{"gene":"FBXL3","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2007,"finding":"FBXL3 (F-box protein with leucine-rich repeats) is required for normal mammalian circadian period determination; the Afh Cys358Ser mutation delays CRY protein degradation and attenuates circadian transcriptional/translational oscillations, establishing FBXL3 as a core regulator of CRY stability in the circadian clock.","method":"ENU mutagenesis screen, in vivo wheel-running assays, Per2::Luciferase tissue-slice bioluminescence, in vitro degradation assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal in vivo and in vitro methods, widely replicated across subsequent labs","pmids":["17463252"],"is_preprint":false},{"year":2013,"finding":"Crystal structures of mammalian CRY2 in apo, FAD-bound, and FBXL3–SKP1-complexed forms reveal that FBXL3 captures CRY2 by inserting its conserved C-terminal tail into the FAD-binding pocket and simultaneously burying the PER-binding interface of CRY2; FAD and PER proteins can competitively disrupt this interaction, providing a mechanism for regulated CRY ubiquitination by SCF(FBXL3).","method":"X-ray crystallography of CRY2 alone and in complex with FBXL3-SKP1; FAD competition assays; structural mutagenesis","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structures with functional validation, highly cited, defining mechanistic study","pmids":["23503662"],"is_preprint":false},{"year":2013,"finding":"SCF(FBXL3) complex formation is substrate-dependent in vivo: Fbxl3 does not associate substantially with Skp1/Cul1 unless its substrate CRY1 is present; a CRY1-binding-deficient Fbxl3 mutant fails to form the SCF complex; the C-terminal LRR domain of Fbxl3 autoinhibits Skp1 binding, suggesting an unknown interactor suppresses SCF assembly until CRY binding relieves inhibition.","method":"Co-immunoprecipitation in transfected mammalian cells; in vitro reconstitution with recombinant proteins; domain-swap mutagenesis","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution plus cell-based Co-IP with mutagenesis, single lab but multiple orthogonal methods","pmids":["24085301"],"is_preprint":false},{"year":2013,"finding":"Genetic epistasis in double-mutant mice shows that FBXL3 regulates the circadian clock through two separable mechanisms: (1) ubiquitin-mediated degradation of CRY proteins (E-box loop), and (2) inactivation of the Rev-Erbα:HDAC3 corepressor complex to regulate RRE-driven transcription; deletion of Rev-erbα rescues the long-period phenotype of Fbxl3-deficient mice.","method":"Double-mutant mouse genetics (Fbxl3-KO × Rev-erbα-KO; Fbxl3 × Cry1 double mutants); circadian behavioral assays; transcriptional reporter assays","journal":"PNAS","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic epistasis with multiple double-mutant combinations and behavioral readouts","pmids":["23471982"],"is_preprint":false},{"year":2013,"finding":"In the SCN, FBXL3-mediated CRY stabilization (via the Afh allele) demonstrates that CRY1 and CRY2 have distinct, non-redundant roles: CRY1 is a more potent transcriptional repressor and period-lengthening factor than CRY2; Fbxl3(Afh/Afh) has no effect on CRY1/CRY2 double-null SCN rhythms, confirming FBXL3's circadian action is exclusively CRY-dependent.","method":"SCN bioluminescence recordings in Cry-deficient mice carrying Fbxl3(Afh); wheel-running behavioral assays; genetic epistasis","journal":"Journal of Neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — rigorous genetic epistasis across multiple CRY-null backgrounds with behavioral and molecular readouts","pmids":["23616524"],"is_preprint":false},{"year":2016,"finding":"CRY2 functions as an essential cofactor within the SCF(FBXL3) E3 ligase complex to recruit T58-phosphorylated c-MYC for ubiquitylation and degradation; CRY1 cannot substitute for CRY2 in this function; loss of CRY2 or FBXL3 stabilizes c-MYC protein.","method":"Co-immunoprecipitation; ubiquitylation assays; CRY1/CRY2 substitution experiments; siRNA knockdown with protein stability measurements","journal":"Molecular Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, ubiquitylation