{"gene":"NEURL3","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2022,"finding":"NEURL3 directly interacts with IRF7 and catalyzes K63-linked poly-ubiquitination on IRF7 at lysine 375, which disrupts IRF7's association with HDAC1, epigenetically enhancing transcription of interferon-stimulated genes and augmenting antiviral immune response. Neurl3-/- mice produced less type I IFNs and showed increased susceptibility to viral infection.","method":"Co-immunoprecipitation, ubiquitination assay with K63-specific linkage analysis, site-directed mutagenesis (K375 site), Neurl3 knockout mice, viral infection assays","journal":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, site-directed mutagenesis of ubiquitination site, in vivo KO mouse model with defined phenotype, multiple orthogonal methods in one study","pmids":["35792897"],"is_preprint":false},{"year":2024,"finding":"NEURL3 promotes K48-linked poly-ubiquitination of Vimentin at lysine 97, leading to Vimentin protein degradation, thereby suppressing epithelial-mesenchymal transition and metastasis in nasopharyngeal carcinoma. Restoration of Vimentin expression fully reversed the tumor-suppressive effect of NEURL3 overexpression.","method":"Mass spectrometry, co-immunoprecipitation, ubiquitination assays with K48-specific linkage analysis, immunofluorescence, in vitro and in vivo overexpression and rescue experiments","journal":"Journal of experimental & clinical cancer research : CR","confidence":"High","confidence_rationale":"Tier 2 / Moderate — mass spectrometry substrate identification, ubiquitination assay with K48 linkage specificity, mutagenesis of ubiquitination site, rescue experiment, in vivo validation; single lab but multiple orthogonal methods","pmids":["38191501"],"is_preprint":false},{"year":2024,"finding":"LINCR/NEURL3 promotes ubiquitin-mediated degradation of MAPK phosphatase-1 (MKP1), a negative regulator of MAP kinases, thereby amplifying TLR-mediated JNK and p38 MAPK signaling. In LINCR-deficient cells, sustained activation of JNK and p38 induced by TLR3, TLR4, and TLR5 agonists was clearly attenuated, and TLR-induced inflammatory cytokine production was significantly reduced.","method":"LINCR-deficient cell lines, TLR agonist stimulation, ubiquitination assays, kinase activation assays, cytokine production assays","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined cellular loss-of-function phenotype with identified substrate (MKP1), ubiquitination assay, multiple TLR contexts tested; single lab","pmids":["38667302"],"is_preprint":false},{"year":2025,"finding":"NEURL3 promotes osteoclast differentiation by increasing ubiquitination of BMP7. Inhibition of BMP7 reversed the pro-osteoclastic effect of NEURL3, and NEURL3 inhibition suppressed osteoclast differentiation in vitro and reduced bone loss in OVX-induced osteoporosis mice in vivo.","method":"Western blotting for osteoclastogenesis markers, ubiquitination assays for BMP7, in vitro BMM osteoclast differentiation model, OVX mouse model, micro-CT","journal":"Applied biochemistry and biotechnology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vitro and in vivo loss-of-function with identified substrate (BMP7), rescue experiment; single lab, single paper","pmids":["39960614"],"is_preprint":false},{"year":2016,"finding":"In half-smooth tongue sole (Cynoglossus semilaevis), neurl3 (neuralized E3 ubiquitin ligase 3) knockdown by RNA interference caused increased transcription of spermatogenesis-related genes, and neurl3 expression levels correlated with testis protein ubiquitination levels, indicating neurl3 regulates testis protein ubiquitination in a dosage-dependent manner during spermatogenesis.","method":"RNA interference knockdown, RT-qPCR for spermatogenesis genes, protein ubiquitination assays in testis tissue","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — correlation-based mechanistic inference in a fish ortholog, RNAi knockdown with indirect ubiquitination readout; single lab, single study, no direct substrate identified","pmids":["27480167"],"is_preprint":false},{"year":2015,"finding":"Targeted overexpression of LINCR in mouse lung epithelium caused hypoplastic lungs with cystic changes and upregulation of Hairy/Enhancer of Split 1 (Hes1), an effector of Notch signaling, producing a phenotype similar to activated Notch1 overexpression, suggesting LINCR acts upstream of or within the Notch signaling pathway in lung epithelial development.","method":"Doxycycline-inducible double-transgenic mouse model with conditional lung epithelial overexpression of LINCR, histological analysis, marker gene expression (Hes1)","journal":"Developmental dynamics : an official publication of the American Association of Anatomists","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis via conditional transgenic OE with phenotypic readout and