{"gene":"ZRANB1","run_date":"2026-06-11T09:02:07","timeline":{"discoveries":[{"year":2008,"finding":"Trabid/ZRANB1 binds K63-linked ubiquitin chains with its three tandem NZF (Npl4 zinc finger) domains and cleaves these chains via its OTU domain; both activities are required for efficient TCF-mediated transcription in cells with high Wnt pathway activity. Epistasis experiments showed Trabid acts below the stabilization of beta-catenin, suggesting it affects the TCF-beta-catenin transcription complex. Trabid also binds to and deubiquitylates APC, a negative regulator of Wnt transcription.","method":"In vitro DUB assay, domain-deletion/point-mutation analysis, Co-IP, epistasis in mammalian and Drosophila cells","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro enzymatic assays with mutagenesis, reciprocal Co-IP, epistasis across two organisms, replicated in multiple cell lines","pmids":["18281465"],"is_preprint":false},{"year":2014,"finding":"Drosophila Trabid interacts with TAK1, reduces its K63-linked ubiquitination (at Lys142) and immune signalling output. The three tandem NZF fingers and catalytic cysteine (C518) are required for Trabid activity. TAB2 participates in the TAK1-Trabid interaction via its zinc finger domain. Loss of Trabid causes chronic IMD pathway activation and reduced lifespan.","method":"Co-IP, ubiquitin site-mapping by mutagenesis, genetic loss-of-function in Drosophila, cell culture screen","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, mutant rescue, in vivo genetic data; single lab","pmids":["24586180"],"is_preprint":false},{"year":2016,"finding":"TRABID/ZRANB1 deubiquitinates and stabilizes the histone demethylase Jmjd2d in dendritic cells, thereby facilitating TLR-induced histone modifications at the Il12 and Il23 promoters. Deletion of Zranb1 in dendritic cells inhibited TLR-induced IL-12 and IL-23 expression, impaired inflammatory T cell differentiation, and protected mice from autoimmune inflammation.","method":"Conditional knockout mouse model, co-IP, ubiquitination assay, ChIP (histone modification), T cell differentiation assays","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with defined cellular phenotype, substrate identification by Co-IP and ubiquitination assay, chromatin-level readout; multiple orthogonal methods in one study","pmids":["26808229"],"is_preprint":false},{"year":2018,"finding":"ZRANB1 binds, deubiquitinates, and stabilizes EZH2 protein; depletion of ZRANB1 leads to EZH2 destabilization and growth inhibition in breast cancer cells.","method":"Co-IP, ubiquitination assay, siRNA knockdown, small-molecule inhibitor, in vivo xenograft model","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional KD phenotype; single lab, multiple orthogonal methods","pmids":["29669287"],"is_preprint":false},{"year":2018,"finding":"Trabid/ZRANB1 forms a complex with Twist1 and specifically cleaves RNF8-induced K63-linked polyubiquitin chains from Twist1, which promotes subsequent K48-linked ubiquitination and proteasomal degradation of Twist1. TRABID activity is activated by AKT-mediated phosphorylation at Ser78/Thr117. Knockdown of Trabid increases Twist1 K63-ubiquitination while abrogating K48-ubiquitination, enhancing HCC growth and metastasis.","method":"Co-IP, in vitro deubiquitination assay, ubiquitin chain-type discrimination assay, phosphorylation site mutagenesis, in vivo xenograft model","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, in vitro DUB assay, phosphosite mutagenesis; single lab with multiple orthogonal methods","pmids":["29748601"],"is_preprint":false},{"year":2021,"finding":"TRABID and E3 ligase UBE3C reciprocally regulate K29/K48-branched ubiquitination of VPS34. This branched ubiquitination enhances VPS34 binding to proteasomes for degradation, suppressing autophagosome formation and maturation. Under ER/proteotoxic stress, UBE3C shifts from phagophores to proteasomes, reducing VPS34 ubiquitination and elevating autophagy. TRABID-mediated VPS34 stabilization is critical for liver lipid metabolism.","method":"Co-IP, ubiquitin chain-type analysis (UBE3C/TRABID knockdown and overexpression), autophagy flux assays, liver-specific mouse models","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal regulation demonstrated by multiple biochemical assays, in vivo mouse data, multiple orthogonal methods across DUB/E3 pair","pmids":["33637724"],"is_preprint":false},{"year":2021,"finding":"TRABID/ZRANB1 stabilizes the E3 ubiquitin ligase HECTD1 by deubiquitinating it; TRABID depletion leads to rapid HECTD1 degradation. HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains and requires K29/K48 branching for full ligase activity. TRABID prefers cleavage of K29- and K33-linked chains.","method":"Catalytic-dead TRABID interactome trapping (MS), Co-IP, UbiCREST, Ub-AQUA proteomics, in vitro autoubiquitination with Ub mutants, siRNA knockdown and CRISPR KO in mammalian cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — substrate trapping by MS, in vitro reconstitution with Ub mutants, UbiCREST linkage analysis, genetic KO validation; multiple rigorous orthogonal methods in one study","pmids":["33853758"],"is_preprint":false},{"year":2021,"finding":"ZRANB1 deubiquitinates Sox9 in colorectal cancer cells, decelerating its ubiquitination and increasing Sox9 stability; stabilized Sox9 then transcriptionally activates USP22 to promote Wnt/β-catenin pathway activity and cancer stem cell features.","method":"Co-IP, ubiquitination assay, CHX chase, reporter assay, xenograft mouse model","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP and ubiquitination assay with functional downstream readouts; single lab","pmids":["34798260"],"is_preprint":false},{"year":2021,"finding":"ZRANB1 directly binds SP1 and stabilizes it by deubiquitination, which in turn upregulates LOXL2 transcription to promote HCC growth and metastasis.","method":"Co-IP, ubiquitination assay, CHX chase, RNA-seq, in vivo xenograft","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP and ubiquitination assay with functional downstream readouts; single lab","pmids":["34765294"],"is_preprint":false},{"year":2022,"finding":"ZRANB1 deubiquitinase activity (demonstrated via C443S catalytic knock-in mice) is required for normal MUC2 mucin expression in colonic goblet cells; Zranb1 C443S mutant mice show decreased MUC2 production and exacerbated DSS-induced colitis.","method":"CRISPR/Cas9 knock-in mouse model (catalytic dead C443S), colonic organoids, DSS colitis model","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — catalytic-dead knock-in mouse with defined intestinal phenotype; single lab","pmids":["36087511"],"is_preprint":false},{"year":2023,"finding":"TRABID deubiquitinates K29-linked polyubiquitin chains on 53BP1 (placed by E3 ligase SPOP), preventing 53BP1 dissociation from DNA double-strand breaks. This prolongs 