assays, genetic substitution experiments, widely cited","pmids":["27840026"],"is_preprint":false},{"year":2019,"finding":"Both CRY1 and CRY2 recruit the cell-cycle kinase TLK2 (when TLK2 is catalytically active) to SCF(FBXL3) for ubiquitin-mediated degradation; CRY overexpression decreases TLK2 abundance and CRY genetic deletion increases TLK2 abundance, establishing a molecular link between circadian and cell-cycle oscillators.","method":"Affinity purification mass spectrometry (APMS); Co-immunoprecipitation; CRY1/CRY2 overexpression and genetic deletion with TLK2 protein quantification; kinase-dead TLK2 mutant","journal":"Scientific Reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — APMS plus Co-IP and genetic KO, single lab","pmids":["30655559"],"is_preprint":false},{"year":2022,"finding":"Loss of fbxl3a function in zebrafish disrupts circadian rhythms of clock gene promoter activity, mRNA expression, and locomotor/sleep-wake cycles, confirming an evolutionarily conserved role for FBXL3 in vertebrate circadian timekeeping via CRY protein degradation.","method":"Zebrafish fbxl3a loss-of-function (exome-identified mutation); circadian promoter-activity and mRNA oscillation assays; locomotor and sleep-wake behavioral assays","journal":"International Journal of Molecular Sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean loss-of-function in vertebrate model with multiple circadian readouts, single lab","pmids":["35216494"],"is_preprint":false},{"year":2025,"finding":"FBXL3 promotes ubiquitination and proteasomal degradation of TCF12 in muscle satellite cells, suppressing MEF2C-driven myogenin expression; Fbxl3 deletion activates MyoD and myogenin via TCF12–MEF2C axis, augmenting myogenic differentiation and regeneration.","method":"Satellite cell-specific Fbxl3 knockout (Pax7-CreER); RNA-seq + GSEA; ChIP-PCR; dual-luciferase reporter assay; ubiquitination assays; AAV-mediated FBXL3 silencing","journal":"Frontiers in Immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with multiple orthogonal molecular methods (ChIP, luciferase, ubiquitination), single lab","pmids":["40755783"],"is_preprint":false},{"year":2025,"finding":"Satellite cell-specific deletion of FBXL3 in mdx mice improves muscle pathology, increases myogenin expression, and enhances regenerative activity, identifying FBXL3 as a negative regulator of muscle repair acting through repression of myogenin.","method":"Satellite cell-specific Fbxl3 deletion in mdx mice; grip strength and endurance tests; histological analysis of centrally nucleated fibers; AAV-mediated FBXL3 silencing in gastrocnemius","journal":"Biochemical and Biophysical Research Communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean conditional KO with functional and histological readouts, single lab","pmids":["40554051"],"is_preprint":false},{"year":2025,"finding":"YAP-TEAD transcriptional cascade directly targets the Fbxl3 promoter in response to mechanical/shaking stimuli; upregulated FBXL3 enhances CRY protein degradation, thereby suppressing circadian clock gene oscillations in iPSC embryoid bodies undergoing osteogenic differentiation.","method":"ATAC-seq; chromatin immunoprecipitation (ChIP) assay; RNA-seq; verteporfin (YAP-TEAD inhibitor) treatment; circadian bioluminescence assays","journal":"Cell Death Discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and ATAC-seq with functional inhibitor rescue, single lab","pmids":["40413171"],"is_preprint":false},{"year":2026,"finding":"EGFR activation triggers SRC-mediated phosphorylation of FBXL3 at Y306, enabling FBXL3 interaction with GLDC in the nucleus; FBXL3 then targets GLDC for K63-linked polyubiquitination at K636, promoting GLDC interaction with SMARCE1/DMAP1 to inhibit STAT1-driven MHC-I gene transcription and enable tumor immune evasion.","method":"Co-immunoprecipitation; ubiquitination assays (K63-linkage specific); site-directed mutagenesis (Y306F FBXL3, K636R GLDC); SRC inhibitor treatment; CD8+ T cell functional assays","journal":"Cell Insight","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with mutagenesis and linkage-specific ubiquitination