pathway placement via Hes1 induction; single lab, single study, mechanism not directly confirmed at molecular level","pmids":["25904058"],"is_preprint":false}],"current_model":"NEURL3 (also known as LINCR/RNF132) is an E3 ubiquitin ligase that catalyzes substrate-specific ubiquitination: it performs K63-linked ubiquitination of IRF7 at K375 to enhance antiviral interferon responses (by displacing HDAC1), K48-linked ubiquitination of Vimentin at K97 to promote its degradation and suppress EMT/metastasis, ubiquitination and degradation of MKP1 to amplify TLR-driven JNK/p38 MAP kinase signaling, and ubiquitination of BMP7 to promote osteoclast differentiation; it has also been linked to Notch signaling pathway activation in lung epithelial development."},"narrative":{"mechanistic_narrative":"NEURL3 (LINCR/RNF132) is a substrate-specific E3 ubiquitin ligase that shapes immune signaling, epithelial-mesenchymal state, and tissue differentiation through distinct linkage-type ubiquitination events on defined targets [PMID:35792897, PMID:38191501, PMID:38667302]. In antiviral immunity, it directly binds IRF7 and catalyzes K63-linked poly-ubiquitination at IRF7 K375, displacing HDAC1 to derepress interferon-stimulated gene transcription; Neurl3-deficient mice produce less type I interferon and are more susceptible to viral infection [PMID:35792897]. In tumor biology, NEURL3 catalyzes K48-linked poly-ubiquitination of Vimentin at K97 to drive its degradation, suppressing epithelial-mesenchymal transition and metastasis in nasopharyngeal carcinoma, an effect fully reversed by Vimentin restoration [PMID:38191501]. It also amplifies TLR-driven JNK and p38 MAPK signaling and inflammatory cytokine output by promoting ubiquitin-mediated degradation of the MAP kinase phosphatase MKP1 [PMID:38667302]. In bone, NEURL3 promotes osteoclast differentiation through ubiquitination of BMP7, and its inhibition reduces bone loss in ovariectomy-induced osteoporosis [PMID:39960614]. Conditional overexpression in mouse lung epithelium produces hypoplastic, cystic lungs with Hes1 induction, placing NEURL3 within Notch signaling during lung epithelial development [PMID:25904058].","teleology":[{"year":2015,"claim":"Before molecular substrates were known, it was unclear what developmental pathway NEURL3/LINCR engaged; conditional overexpression connected it to Notch-driven lung epithelial morphogenesis.","evidence":"Doxycycline-inducible lung epithelial overexpression in transgenic mice with histology and Hes1 marker readout","pmids":["25904058"],"confidence":"Medium","gaps":["No direct ubiquitination substrate identified in this Notch context","Mechanistic link to Notch is inferred from Hes1 induction, not biochemically defined","Loss-of-function phenotype not tested"]},{"year":2016,"claim":"To test whether NEURL3 functions as a ubiquitination regulator in vivo, knockdown in a fish ortholog tied its dosage to testis protein ubiquitination during spermatogenesis.","evidence":"RNAi knockdown in Cynoglossus semilaevis with RT-qPCR and bulk testis ubiquitination readout","pmids":["27480167"],"confidence":"Low","gaps":["Correlation-based with no direct substrate","Ortholog in a non-mammalian species","Ubiquitination readout is indirect and bulk"]},{"year":2022,"claim":"The first defined catalytic mechanism established NEURL3 as a K63-linkage E3 ligase that ubiquitinates IRF7 to boost antiviral interferon responses, answering how it acts at the molecular level.","evidence":"Reciprocal Co-IP, K63-specific ubiquitination assay, K375 site-directed mutagenesis, and Neurl3 knockout mice with viral infection assays","pmids":["35792897"],"confidence":"High","gaps":["Structural basis of IRF7 recognition unknown","Whether HDAC1 displacement is direct or downstream of ubiquitination not resolved"]},{"year":2024,"claim":"NEURL3 was shown to switch linkage type and direction of effect, performing K48-linked degradative ubiquitination of Vimentin to suppress EMT and metastasis, establishing a tumor-suppressive role.","evidence":"Mass spectrometry substrate ID, K48-specific ubiquitination assay, K97 mutagenesis, and in vivo overexpression/rescue in nasopharyngeal carcinoma models","pmids":["38191501"],"confidence":"High","gaps":["What determines K63 versus K48 linkage choice across substrates is unknown","Single tumor type tested"]},{"year":2024,"claim":"A separate loss-of-function study placed NEURL3 in innate immune signaling amplification by degrading the MAP kinase phosphatase MKP1, defining how it sustains TLR-driven JNK/p38 activation.","evidence":"LINCR-deficient cells with TLR3/4/5 agonist stimulation, ubiquitination and kinase activation assays, cytokine production readout","pmids":["38667302"],"confidence":"Medium","gaps":["Ubiquitin linkage type on MKP1 not specified","Single lab; no in vivo confirmation","Direct interaction