53BP1 retention at DSBs, suppresses homologous recombination, and causes chromosomal instability. TRABID overexpression in prostate cancer cells sensitizes them to PARP inhibitors.","method":"Co-IP, ubiquitination assay (K29-specific), TRABID knockdown/overexpression, HR/NHEJ reporter assays, PARP inhibitor sensitivity assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and linkage-specific ubiquitination assay with functional DNA-repair readouts; single lab, multiple orthogonal methods","pmids":["37002234"],"is_preprint":false},{"year":2023,"finding":"TRABID is upregulated in mitosis and stabilizes the chromosomal passenger complex (CPC) by removing K29-linked polyubiquitin chains from Aurora B and Survivin. TRABID inhibition causes micronuclei through combined mitotic and autophagy defects, protects cGAS from autophagic degradation, and activates the cGAS/STING innate immunity pathway.","method":"Co-IP, ubiquitin chain-type assay, TRABID KO/knockdown, mitotic cell analysis, cGAS/STING reporter, in vivo tumor immunotherapy models","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple substrates identified biochemically (K29-DUB on Aurora B and Survivin), mechanistic pathway validated in vitro and in vivo, multiple orthogonal methods in one study","pmids":["37237031"],"is_preprint":false},{"year":2023,"finding":"ZRANB1 functions as an E3 ubiquitin ligase (not only a DUB) for SLC7A11: it ubiquitinates and targets SLC7A11 for degradation, thereby inhibiting glutathione synthesis and sensitizing cancer cells to ferroptosis. The region spanning residues 463–584 is required for this E3 ligase activity.","method":"sgRNA whole-DUB screen, co-IP, in vitro ubiquitination assay, domain-deletion mutagenesis, GSH measurement, lipid peroxidation assay","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — in vitro ubiquitination assay with domain mutagenesis establishing E3 activity; single lab","pmids":["37831441"],"is_preprint":false},{"year":2023,"finding":"Patient missense mutations in ZRANB1 impair either its DUB catalytic activity or its binding to STRIPAK complex. Both defects impede trafficking of APC to microtubule plus-ends, causing APC hyperubiquitylation and mislocalization, and severely compromise neuronal growth cone formation and neurite outgrowth trajectory. The proposed model is that STRIPAK recruits Trabid to deubiquitylate APC.","method":"Knock-in mouse models (patient mutations), live-cell imaging, neuronal culture, immunofluorescence, DUB activity assay, Co-IP with STRIPAK components, APC localization analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent patient-mutation knock-in mouse models, multiple orthogonal methods (DUB assay, Co-IP, live imaging, in vivo neuronal phenotyping) in one study","pmids":["38099646"],"is_preprint":false},{"year":2012,"finding":"Small molecules identified as TRABID DUB inhibitors via virtual screening and in vitro DUB assay did not inhibit β-catenin-mediated transcription. Furthermore, shRNA knockdown of TRABID or expression of a DUB-activity-deficient TRABID mutant showed little effect on β-catenin-mediated transcription (negative result).","method":"Structure-based virtual screening, in vitro DUB assay, β-catenin transcription reporter, shRNA knockdown, DUB-dead mutant overexpression","journal":"BMC chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro DUB assay with mutagenesis and functional reporter; single lab; negative finding regarding Wnt/β-catenin role","pmids":["22584113"],"is_preprint":false},{"year":2025,"finding":"Mitochondrial PTRH2 interacts with TRABID and mt-ND5 (complex I subunit). In cells lacking PTRH2, TRABID aberrantly deubiquitylates mt-ND5, increasing its stability and promoting complex I activity and ATP production, leading to mitochondrial Ca2+ overload under stress. Re-expression of PTRH2 blocks TRABID-mediated mt-ND5 deubiquitylation, resulting in mt-ND5 polyubiquitylation and proteasomal degradation.","method":"Immunoprecipitation/mass spectrometry proteomics, co-IP, ubiquitination assay, PTRH2 knockout/re-expression, mitochondrial Ca2+ measurement, complex I activity assay","journal":"PNAS nexus","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — IP-MS substrate identification, co-IP, ubiquitination assay with functional rescue; single lab","pmids":["40496187"],"is_preprint":false},{"year":2025,"finding":"TRABID removes K29-linked ubiquitination from the H3K9me3 methyltransferase SUV39H1, antagonizing the TRIP12 E3 ligase. K29-linked ubiquitination is essential for proteasomal degradation of SUV39H1, and TRABID-mediated reversal of this modification stabilizes SUV39H1, thereby controlling the H3K9me3 epigenetic landscape.","method":"Cell-based ubiquitin replacement strategy (conditional chain-type abrogation), ubiquitination assays, TRABID/TRIP12 genetic manipulation, H3K9me3 ChIP","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — engineered ubiquitin replacement system with ChIP readout; preprint, single lab, novel orthogonal approach","pmids":["bio_10.1101_2024.10.29.620783"],"is_preprint":true},{"year":2025,"finding":"ZRANB1 regulates K33-linked deubiquitination of cathepsin B (CTSB), stabilizing CTSB expression. In HBV-positive HCC cells, the MINPP1-ZRANB1-CTSB axis promotes ferroptosis; this axis is inactive in HBV-negative cells unless HBV is introduced.","method":"Co-immunoprecipitation, ubiquitin modification analysis (K33-linkage), immunofluorescence, in vivo tumor experiments","journal":"Biology direct","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP and ubiquitination assay; single lab, limited mechanistic follow-up","pmids":["41035046"],"is_preprint":false},{"year":2026,"finding":"ZRANB1 deubiquitinates and stabilizes SF3B3 (a spliceosomal protein), preventing its UPS-dependent degradation. Stabilization of SF3B3 by ZRANB1 modulates alternative splicing of CHEK2, specifically suppressing production of the tumor-suppressive exon-4-skipped isoform in urothelial bladder cancer.","method":"Co-immunoprecipitation coupled with mass spectrometry, ubiquitination assay, alternative splicing analysis, in vitro and in vivo tumor models","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — IP-MS substrate identification, ubiquitination assay, splicing readout; single lab","pmids":["42265067"],"is_preprint":false},{"year":2026,"finding":"UCHL5 directly interacts with ZRANB1 (co-IP) and extends ZRANB1 protein half-life by more than 2-fold through deubiquitination, establishing UCHL5 as an upstream stabilizer of ZRANB1.","method":"Co-immunoprecipitation, CHX chase, protein half-life measurement, CRISPR KO and overexpression","journal":"Cancer biology & therapy","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP and CHX chase; single lab, no in vitro reconstitution","pmids":["42037453"],"is_preprint":false},{"year":2026,"finding":"ZRANB1 directly binds EZH2 (confirmed by in vitro pull-down) and deubiquitinates EZH2 to stabilize it; stabilized EZH2 in turn maintains MYCN stability in a ternary ZRANB1-EZH2-MYCN complex. DUB activity is required for MYCN stabilization.","method":"Co-IP, in vitro pull-down, CHX chase, ubiquitination assay, catalytic-dead mutant, xenograft model","journal":"Cell biology and toxicology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro pull-down and ubiquitination assay with catalytic-dead mutant controls; single lab","pmids":["41949670"],"is_preprint":false}],"current_model":"ZRANB1/TRABID is an OTU-domain deubiquitinase with preference for cleaving K29-, K33-, and K63-linked ubiquitin chains (via its NZF fingers for chain binding and OTU domain for catalysis) that acts on a broad substrate range including APC, VPS34 (opposing UBE3C-mediated K29/K48-branched ubiquitination to regulate autophagy), EZH2, HECTD1, Jmjd2d, Twist1, Sox9, SP1, Aurora B/Survivin (CPC), 53BP1, SLC7A11, mt-ND5, SUV39H1, SF3B3, and CTSB; it also unexpectedly possesses E3 ligase activity toward SLC7A11; through these substrates it controls Wnt/TCF transcription, innate immune cytokine expression, autophagy-UPS crosstalk, mitotic chromosome segregation, cGAS/STING anti-tumor immunity, DNA repair pathway choice (NHEJ vs HR), neurite outgrowth via APC trafficking, ferroptosis sensitivity, and liver lipid metabolism."},"narrative":{"mechanistic_narrative":"ZRANB1 (TRABID) is an OTU-family deubiquitinase that uses three tandem NZF zinc-finger domains to bind atypical polyubiquitin chains and its OTU catalytic domain to cleave them, with biochemical preference for K29-, K33-, and K63-linked linkages [PMID:18281465, PMID:33853758]. Its principal cellular function is to stabilize a broad set of substrates by removing degradative or regulatory ubiquitin chains, thereby controlling diverse downstream programs. In chromatin and transcription it deubiquitinates and stabilizes the histone demethylase Jmjd2d to license TLR-induced IL-12/IL-23 expression and inflammatory T-cell differentiation [PMID:26808229], the methyltransferase SUV39H1 to shape the H3K9me3 landscape [PMID:bio_10.1101_2024.10.29.620783], and the polycomb subunit EZH2 to support cancer cell growth [PMID:29669287, PMID:41949670]. It also operates at the ubiquitin-proteasome/autophagy interface, where it opposes the E3 ligase UBE3C by removing K29/K48-branched chains from VPS34 to promote autophagosome formation and govern liver lipid metabolism [PMID:33637724], and stabilizes the E3 ligase HECTD1 [PMID:33853758]. In mitosis ZRANB1 stabilizes the chromosomal passenger complex by stripping K29-linked chains from Aurora B and Survivin, and its inhibition couples mitotic defects to cGAS/STING innate-immune activation [PMID:37237031]. In the DNA damage response it removes SPOP-deposited K29 chains from 53BP1 to prolong 53BP1 retention at double-strand breaks and bias repair away from homologous recombination [PMID:37002234]. Beyond canonical DUB activity, ZRANB1 unexpectedly acts as an E3 ligase toward SLC7A11, targeting it for degradation to sensitize cells to ferroptosis [PMID:37831441]. ZRANB1 mediates STRIPAK-directed deubiquitination of APC to enable APC trafficking to microtubule plus-ends; patient missense mutations that impair either DUB activity or STRIPAK binding disrupt growth-cone formation and neurite outgrowth [PMID:38099646].","teleology":[{"year":2008,"claim":"Established the founding biochemical logic of the enzyme: how it recognizes and cleaves ubiquitin chains and links that activity to a transcriptional output.","evidence":"In vitro DUB assays with domain-deletion/point mutants, Co-IP, and epistasis across mammalian and Drosophila cells","pmids":["18281465"],"confidence":"High","gaps":["Chain-linkage preference beyond K63 not yet resolved","Direct substrate underlying the TCF effect not fully defined"]},{"year":2012,"claim":"Challenged the proposed Wnt/beta-catenin role by showing DUB inhibition and catalytic-dead mutants had little effect on beta-catenin transcription, indicating context dependence of the early model.","evidence":"Structure-based virtual screening, in vitro DUB assay, beta-catenin reporter, shRNA and DUB-dead mutant (negative result)","pmids":["22584113"],"confidence":"Medium","gaps":["Negative result; does not exclude cell-type-specific Wnt regulation","Inhibitor potency/selectivity in cells not established"]},{"year":2014,"claim":"Extended the enzyme into innate immune signalling, showing it tunes K63-ubiquitination of TAK1 and immune output in vivo.","evidence":"Co-IP, ubiquitin site-mapping, Drosophila loss-of-function genetics","pmids":["24586180"],"confidence":"Medium","gaps":["Mammalian conservation of TAK1 regulation not shown here","Single lab"]},{"year":2016,"claim":"Provided the first mammalian genetic proof that DUB-mediated substrate stabilization (Jmjd2d) controls a defined chromatin and immune phenotype.","evidence":"Conditional KO mouse, Co-IP, ubiquitination assay, ChIP, T-cell differentiation assays","pmids":["26808229"],"confidence":"High","gaps":["Chain linkage on Jmjd2d not specified","Direct vs indirect promoter effects not fully separated"]},{"year":2018,"claim":"Defined regulated substrate selection — AKT phosphorylation activates the enzyme to edit K63 chains on Twist1, redirecting it toward K48 degradation — and added EZH2 stabilization as an oncogenic axis.","evidence":"In vitro DUB and chain-discrimination assays, phosphosite mutagenesis, Co-IP, xenografts","pmids":["29748601","29669287"],"confidence":"Medium","gaps":["Upstream regulation generalizability beyond AKT unknown","Single-lab substrate sets"]},{"year":2021,"claim":"Pinned down K29/K33 chain-cleavage preference and embedded the enzyme in UPS-autophagy crosstalk by showing reciprocal control of branched VPS34 ubiquitination with UBE3C and stabilization of E3 ligases (HECTD1) and transcription factors (Sox9, SP1).","evidence":"Catalytic-dead interactome trapping/MS, UbiCREST, Ub-AQUA, reciprocal E3/DUB perturbation, autophagy flux and liver mouse models","pmids":["33637724","33853758","34798260","34765294"],"confidence":"High","gaps":["How branched-chain specificity is achieved structurally unclear","Substrate-recruitment determinants not mapped"]},{"year":2022,"claim":"Used a catalytic-dead knock-in mouse to show DUB activity is physiologically required for MUC2 mucin production and intestinal barrier protection.","evidence":"C443S knock-in mouse, colonic organoids, DSS colitis model","pmids":["36087511"],"confidence":"Medium","gaps":["Direct substrate driving MUC2 phenotype not identified","Single lab"]},{"year":2023,"claim":"Expanded the enzyme into genome maintenance, mitosis, ferroptosis, and neurodevelopment, and overturned its classification as a pure DUB by demonstrating E3 ligase activity toward SLC7A11.","evidence":"K29-specific ubiquitination/DUB