assays, single lab","pmids":["41728086"],"is_preprint":false}],"current_model":"FBXL3 is the substrate-recognition subunit of the SCF(FBXL3) E3 ubiquitin ligase complex that targets CRY1 and CRY2 for ubiquitination and proteasomal degradation by inserting its C-terminal tail into the CRY FAD-binding pocket (competitively regulated by FAD and PER proteins), thereby driving circadian clock oscillations with ~24 h period; beyond the clock, FBXL3 uses CRY2 as a cofactor to ubiquitinate c-MYC (T58-phosphorylated) and TLK2, promotes K63-linked ubiquitination of GLDC following SRC-mediated Y306 phosphorylation to suppress MHC-I expression, and negatively regulates myogenic regeneration by promoting degradation of the transcription factor TCF12, collectively establishing FBXL3 as a multifunctional SCF ubiquitin ligase that integrates circadian timing, cell proliferation, immune evasion, and muscle differentiation."},"narrative":{"mechanistic_narrative":"FBXL3 is the substrate-recognition subunit of an SCF (SKP1–CUL1–F-box) E3 ubiquitin ligase whose central, conserved role is to set the period of the mammalian circadian clock by driving ubiquitin-mediated degradation of the cryptochrome repressors CRY1 and CRY2 [PMID:17463252, PMID:35216494]. Structurally, FBXL3 captures CRY by inserting its C-terminal tail into the cryptochrome FAD-binding pocket while burying the PER-binding surface, so that FAD and PER proteins competitively oppose FBXL3 engagement and thereby gate the timing of CRY turnover [PMID:23503662]. SCF(FBXL3) assembly is itself substrate-driven: the C-terminal LRR domain autoinhibits SKP1 binding until CRY binding relieves this inhibition, so the ligase forms productively only in the presence of its substrate [PMID:24085301]. Beyond promoting CRY degradation through the E-box loop, FBXL3 also acts genetically through inactivation of the REV-ERBα:HDAC3 corepressor complex on RRE-driven transcription, the two arms together accounting for its long-period phenotype [PMID:23471982]. FBXL3 additionally repurposes cryptochromes as substrate-recruiting cofactors for non-clock targets: CRY2 is an essential cofactor for ubiquitylation of T58-phosphorylated c-MYC [PMID:27840026], and CRY1/CRY2 recruit the active cell-cycle kinase TLK2 for degradation, linking the clock to proliferation [PMID:30655559]. In muscle satellite cells FBXL3 degrades the transcription factor TCF12 to suppress the MEF2C–myogenin axis, acting as a negative regulator of myogenic differentiation and muscle repair [PMID:40755783, PMID:40554051]. In a distinct nuclear, non-degradative role downstream of EGFR/SRC signaling, SRC-mediated phosphorylation of FBXL3 at Y306 enables K63-linked polyubiquitination of GLDC, promoting GLDC-driven repression of MHC-I transcription and tumor immune evasion [PMID:41728086].","teleology":[{"year":2007,"claim":"Established that a previously uncharacterized F-box protein governs circadian period, defining FBXL3 as a core clock component by controlling CRY protein stability.","evidence":"ENU mutagenesis screen with the Afh (Cys358Ser) allele, in vivo wheel-running, Per2::Luciferase tissue bioluminescence, and in vitro degradation assays in mouse","pmids":["17463252"],"confidence":"High","gaps":["Did not resolve the structural basis of CRY recognition","Did not address non-clock substrates"]},{"year":2013,"claim":"Resolved how FBXL3 recognizes its substrate and how that recognition is regulated, showing tail insertion into the CRY FAD pocket and competition by FAD and PER.","evidence":"X-ray crystallography of CRY2 apo, FAD-bound, and FBXL3–SKP1-complexed forms, plus FAD competition and structural mutagenesis","pmids":["23503662"],"confidence":"High","gaps":["Did not quantify in-cell competition kinetics between FAD/PER and FBXL3","Structure of the full SCF holocomplex on CRY not determined"]},{"year":2013,"claim":"Showed that SCF(FBXL3) assembly is substrate-gated, with LRR autoinhibition of SKP1 binding relieved by CRY engagement — explaining how ligase activity is coupled to substrate availability.","evidence":"Co-IP in transfected cells, in vitro reconstitution