with MKP1 not fully characterized"]},{"year":2025,"claim":"NEURL3 was extended to bone biology, where ubiquitination of BMP7 drives osteoclast differentiation, linking the ligase to osteoporosis pathology.","evidence":"BMM osteoclast differentiation model, BMP7 ubiquitination assays, rescue experiments, and OVX mouse model with micro-CT","pmids":["39960614"],"confidence":"Medium","gaps":["Ubiquitin linkage type on BMP7 not defined","Single lab, single study","Direct binding versus indirect effect not resolved"]},{"year":null,"claim":"How NEURL3 selects among structurally diverse substrates and chooses degradative (K48) versus signaling (K63) ubiquitin linkages across immune, epithelial, and skeletal contexts remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of substrate recognition","No unifying determinant of linkage-type selection identified","Tissue-specific regulation of NEURL3 expression and activity uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3]}],"localization":[],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2]}],"complexes":[],"partners":["IRF7","VIM","DUSP1","BMP7"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"A8MQ27","full_name":"E3 ubiquitin-protein ligase NEURL1B","aliases":["Neuralized-2","NEUR2","Neuralized-like protein 1B","Neuralized-like protein 3","RING-type E3 ubiquitin transferase NEURL1B"],"length_aa":555,"mass_kda":59.3,"function":"E3 ubiquitin-protein ligase involved in regulation of the Notch pathway through influencing the stability and activity of several Notch ligands","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/A8MQ27/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEURL3","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":74,"dependency_fraction":0.02702702702702703},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NEURL3","total_profiled":1310},"omim":[{"mim_id":"617206","title":"NEURALIZED E3 UBIQUITIN PROTEIN LIGASE 3; NEURL3","url":"https://www.omim.org/entry/617206"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"kidney","ntpm":15.2},{"tissue":"pancreas","ntpm":24.5},{"tissue":"salivary gland","ntpm":28.5}],"url":"https://www.proteinatlas.org/search/NEURL3"},"hgnc":{"alias_symbol":["Lincr","LOC93082","RNF132"],"prev_symbol":[]},"alphafold":{"accession":"A8MQ27","domains":[{"cath_id":"2.60.120.920","chopping":"42-227","consensus_level":"high","plddt":81.7661,"start":42,"end":227},{"cath_id":"2.60.120.920","chopping":"283-437","consensus_level":"high","plddt":82.429,"start":283,"end":437},{"cath_id":"3.30.40.10","chopping":"503-552","consensus_level":"high","plddt":87.6526,"start":503,"end":552}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/A8MQ27","model_url":"https://alphafold.ebi.ac.uk/files/AF-A8MQ27-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-A8MQ27-F1-predicted_aligned_error_v6.png","plddt_mean":70.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEURL3","jax_strain_url":"https://www.jax.org/strain/search?query=NEURL3"},"sequence":{"accession":"A8MQ27","fasta_url":"https://rest.uniprot.org/uniprotkb/A8MQ27.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/A8MQ27/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/A8MQ27"}},"corpus_meta":[{"pmid":"27480167","id":"PMC_27480167","title":"Ubiquitin ligase gene neurl3 plays a role in spermatogenesis of half-smooth tongue sole (Cynoglossus semilaevis) by regulating testis protein ubiquitination.","date":"2016","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/27480167","citation_count":23,"is_preprint":false},{"pmid":"35792897","id":"PMC_35792897","title":"E3 ubiquitin ligase NEURL3 promotes innate antiviral response through catalyzing K63-linked ubiquitination of IRF7.","date":"2022","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/35792897","citation_count":19,"is_preprint":false},{"pmid":"31790618","id":"PMC_31790618","title":"Correlation between LincR-Gng2-5'and LincR-Epas1-3'as with the severity of multiple sclerosis in Egyptian patients.","date":"2019","source":"The International journal of neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/31790618","citation_count":10,"is_preprint":false},{"pmid":"38191501","id":"PMC_38191501","title":"The E3 ligase NEURL3 suppresses epithelial-mesenchymal transition and metastasis in nasopharyngeal carcinoma by promoting vimentin degradation.","date":"2024","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/38191501","citation_count":9,"is_preprint":false},{"pmid":"38262392","id":"PMC_38262392","title":"LincR-PPP2R5C Promotes Th2 Cell Differentiation Through PPP2R5C/PP2A by Forming an RNA-DNA Triplex in Allergic Asthma.","date":"2024","source":"Allergy, asthma & immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/38262392","citation_count":7,"is_preprint":false},{"pmid":"39018689","id":"PMC_39018689","title":"LincR-PPP2R5C regulates IL-1β ubiquitination in macrophages and promotes airway inflammation and emphysema in a murine model of COPD.