assays, HR/NHEJ reporters, CPC/cGAS-STING analyses, whole-DUB sgRNA screen with in vitro ubiquitination, patient-mutation knock-in mice and neuronal imaging","pmids":["37002234","37237031","37831441","38099646"],"confidence":"High","gaps":["Mechanism switching between DUB and E3 modes unresolved","STRIPAK-mediated recruitment to APC structurally undefined"]},{"year":2025,"claim":"Added mitochondrial (mt-ND5/complex I) and epigenetic (SUV39H1) substrates, showing scaffold-dependent restriction (PTRH2) and K29-linkage editing against specific E3 ligases.","evidence":"IP-MS, co-IP, ubiquitination assays, PTRH2 KO/re-expression, complex I and Ca2+ assays; engineered ubiquitin-replacement system with ChIP (preprint)","pmids":["40496187","bio_10.1101_2024.10.29.620783"],"confidence":"Medium","gaps":["Mitochondrial localization mechanism of the enzyme unclear","SUV39H1 finding is a preprint, single lab"]},{"year":2026,"claim":"Linked the enzyme to splicing control via SF3B3 stabilization and CHEK2 isoform choice, and added EZH2-MYCN and CTSB axes plus an upstream stabilizer (UCHL5).","evidence":"IP-MS, ubiquitination assays, splicing analysis, ternary-complex pull-downs, CHX chase, tumor models","pmids":["42265067","41949670","41035046","42037453"],"confidence":"Medium","gaps":["UCHL5 and CTSB axes rest on single Co-IP/CHX without reconstitution","Direct vs indirect splicing effects not fully separated"]},{"year":null,"claim":"How a single enzyme switches between deubiquitinase and E3 ligase activity, and what governs its substrate and chain-linkage selectivity in each cellular context, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of DUB-vs-E3 mode switching","Determinants of substrate targeting across compartments unknown","Physiological hierarchy among the many reported substrates undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,5,6,10,11,12]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,6,11]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,10,16]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[15]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5,11]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,5,6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2,11]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[11]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,16]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[12]}],"complexes":["STRIPAK","chromosomal passenger complex (CPC)"],"partners":["VPS34","UBE3C","HECTD1","EZH2","53BP1","APC","PTRH2","SF3B3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UGI0","full_name":"Ubiquitin thioesterase ZRANB1","aliases":["TRAF-binding domain-containing protein","hTrabid","Zinc finger Ran-binding domain-containing protein 1"],"length_aa":708,"mass_kda":81.0,"function":"Ubiquitin thioesterase, which specifically hydrolyzes 'Lys-29'-linked and 'Lys-33'-linked diubiquitin (PubMed:22157957, PubMed:23827681, PubMed:25752573, PubMed:25752577). Also cleaves 'Lys-63'-linked chains, but with 40-fold less efficiency compared to 'Lys-29'-linked ones (PubMed:18281465). Positive regulator of the Wnt signaling pathway that deubiquitinates APC protein, a negative regulator of Wnt-mediated transcription (PubMed:18281465). Acts as a regulator of autophagy by mediating deubiquitination of PIK3C3/VPS34, thereby promoting autophagosome maturation (PubMed:33637724). Plays a role in the regulation of cell morphology and cytoskeletal organization (PubMed:21834987). Required in the stress fiber dynamics and cell migration (PubMed:21834987)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9UGI0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZRANB1","classification":"Not Classified","n_dependent_lines":25,"n_total_lines":1208,"dependency_fraction":0.020695364238410598},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZRANB1","total_profiled":1310},"omim":[{"mim_id":"618649","title":"HECT DOMAIN E3 UBIQUITIN PROTEIN LIGASE 1; HECTD1","url":"https://www.omim.org/entry/618649"},{"mim_id":"611749","title":"ZINC FINGER RANBP2-TYPE DOMAIN-CONTAINING PROTEIN 1; ZRANB1","url":"https://www.omim.org/entry/611749"},{"mim_id":"611748","title":"OTU DOMAIN-CONTAINING PROTEIN 7B; OTUD7B","url":"https://www.omim.org/entry/611748"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZRANB1"},"hgnc":{"alias_symbol":["TRABID"],"prev_symbol":[]},"alphafold":{"accession":"Q9UGI0","domains":[{"cath_id":"-","chopping":"1-33","consensus_level":"medium","plddt":80.6215,"start":1,"end":33},{"cath_id":"1.25.40.560","chopping":"244-340","consensus_level":"high","plddt":89.7657,"start":244,"end":340},{"cath_id":"3.90.70.80","chopping":"355-595_611-688","consensus_level":"high","plddt":93.4819,"start":355,"end":688}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UGI0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UGI0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UGI0-F1-predicted_aligned_error_v6.png","plddt_mean":76.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZRANB1","jax_strain_url":"https://www.jax.org/strain/search?query=ZRANB1"},"sequence":{"accession":"Q9UGI0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UGI0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UGI0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UGI0"}},"corpus_meta":[{"pmid":"18281465","id":"PMC_18281465","title":"Trabid, a new positive regulator of Wnt-induced transcription with preference for binding and cleaving K63-linked ubiquitin chains.","date":"2008","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/18281465","citation_count":98,"is_preprint":false},{"pmid":"26808229","id":"PMC_26808229","title":"Epigenetic regulation of the expression of Il12 and Il23 and autoimmune inflammation by the deubiquitinase Trabid.","date":"2016","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/26808229","citation_count":87,"is_preprint":false},{"pmid":"33637724","id":"PMC_33637724","title":"VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, proteostasis and liver metabolism.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33637724","citation_count":73,"is_preprint":false},{"pmid":"29669287","id":"PMC_29669287","title":"ZRANB1 Is an EZH2 Deubiquitinase and a Potential Therapeutic Target in Breast Cancer.