with recombinant proteins, and domain-swap mutagenesis","pmids":["24085301"],"confidence":"High","gaps":["The inferred autoinhibition-relieving interactor was not identified","Single-lab biochemistry"]},{"year":2013,"claim":"Separated FBXL3's clock action into two genetically distinct arms — CRY degradation and REV-ERBα:HDAC3 inactivation — broadening its role beyond the E-box loop.","evidence":"Double-mutant mouse genetics (Fbxl3-KO × Rev-erbα-KO; Fbxl3 × Cry1) with circadian behavioral and reporter assays","pmids":["23471982"],"confidence":"High","gaps":["Molecular mechanism by which FBXL3 inactivates REV-ERBα:HDAC3 not defined","Whether the RRE arm involves direct FBXL3 substrate ubiquitination unclear"]},{"year":2013,"claim":"Confirmed that FBXL3's circadian function is exclusively CRY-dependent and that CRY1 and CRY2 are non-redundant period determinants.","evidence":"SCN bioluminescence and wheel-running in Cry-deficient mice carrying Fbxl3(Afh); genetic epistasis","pmids":["23616524"],"confidence":"High","gaps":["Did not address tissue-specific CRY targeting outside the SCN"]},{"year":2016,"claim":"Revealed a non-clock function in which CRY2 serves as a cofactor enabling FBXL3 to degrade oncogenic c-MYC, connecting the ligase to growth control.","evidence":"Reciprocal Co-IP, ubiquitylation assays, CRY1/CRY2 substitution, and siRNA knockdown with protein stability measurements","pmids":["27840026"],"confidence":"High","gaps":["In vivo tumor relevance of c-MYC targeting not established","Basis of CRY2-specific (vs CRY1) cofactor function not structurally defined"]},{"year":2019,"claim":"Extended the cofactor model to TLK2, linking circadian and cell-cycle oscillators through CRY-dependent FBXL3 substrate recruitment.","evidence":"APMS, Co-IP, CRY overexpression/deletion with TLK2 quantification, and kinase-dead TLK2 mutant","pmids":["30655559"],"confidence":"Medium","gaps":["Physiological consequences of TLK2 turnover not characterized","Single-lab data"]},{"year":2022,"claim":"Demonstrated evolutionary conservation of FBXL3's circadian role in a non-mammalian vertebrate.","evidence":"Zebrafish fbxl3a loss-of-function with circadian promoter, mRNA oscillation, and sleep-wake behavioral assays","pmids":["35216494"],"confidence":"Medium","gaps":["Did not test non-clock substrates in fish","Single-lab study"]},{"year":2025,"claim":"Identified TCF12 as an FBXL3 degradation target in satellite cells, defining FBXL3 as a negative regulator of myogenic differentiation via the MEF2C–myogenin axis.","evidence":"Satellite-cell-specific Fbxl3 KO, RNA-seq/GSEA, ChIP-PCR, dual-luciferase, ubiquitination assays, and AAV silencing","pmids":["40755783"],"confidence":"Medium","gaps":["Whether TCF12 targeting requires a CRY cofactor not tested","Single-lab study"]},{"year":2025,"claim":"Showed the muscle-repair relevance of FBXL3 loss in a dystrophic model, supporting it as a brake on regeneration.","evidence":"Satellite-cell-specific Fbxl3 deletion in mdx mice with grip/endurance tests, histology, and AAV silencing","pmids":["40554051"],"confidence":"Medium","gaps":["Long-term therapeutic durability not assessed","Single-lab study"]},{"year":2025,"claim":"Placed Fbxl3 as a transcriptional output of YAP-TEAD mechanotransduction that feeds back to suppress clock oscillations.","evidence":"ATAC-seq, ChIP, RNA-seq, verteporfin inhibition, and circadian bioluminescence in iPSC embryoid bodies","pmids":["40413171"],"confidence":"Medium","gaps":["Direct YAP-TEAD binding at the Fbxl3 promoter in vivo not fully resolved","Single-lab study"]},{"year":2026,"claim":"Uncovered a non-degradative, phosphorylation-gated nuclear function in which FBXL3 mediates K63-linked GLDC ubiquitination to repress MHC-I and drive immune evasion.","evidence":"Co-IP, K63-linkage-specific ubiquitination assays, Y306F/K636R mutagenesis, SRC inhibition, and CD8+ T cell assays","pmids":["41728086"],"confidence":"Medium","gaps":["Whether this requires SCF holocomplex or a CRY cofactor not addressed","In vivo tumor immunity validation limited","Single-lab study"]},{"year":null,"claim":"It remains unknown how FBXL3 selects between its degradative clock/cell-cycle substrates and its non-degradative K63-ubiquitination nuclear targets, and what governs cofactor-dependent versus cofactor-independent substrate recruitment across tissues.