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39018689","citation_count":5,"is_preprint":false},{"pmid":"25904058","id":"PMC_25904058","title":"Overexpression of LINCR in the developing mouse lung epithelium inhibits distal differentiation and induces cystic changes.","date":"2015","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/25904058","citation_count":5,"is_preprint":false},{"pmid":"38667302","id":"PMC_38667302","title":"The E3 Ubiquitin Protein Ligase LINCR Amplifies the TLR-Mediated Signals through Direct Degradation of MKP1.","date":"2024","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/38667302","citation_count":4,"is_preprint":false},{"pmid":"37230320","id":"PMC_37230320","title":"Divergent expression of Neurl3 from hemogenic endothelial cells to hematopoietic stem progenitor cells during development.","date":"2023","source":"Journal of genetics and genomics = Yi chuan xue bao","url":"https://pubmed.ncbi.nlm.nih.gov/37230320","citation_count":3,"is_preprint":false},{"pmid":"39025723","id":"PMC_39025723","title":"A micropeptide TREMP encoded by lincR-PPP2R5C promotes Th2 cell differentiation by interacting with PYCR1 in allergic airway inflammation.","date":"2024","source":"Allergology international : official journal of the Japanese Society of Allergology","url":"https://pubmed.ncbi.nlm.nih.gov/39025723","citation_count":3,"is_preprint":false},{"pmid":"39729722","id":"PMC_39729722","title":"LincR-PPP2R5C regulates the PP2A signaling pathway in the macrophage-myofibroblast transition in a mouse model of epidural fibrosis.","date":"2024","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39729722","citation_count":2,"is_preprint":false},{"pmid":"39155740","id":"PMC_39155740","title":"LincR-PPP2R5C Deficiency Alleviates Airway Remodeling by Inhibiting Epithelial-Mesenchymal Transition Through the PP2A/TGF-β1 Signaling Pathway in Chronic Experimental Allergic Asthma.","date":"2024","source":"Allergy, asthma & immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/39155740","citation_count":2,"is_preprint":false},{"pmid":"39287443","id":"PMC_39287443","title":"LincR-PPP2R5C deficiency enhancing the fungicidal activity of neutrophils in pulmonary cryptococcosis is linked to the upregulation of IL-4.","date":"2024","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/39287443","citation_count":2,"is_preprint":false},{"pmid":"40918133","id":"PMC_40918133","title":"Comprehensive analysis based on the ubiquitination- and deubiquitylation-related genes reveals the function of NEURL3 in esophageal squamous cell carcinoma.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40918133","citation_count":1,"is_preprint":false},{"pmid":"39960614","id":"PMC_39960614","title":"Inhibition of NEURL3 Suppresses Osteoclast Differentiation via BMP7 Ubiquitination Modulation.","date":"2025","source":"Applied biochemistry and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/39960614","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11002,"output_tokens":1838,"usd":0.030288,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8684,"output_tokens":2439,"usd":0.052198,"stage2_stop_reason":"end_turn"},"total_usd":0.082486,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"NEURL3 directly interacts with IRF7 and catalyzes K63-linked poly-ubiquitination on IRF7 at lysine 375, which disrupts IRF7's association with HDAC1, epigenetically enhancing transcription of interferon-stimulated genes and augmenting antiviral immune response. Neurl3-/- mice produced less type I IFNs and showed increased susceptibility to viral infection.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with K63-specific linkage analysis, site-directed mutagenesis (K375 site), Neurl3 knockout mice, viral infection assays\",\n      \"journal\": \"FASEB journal : official publication of the Federation of American Societies for Experimental Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, site-directed mutagenesis of ubiquitination site, in vivo KO mouse model with defined phenotype, multiple orthogonal methods in one study\",\n      \"pmids\": [\"35792897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NEURL3 promotes K48-linked poly-ubiquitination of Vimentin at lysine 97, leading to Vimentin protein degradation, thereby suppressing epithelial-mesenchymal transition and metastasis in nasopharyngeal carcinoma. Restoration of Vimentin expression fully reversed the tumor-suppressive effect of NEURL3 overexpression.