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/29669287","citation_count":51,"is_preprint":false},{"pmid":"24586180","id":"PMC_24586180","title":"Loss of Trabid, a new negative regulator of the drosophila immune-deficiency pathway at the level of TAK1, reduces life span.","date":"2014","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24586180","citation_count":49,"is_preprint":false},{"pmid":"29748605","id":"PMC_29748605","title":"Targeting circular RNA-ZRANB1 for therapeutic intervention in retinal neurodegeneration.","date":"2018","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/29748605","citation_count":43,"is_preprint":false},{"pmid":"29748601","id":"PMC_29748601","title":"Trabid inhibits hepatocellular carcinoma growth and metastasis by cleaving RNF8-induced K63 ubiquitination of Twist1.","date":"2018","source":"Cell death and 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models.","date":"2020","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/32777532","citation_count":28,"is_preprint":false},{"pmid":"33853758","id":"PMC_33853758","title":"The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1.","date":"2021","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33853758","citation_count":24,"is_preprint":false},{"pmid":"37002234","id":"PMC_37002234","title":"TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37002234","citation_count":22,"is_preprint":false},{"pmid":"34765294","id":"PMC_34765294","title":"Deubiquitinase ZRANB1 drives hepatocellular carcinoma progression through SP1-LOXL2 axis.","date":"2021","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/34765294","citation_count":19,"is_preprint":false},{"pmid":"37831441","id":"PMC_37831441","title":"The deubiquitinase ZRANB1 is an E3 ubiquitin ligase for SLC7A11 and regulates ferroptotic resistance.","date":"2023","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/37831441","citation_count":18,"is_preprint":false},{"pmid":"22584113","id":"PMC_22584113","title":"Identification Of Small Molecule TRABID Deubiquitinase Inhibitors By Computation-Based Virtual Screen.","date":"2012","source":"BMC chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/22584113","citation_count":15,"is_preprint":false},{"pmid":"23743024","id":"PMC_23743024","title":"UBE3B and ZRANB1 polymorphisms and transcript abundance are associated with water holding capacity of porcine M. longissimus dorsi.","date":"2013","source":"Meat 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disease","url":"https://pubmed.ncbi.nlm.nih.gov/42265067","citation_count":0,"is_preprint":false},{"pmid":"42037453","id":"PMC_42037453","title":"UCHL5 suppresses thyroid carcinoma progression via ZRANB1 stabilization and ferroptosis regulation.","date":"2026","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/42037453","citation_count":0,"is_preprint":false},{"pmid":"41949670","id":"PMC_41949670","title":"ZRANB1 depletion inhibits neuroblastoma progression by destabilizing MYCN through EZH2-mediated deubiquitination.","date":"2026","source":"Cell biology and toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/41949670","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.29.620783","title":"Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity","date":"2024-11-02","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.29.620783","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.17.613539","title":"Decoding polyubiquitin regulation of K  <sub>V</sub>  7. 1 functional expression with engineered linkage-selective deubiquitinases","date":"2024-09-17","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.17.613539","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15085,"output_tokens":5524,"usd":0.064058,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13910,"output_tokens":3878,"usd":0.08325,"stage2_stop_reason":"end_turn"},"total_usd":0.147308,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"Trabid/ZRANB1 binds K63-linked ubiquitin chains with its three tandem NZF (Npl4 zinc finger) domains and cleaves these chains via its OTU domain; both activities are required for efficient TCF-mediated transcription in cells with high Wnt pathway activity. Epistasis experiments showed Trabid acts below the stabilization of beta-catenin, suggesting it affects the TCF-beta-catenin transcription complex. Trabid also binds to and deubiquitylates APC, a negative regulator of Wnt transcription.\",\n      \"method\": \"In vitro DUB assay, domain-deletion/point-mutation analysis, Co-IP, epistasis in mammalian and Drosophila cells\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro enzymatic assays with mutagenesis, reciprocal Co-IP, epistasis across two organisms, replicated in multiple cell lines\",\n      \"pmids\": [\"18281465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Drosophila Trabid interacts with TAK1, reduces its K63-linked ubiquitination (at Lys142) and immune signalling output. The three tandem NZF fingers and catalytic cysteine (C518) are required for Trabid activity. TAB2 participates in the TAK1-Trabid interaction via its zinc finger domain. Loss of Trabid causes chronic IMD pathway activation and reduced lifespan.\",\n      \"method\": \"Co-IP, ubiquitin site-mapping by mutagenesis, genetic loss-of-function in Drosophila, cell culture screen\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, mutant rescue, in vivo genetic data; single lab\",\n      \"pmids\": [\"24586180\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TRABID/ZRANB1 deubiquitinates and stabilizes the histone demethylase Jmjd2d in dendritic cells, thereby facilitating TLR-induced histone modifications at the Il12 and Il23 promoters. Deletion of Zranb1 in dendritic cells inhibited TLR-induced IL-12 and IL-23 expression, impaired inflammatory T cell differentiation, and protected mice from autoimmune inflammation.\",\n      \"method\": \"Conditional knockout mouse model, co-IP, ubiquitination assay, ChIP (histone modification), T cell differentiation assays\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with defined cellular phenotype, substrate identification by Co-IP and ubiquitination assay, chromatin-level readout; multiple orthogonal methods in one study\",\n      \"pmids\": [\"26808229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ZRANB1 binds, deubiquitinates, and stabilizes EZH2 protein; depletion of ZRANB1 leads to EZH2 destabilization and growth inhibition in breast cancer cells.\",\n      \"method\": \"Co-IP, ubiquitination assay, siRNA knockdown, small-molecule inhibitor, in vivo xenograft model\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay with functional KD phenotype; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"29669287\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Trabid/ZRANB1 forms a complex with Twist1 and specifically cleaves RNF8-induced K63-linked polyubiquitin chains from Twist1, which promotes subsequent K48-linked ubiquitination and proteasomal degradation of Twist1. TRABID activity is activated by AKT-mediated phosphorylation at Ser78/Thr117. Knockdown of Trabid increases Twist1 K63-ubiquitination while abrogating K48-ubiquitination, enhancing HCC growth and metastasis.