-exome sequencing (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.06.20.599934\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Basis of flagellum-specific (vs ciliary) requirement unexplained\", \"Direct binding interface undefined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified DNAH3 as an additional heavy-chain partner whose loss disrupts DNALI1 localization, reinforcing that DNALI1 depends on multiple IDA heavy chains for proper assembly.\",\n      \"evidence\": \"Co-IP with mass spectrometry, comparative proteomics, Dnah3 knockout mouse, immunofluorescence, and TEM\",\n      \"pmids\": [\"41731497\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DNAH3 and DNAH12 act in the same or distinct IDA subspecies unclear\", \"Direct binding vs co-assembly dependence not separated\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNALI1's axonemal/manchette transport functions mechanistically relate to its pathological autophagy-modulating activity, and what molecular determinant governs each, remains unresolved.\",\n      \"evidence\": \"No timeline discovery connects the two functional contexts\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No shared molecular mechanism identified\", \"No structural model of DNALI1 within any complex\", \"Autophagy target of DNALI1 unidentified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [1, 2, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 5, 6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\"inner dynein arm\", \"MEIG1/PACRG complex\"],\n    \"partners\": [\"DYNC1H1\", \"PACRG\", \"MEIG1\", \"DNAH1\", \"DNAH7\", \"DNAH3\", \"DNAH12\", \"SPAG16L\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}