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, ubiquitination assays with K48-specific linkage analysis, immunofluorescence, in vitro and in vivo overexpression and rescue experiments\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mass spectrometry substrate identification, ubiquitination assay with K48 linkage specificity, mutagenesis of ubiquitination site, rescue experiment, in vivo validation; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"38191501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LINCR/NEURL3 promotes ubiquitin-mediated degradation of MAPK phosphatase-1 (MKP1), a negative regulator of MAP kinases, thereby amplifying TLR-mediated JNK and p38 MAPK signaling. In LINCR-deficient cells, sustained activation of JNK and p38 induced by TLR3, TLR4, and TLR5 agonists was clearly attenuated, and TLR-induced inflammatory cytokine production was significantly reduced.\",\n      \"method\": \"LINCR-deficient cell lines, TLR agonist stimulation, ubiquitination assays, kinase activation assays, cytokine production assays\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined cellular loss-of-function phenotype with identified substrate (MKP1), ubiquitination assay, multiple TLR contexts tested; single lab\",\n      \"pmids\": [\"38667302\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEURL3 promotes osteoclast differentiation by increasing ubiquitination of BMP7. Inhibition of BMP7 reversed the pro-osteoclastic effect of NEURL3, and NEURL3 inhibition suppressed osteoclast differentiation in vitro and reduced bone loss in OVX-induced osteoporosis mice in vivo.\",\n      \"method\": \"Western blotting for osteoclastogenesis markers, ubiquitination assays for BMP7, in vitro BMM osteoclast differentiation model, OVX mouse model, micro-CT\",\n      \"journal\": \"Applied biochemistry and biotechnology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vitro and in vivo loss-of-function with identified substrate (BMP7), rescue experiment; single lab, single paper\",\n      \"pmids\": [\"39960614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In half-smooth tongue sole (Cynoglossus semilaevis), neurl3 (neuralized E3 ubiquitin ligase 3) knockdown by RNA interference caused increased transcription of spermatogenesis-related genes, and neurl3 expression levels correlated with testis protein ubiquitination levels, indicating neurl3 regulates testis protein ubiquitination in a dosage-dependent manner during spermatogenesis.\",\n      \"method\": \"RNA interference knockdown, RT-qPCR for spermatogenesis genes, protein ubiquitination assays in testis tissue\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — correlation-based mechanistic inference in a fish ortholog, RNAi knockdown with indirect ubiquitination readout; single lab, single study, no direct substrate identified\",\n      \"pmids\": [\"27480167\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Targeted overexpression of LINCR in mouse lung epithelium caused hypoplastic lungs with cystic changes and upregulation of Hairy/Enhancer of Split 1 (Hes1), an effector of Notch signaling, producing a phenotype similar to activated Notch1 overexpression, suggesting LINCR acts upstream of or within the Notch signaling pathway in lung epithelial development.\",\n      \"method\": \"Doxycycline-inducible double-transgenic mouse model with conditional lung epithelial overexpression of LINCR, histological analysis, marker gene expression (Hes1)\",\n      \"journal\": \"Developmental dynamics : an official publication of the American Association of Anatomists\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis via conditional transgenic OE with phenotypic readout and pathway placement via Hes1 induction; single lab, single study, mechanism not directly confirmed at molecular level\",\n      \"pmids\": [\"25904058\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NEURL3 (also known as LINCR/RNF132) is an E3 ubiquitin ligase that catalyzes substrate-specific ubiquitination: it performs K63-linked ubiquitination of IRF7 at K375 to enhance antiviral interferon responses (by displacing HDAC1), K48-linked ubiquitination of Vimentin at K97 to promote its degradation and suppress EMT/metastasis, ubiquitination and degradation of MKP1 to amplify TLR-driven JNK/p38 MAP kinase signaling, and ubiquitination of BMP7 to promote osteoclast differentiation; it has also been linked to Notch signaling pathway activation in lung epithelial development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEURL3 (LINCR/RNF132) is a substrate-specific E3 ubiquitin ligase that shapes immune signaling, epithelial-mesenchymal state, and tissue differentiation through distinct linkage-type ubiquitination events on defined targets [#0, #1, #2]. In antiviral immunity, it directly binds IRF7 and catalyzes K63-linked poly-ubiquitination at IRF7 K375, displacing HDAC1 to derepress interferon-stimulated gene transcription; Neurl3-deficient mice produce less type I interferon and are more susceptible to viral infection [#0]. In tumor biology, NEURL3 catalyzes K48-linked poly-ubiquitination of Vimentin at K97 to drive its