\",\n      \"method\": \"Co-IP, in vitro deubiquitination assay, ubiquitin chain-type discrimination assay, phosphorylation site mutagenesis, in vivo xenograft model\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, in vitro DUB assay, phosphosite mutagenesis; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"29748601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRABID and E3 ligase UBE3C reciprocally regulate K29/K48-branched ubiquitination of VPS34. This branched ubiquitination enhances VPS34 binding to proteasomes for degradation, suppressing autophagosome formation and maturation. Under ER/proteotoxic stress, UBE3C shifts from phagophores to proteasomes, reducing VPS34 ubiquitination and elevating autophagy. TRABID-mediated VPS34 stabilization is critical for liver lipid metabolism.\",\n      \"method\": \"Co-IP, ubiquitin chain-type analysis (UBE3C/TRABID knockdown and overexpression), autophagy flux assays, liver-specific mouse models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal regulation demonstrated by multiple biochemical assays, in vivo mouse data, multiple orthogonal methods across DUB/E3 pair\",\n      \"pmids\": [\"33637724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRABID/ZRANB1 stabilizes the E3 ubiquitin ligase HECTD1 by deubiquitinating it; TRABID depletion leads to rapid HECTD1 degradation. HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains and requires K29/K48 branching for full ligase activity. TRABID prefers cleavage of K29- and K33-linked chains.\",\n      \"method\": \"Catalytic-dead TRABID interactome trapping (MS), Co-IP, UbiCREST, Ub-AQUA proteomics, in vitro autoubiquitination with Ub mutants, siRNA knockdown and CRISPR KO in mammalian cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — substrate trapping by MS, in vitro reconstitution with Ub mutants, UbiCREST linkage analysis, genetic KO validation; multiple rigorous orthogonal methods in one study\",\n      \"pmids\": [\"33853758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZRANB1 deubiquitinates Sox9 in colorectal cancer cells, decelerating its ubiquitination and increasing Sox9 stability; stabilized Sox9 then transcriptionally activates USP22 to promote Wnt/β-catenin pathway activity and cancer stem cell features.\",\n      \"method\": \"Co-IP, ubiquitination assay, CHX chase, reporter assay, xenograft mouse model\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP and ubiquitination assay with functional downstream readouts; single lab\",\n      \"pmids\": [\"34798260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZRANB1 directly binds SP1 and stabilizes it by deubiquitination, which in turn upregulates LOXL2 transcription to promote HCC growth and metastasis.\",\n      \"method\": \"Co-IP, ubiquitination assay, CHX chase, RNA-seq, in vivo xenograft\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP and ubiquitination assay with functional downstream readouts; single lab\",\n      \"pmids\": [\"34765294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ZRANB1 deubiquitinase activity (demonstrated via C443S catalytic knock-in mice) is required for normal MUC2 mucin expression in colonic goblet cells; Zranb1 C443S mutant mice show decreased MUC2 production and exacerbated DSS-induced colitis.\",\n      \"method\": \"CRISPR/Cas9 knock-in mouse model (catalytic dead C443S), colonic organoids, DSS colitis model\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — catalytic-dead knock-in mouse with defined intestinal phenotype; single lab\",\n      \"pmids\": [\"36087511\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRABID deubiquitinates K29-linked polyubiquitin chains on 53BP1 (placed by E3 ligase SPOP), preventing 53BP1 dissociation from DNA double-strand breaks. This prolongs 53BP1 retention at DSBs, suppresses homologous recombination, and causes chromosomal instability. TRABID overexpression in prostate cancer cells sensitizes them to PARP inhibitors.\",\n      \"method\": \"Co-IP, ubiquitination assay (K29-specific), TRABID knockdown/overexpression, HR/NHEJ reporter assays, PARP inhibitor sensitivity assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and linkage-specific ubiquitination assay with functional DNA-repair readouts; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37002234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TRABID is upregulated in mitosis and stabilizes the chromosomal passenger complex (CPC) by removing K29-linked polyubiquitin chains from Aurora B and Survivin. TRABID inhibition causes micronuclei through combined mitotic and autophagy defects, protects cGAS from autophagic degradation, and activates the cGAS/STING innate immunity pathway.\",\n      \"method\": \"Co-IP, ubiquitin chain-type assay, TRABID KO/knockdown, mitotic cell analysis, cGAS/STING reporter, in vivo tumor immunotherapy models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple substrates identified biochemically (K29-DUB on Aurora B and Survivin), mechanistic pathway validated in vitro and in vivo, multiple orthogonal methods in one study\",\n      \"pmids\": [\"37237031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ZRANB1 functions as an E3 ubiquitin ligase (not only a DUB) for SLC7A11: it ubiquitinates and targets SLC7A11 for degradation, thereby inhibiting glutathione synthesis and sensitizing cancer cells to ferroptosis. The region spanning residues 463–584 is required for this E3 ligase activity.\",\n      \"method\": \"sgRNA whole-DUB screen, co-IP, in vitro ubiquitination assay, domain-deletion mutagenesis, GSH measurement, lipid peroxidation assay\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ubiquitination assay with domain mutagenesis establishing E3 activity; single lab\",\n      \"pmids\": [\"37831441\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Patient missense mutations in ZRANB1 impair either its DUB catalytic activity or its binding to STRIPAK complex. Both defects impede trafficking of APC to microtubule plus-ends, causing APC hyperubiquitylation and mislocalization, and severely compromise neuronal growth cone formation and neurite outgrowth trajectory. The proposed model is that STRIPAK recruits Trabid to deubiquitylate APC.\",\n      \"method\": \"Knock-in mouse models (patient mutations), live-cell imaging, neuronal culture, immunofluorescence, DUB activity assay, Co-IP with STRIPAK components, APC localization analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent patient-mutation knock-in mouse models, multiple orthogonal methods (DUB assay, Co-IP, live imaging, in vivo neuronal phenotyping) in one study\",\n      \"pmids\": [\"38099646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Small molecules identified as TRABID DUB inhibitors via virtual screening and in vitro DUB assay did not inhibit β-catenin-mediated transcription. Furthermore, shRNA knockdown of TRABID or expression of a DUB-activity-deficient TRABID mutant showed little effect on β-catenin-mediated transcription (negative result).