degradation, suppressing epithelial-mesenchymal transition and metastasis in nasopharyngeal carcinoma, an effect fully reversed by Vimentin restoration [#1]. It also amplifies TLR-driven JNK and p38 MAPK signaling and inflammatory cytokine output by promoting ubiquitin-mediated degradation of the MAP kinase phosphatase MKP1 [#2]. In bone, NEURL3 promotes osteoclast differentiation through ubiquitination of BMP7, and its inhibition reduces bone loss in ovariectomy-induced osteoporosis [#3]. Conditional overexpression in mouse lung epithelium produces hypoplastic, cystic lungs with Hes1 induction, placing NEURL3 within Notch signaling during lung epithelial development [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Before molecular substrates were known, it was unclear what developmental pathway NEURL3/LINCR engaged; conditional overexpression connected it to Notch-driven lung epithelial morphogenesis.\",\n      \"evidence\": \"Doxycycline-inducible lung epithelial overexpression in transgenic mice with histology and Hes1 marker readout\",\n      \"pmids\": [\"25904058\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct ubiquitination substrate identified in this Notch context\", \"Mechanistic link to Notch is inferred from Hes1 induction, not biochemically defined\", \"Loss-of-function phenotype not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"To test whether NEURL3 functions as a ubiquitination regulator in vivo, knockdown in a fish ortholog tied its dosage to testis protein ubiquitination during spermatogenesis.\",\n      \"evidence\": \"RNAi knockdown in Cynoglossus semilaevis with RT-qPCR and bulk testis ubiquitination readout\",\n      \"pmids\": [\"27480167\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Correlation-based with no direct substrate\", \"Ortholog in a non-mammalian species\", \"Ubiquitination readout is indirect and bulk\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The first defined catalytic mechanism established NEURL3 as a K63-linkage E3 ligase that ubiquitinates IRF7 to boost antiviral interferon responses, answering how it acts at the molecular level.\",\n      \"evidence\": \"Reciprocal Co-IP, K63-specific ubiquitination assay, K375 site-directed mutagenesis, and Neurl3 knockout mice with viral infection assays\",\n      \"pmids\": [\"35792897\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of IRF7 recognition unknown\", \"Whether HDAC1 displacement is direct or downstream of ubiquitination not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"NEURL3 was shown to switch linkage type and direction of effect, performing K48-linked degradative ubiquitination of Vimentin to suppress EMT and metastasis, establishing a tumor-suppressive role.\",\n      \"evidence\": \"Mass spectrometry substrate ID, K48-specific ubiquitination assay, K97 mutagenesis, and in vivo overexpression/rescue in nasopharyngeal carcinoma models\",\n      \"pmids\": [\"38191501\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"What determines K63 versus K48 linkage choice across substrates is unknown\", \"Single tumor type tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A separate loss-of-function study placed NEURL3 in innate immune signaling amplification by degrading the MAP kinase phosphatase MKP1, defining how it sustains TLR-driven JNK/p38 activation.\",\n      \"evidence\": \"LINCR-deficient cells with TLR3/4/5 agonist stimulation, ubiquitination and kinase activation assays, cytokine production readout\",\n      \"pmids\": [\"38667302\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage type on MKP1 not specified\", \"Single lab; no in vivo confirmation\", \"Direct interaction with MKP1 not fully characterized\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"NEURL3 was extended to bone biology, where ubiquitination of BMP7 drives osteoclast differentiation, linking the ligase to osteoporosis pathology.\",\n      \"evidence\": \"BMM osteoclast differentiation model, BMP7 ubiquitination assays, rescue experiments, and OVX mouse model with micro-CT\",\n      \"pmids\": [\"39960614\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin linkage type on BMP7 not defined\", \"Single lab, single study\", \"Direct binding versus indirect effect not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NEURL3 selects among structurally diverse substrates and chooses degradative (K48) versus signaling (K63) ubiquitin linkages across immune, epithelial, and skeletal contexts remains unresolved.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of substrate recognition\", \"No unifying determinant of linkage-type selection identified\", \"Tissue-specific regulation of NEURL3 expression and activity uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"IRF7\", \"VIM\", \"DUSP1\", \"BMP7\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}