\",\n      \"method\": \"Structure-based virtual screening, in vitro DUB assay, β-catenin transcription reporter, shRNA knockdown, DUB-dead mutant overexpression\",\n      \"journal\": \"BMC chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro DUB assay with mutagenesis and functional reporter; single lab; negative finding regarding Wnt/β-catenin role\",\n      \"pmids\": [\"22584113\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Mitochondrial PTRH2 interacts with TRABID and mt-ND5 (complex I subunit). In cells lacking PTRH2, TRABID aberrantly deubiquitylates mt-ND5, increasing its stability and promoting complex I activity and ATP production, leading to mitochondrial Ca2+ overload under stress. Re-expression of PTRH2 blocks TRABID-mediated mt-ND5 deubiquitylation, resulting in mt-ND5 polyubiquitylation and proteasomal degradation.\",\n      \"method\": \"Immunoprecipitation/mass spectrometry proteomics, co-IP, ubiquitination assay, PTRH2 knockout/re-expression, mitochondrial Ca2+ measurement, complex I activity assay\",\n      \"journal\": \"PNAS nexus\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — IP-MS substrate identification, co-IP, ubiquitination assay with functional rescue; single lab\",\n      \"pmids\": [\"40496187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TRABID removes K29-linked ubiquitination from the H3K9me3 methyltransferase SUV39H1, antagonizing the TRIP12 E3 ligase. K29-linked ubiquitination is essential for proteasomal degradation of SUV39H1, and TRABID-mediated reversal of this modification stabilizes SUV39H1, thereby controlling the H3K9me3 epigenetic landscape.\",\n      \"method\": \"Cell-based ubiquitin replacement strategy (conditional chain-type abrogation), ubiquitination assays, TRABID/TRIP12 genetic manipulation, H3K9me3 ChIP\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — engineered ubiquitin replacement system with ChIP readout; preprint, single lab, novel orthogonal approach\",\n      \"pmids\": [\"bio_10.1101_2024.10.29.620783\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZRANB1 regulates K33-linked deubiquitination of cathepsin B (CTSB), stabilizing CTSB expression. In HBV-positive HCC cells, the MINPP1-ZRANB1-CTSB axis promotes ferroptosis; this axis is inactive in HBV-negative cells unless HBV is introduced.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitin modification analysis (K33-linkage), immunofluorescence, in vivo tumor experiments\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP and ubiquitination assay; single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"41035046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZRANB1 deubiquitinates and stabilizes SF3B3 (a spliceosomal protein), preventing its UPS-dependent degradation. Stabilization of SF3B3 by ZRANB1 modulates alternative splicing of CHEK2, specifically suppressing production of the tumor-suppressive exon-4-skipped isoform in urothelial bladder cancer.\",\n      \"method\": \"Co-immunoprecipitation coupled with mass spectrometry, ubiquitination assay, alternative splicing analysis, in vitro and in vivo tumor models\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — IP-MS substrate identification, ubiquitination assay, splicing readout; single lab\",\n      \"pmids\": [\"42265067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UCHL5 directly interacts with ZRANB1 (co-IP) and extends ZRANB1 protein half-life by more than 2-fold through deubiquitination, establishing UCHL5 as an upstream stabilizer of ZRANB1.\",\n      \"method\": \"Co-immunoprecipitation, CHX chase, protein half-life measurement, CRISPR KO and overexpression\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP and CHX chase; single lab, no in vitro reconstitution\",\n      \"pmids\": [\"42037453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZRANB1 directly binds EZH2 (confirmed by in vitro pull-down) and deubiquitinates EZH2 to stabilize it; stabilized EZH2 in turn maintains MYCN stability in a ternary ZRANB1-EZH2-MYCN complex. DUB activity is required for MYCN stabilization.\",\n      \"method\": \"Co-IP, in vitro pull-down, CHX chase, ubiquitination assay, catalytic-dead mutant, xenograft model\",\n      \"journal\": \"Cell biology and toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro pull-down and ubiquitination assay with catalytic-dead mutant controls; single lab\",\n      \"pmids\": [\"41949670\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZRANB1/TRABID is an OTU-domain deubiquitinase with preference for cleaving K29-, K33-, and K63-linked ubiquitin chains (via its NZF fingers for chain binding and OTU domain for catalysis) that acts on a broad substrate range including APC, VPS34 (opposing UBE3C-mediated K29/K48-branched ubiquitination to regulate autophagy), EZH2, HECTD1, Jmjd2d, Twist1, Sox9, SP1, Aurora B/Survivin (CPC), 53BP1, SLC7A11, mt-ND5, SUV39H1, SF3B3, and CTSB; it also unexpectedly possesses E3 ligase activity toward SLC7A11; through these substrates it controls Wnt/TCF transcription, innate immune cytokine expression, autophagy-UPS crosstalk, mitotic chromosome segregation, cGAS/STING anti-tumor immunity, DNA repair pathway choice (NHEJ vs HR), neurite outgrowth via APC trafficking, ferroptosis sensitivity, and liver lipid metabolism.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZRANB1 (TRABID) is an OTU-family deubiquitinase that uses three tandem NZF zinc-finger domains to bind atypical polyubiquitin chains and its OTU catalytic domain to cleave them, with biochemical preference for K29-, K33-, and K63-linked linkages [#0, #6]. Its principal cellular function is to stabilize a broad set of substrates by removing degradative or regulatory ubiquitin chains, thereby controlling diverse downstream programs. In chromatin and transcription it deubiquitinates and stabilizes the histone demethylase Jmjd2d to license TLR-induced IL-12/IL-23 expression and inflammatory T-cell differentiation [#2], the methyltransferase SUV39H1 to shape the H3K9me3 landscape [#16], and the polycomb subunit EZH2 to support cancer cell growth [#3, #20]. It also operates at the ubiquitin-proteasome/autophagy interface, where it opposes the E3 ligase UBE3C by removing K29/K48-branched chains from VPS34 to promote autophagosome formation and govern liver lipid metabolism [#5], and stabilizes the E3 ligase HECTD1 [#6]. In mitosis ZRANB1 stabilizes the chromosomal passenger complex by stripping K29-linked chains from Aurora B and Survivin, and its inhibition couples mitotic defects to cGAS/STING innate-immune activation [#11]. In the DNA damage response it removes SPOP-deposited K29 chains from 53BP1 to prolong 53BP1 retention at double-strand breaks and bias repair away from homologous recombination [#10]. Beyond canonical DUB activity, ZRANB1 unexpectedly acts as an E3 ligase toward SLC7A11, targeting it for degradation to sensitize cells to ferroptosis [#12]. ZRANB1 mediates STRIPAK-directed deubiquitination of APC to enable APC trafficking to microtubule plus-ends; patient missense mutations that impair either DUB activity or STRIPAK binding disrupt growth-cone formation and neurite outgrowth [#13].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established the founding biochemical logic of the enzyme: how it recognizes and cleaves ubiquitin chains and links that activity to a transcriptional output.\",\n      \"evidence\": \"In vitro DUB assays with domain-deletion/point mutants, Co-IP, and epistasis across mammalian and Drosophila cells\",\n      \"pmids\": [\"18281465\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Chain-linkage preference beyond K63 not yet resolved\", \"Direct substrate underlying the TCF effect not fully defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Challenged the proposed Wnt/beta-catenin role by showing DUB inhibition and catalytic-dead mutants had little effect on beta-catenin transcription, indicating context dependence of the early model.\",\n      \"evidence\": \"Structure-based virtual screening, in vitro DUB assay, beta-catenin reporter, shRNA and DUB-dead mutant (negative result)\",\n      \"pmids\": [\"22584113\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative result; does not exclude cell-type-specific Wnt regulation\", \"Inhibitor potency/selectivity in cells not established\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Extended the enzyme into innate immune signalling, showing it tunes K63-ubiquitination of TAK1 and immune output in vivo.\",\n      \"evidence\": \"Co-IP, ubiquitin site-mapping, Drosophila loss-of-function genetics\",\n      \"pmids\": [\"24586180\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mammalian conservation of TAK1 regulation not shown here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Provided the first mammalian genetic proof that DUB-mediated substrate stabilization (Jmjd2d) controls a defined chromatin and immune phenotype.\",\n      \"evidence\": \"Conditional KO mouse, Co-IP, ubiquitination assay, ChIP, T-cell differentiation assays\",\n      \"pmids\": [\"26808229\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Chain linkage on Jmjd2d not specified\", \"Direct vs indirect promoter effects not fully separated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined regulated substrate selection — AKT phosphorylation activates the enzyme to edit K63 chains on Twist1, redirecting it toward K48 degradation — and added EZH2 stabilization as an oncogenic axis.\",\n      \"evidence\": \"In vitro DUB and chain-discrimination assays, phosphosite mutagenesis, Co-IP, xenografts\",\n      \"pmids\": [\"29748601\", \"29669287\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Upstream regulation generalizability beyond AKT unknown\", \"Single-lab substrate sets\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Pinned down K29/K33 chain-cleavage preference and embedded the enzyme in UPS-autophagy crosstalk by showing reciprocal control of branched VPS34 ubiquitination with UBE3C and stabilization of E3 ligases (HECTD1) and transcription factors (Sox9, SP1).\",\n      \"evidence\": \"Catalytic-dead interactome trapping/MS, UbiCREST, Ub-AQUA, reciprocal E3/DUB perturbation, autophagy flux and liver mouse models\",\n      \"pmids\": [\"33637724\", \"33853758\", \"34798260\", \"34765294\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How branched-chain specificity is achieved structurally unclear\", \"Substrate-recruitment determinants not mapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Used a catalytic-dead knock-in mouse to show DUB activity is physiologically required for MUC2 mucin production and intestinal barrier protection.\",\n      \"evidence\": \"C443S knock-in mouse, colonic organoids, DSS colitis model\",\n      \"pmids\": [\"36087511\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrate driving MUC2 phenotype not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Expanded the enzyme into genome maintenance, mitosis, ferroptosis, and neurodevelopment, and overturned its classification as a pure DUB by demonstrating E3 ligase activity toward SLC7A11.\",\n      \"evidence\": \"K29-specific ubiquitination/DUB assays, HR/NHEJ reporters, CPC/cGAS-STING analyses, whole-DUB sgRNA screen with in vitro ubiquitination, patient-mutation knock-in mice and neuronal imaging\",\n      \"pmids\": [\"37002234\", \"37237031\", \"37831441\", \"38099646\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism switching between DUB and E3 modes unresolved\", \"STRIPAK-mediated recruitment to APC structurally undefined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Added mitochondrial (mt-ND5/complex I) and epigenetic (SUV39H1) substrates, showing scaffold-dependent restriction (PTRH2) and K29-linkage editing against specific E3 ligases.\",\n      \"evidence\": \"IP-MS, co-IP, ubiquitination assays, PTRH2 KO/re-expression, complex I and Ca2+ assays; engineered ubiquitin-replacement system with ChIP (preprint)\",\n      \"pmids\": [\"40496187\", \"bio_10.1101_2024.10.29.620783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mitochondrial localization mechanism of the enzyme unclear\", \"SUV39H1 finding is a preprint, single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Linked the enzyme to splicing control via SF3B3 stabilization and CHEK2 isoform choice, and added EZH2-MYCN and CTSB axes plus an upstream stabilizer (UCHL5).\",\n      \"evidence\": \"IP-MS, ubiquitination assays, splicing analysis, ternary-complex pull-downs, CHX chase, tumor models\",\n      \"pmids\": [\"42265067\", \"41949670\", \"41035046\", \"42037453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"UCHL5 and CTSB axes rest on single Co-IP/CHX without reconstitution\", \"Direct vs indirect splicing effects not fully separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single enzyme switches between deubiquitinase and E3 ligase activity, and what governs its substrate and chain-linkage selectivity in each cellular context, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of DUB-vs-E3 mode switching\", \"Determinants of substrate targeting across compartments unknown\", \"Physiological hierarchy among the many reported substrates undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 5, 6, 10, 11, 12]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 6, 11]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 10, 16]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5, 11]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 5, 6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 11]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 16]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"complexes\": [\"STRIPAK\", \"chromosomal passenger complex (CPC)\"],\n    \"partners\": [\"VPS34\", \"UBE3C\", \"HECTD1\", \"EZH2\", \"53BP1\", \"APC\", \"PTRH2\", \"SF3B3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}