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating CRY-cofactor recruitment with phospho-gated targeting","The autoinhibition-relieving interactor of the LRR domain is unidentified","Mechanism of REV-ERBα:HDAC3 inactivation undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,5,8,11]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,5,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,2,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-9909396","term_label":"Circadian clock","supporting_discovery_ids":[0,1,3,7,10]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,5,8,11]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5,6]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[8,9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[11]}],"complexes":["SCF(FBXL3) (SKP1-CUL1-FBXL3) E3 ubiquitin ligase"],"partners":["CRY1","CRY2","SKP1","CUL1","TLK2","TCF12","GLDC","SRC"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UKT7","full_name":"F-box/LRR-repeat protein 3","aliases":["F-box and leucine-rich repeat protein 3A","F-box/LRR-repeat protein 3A"],"length_aa":428,"mass_kda":48.7,"function":"Substrate-recognition component of the SCF(FBXL3) E3 ubiquitin ligase complex involved in circadian rhythm function. Plays a key role in the maintenance of both the speed and the robustness of the circadian clock oscillation (PubMed:17463251, PubMed:23452855, PubMed:27565346). The SCF(FBXL3) complex mainly acts in the nucleus and mediates ubiquitination and subsequent degradation of CRY1 and CRY2 (PubMed:17463251, PubMed:23452855, PubMed:27565346). Activity of the SCF(FBXL3) complex is counteracted by the SCF(FBXL21) complex (PubMed:23452855)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9UKT7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FBXL3","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FBXL3","total_profiled":1310},"omim":[{"mim_id":"609087","title":"F-BOX AND LEUCINE-RICH REPEAT PROTEIN 21; FBXL21","url":"https://www.omim.org/entry/609087"},{"mim_id":"606220","title":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH SHORT STATURE, FACIAL ANOMALIES, AND SPEECH DEFECTS; IDDSFAS","url":"https://www.omim.org/entry/606220"},{"mim_id":"605653","title":"F-BOX AND LEUCINE-RICH REPEAT PROTEIN 3; FBXL3","url":"https://www.omim.org/entry/605653"},{"mim_id":"603732","title":"CRYPTOCHROME 2; CRY2","url":"https://www.omim.org/entry/603732"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nuclear bodies","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FBXL3"},"hgnc":{"alias_symbol":["FBL3","FBL3A"],"prev_symbol":["FBXL3A"]},"alphafold":{"accession":"Q9UKT7","domains":[{"cath_id":"1.20.1280.50","chopping":"40-75","consensus_level":"medium","plddt":92.1947,"start":40,"end":75},{"cath_id":"3.80.10.10","chopping":"83-415","consensus_level":"medium","plddt":95.0652,"start":83,"end":415}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKT7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKT7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKT7-F1-predicted_aligned_error_v6.png","plddt_mean":90.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FBXL3","jax_strain_url":"https://www.jax.org/strain/search?query=FBXL3"},"sequence":{"accession":"Q9UKT7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UKT7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UKT7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKT7"}},"corpus_meta":[{"pmid":"17463252","id":"PMC_17463252","title":"The after-hours mutant reveals a role for Fbxl3 in determining mammalian circadian period.","date":"2007","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/17463252","citation_count":387,"is_preprint":false},{"pmid":"23503662","id":"PMC_23503662","title":"SCF(FBXL3) ubiquitin ligase targets cryptochromes at their cofactor pocket.","date":"2013","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/23503662","citation_count":198,"is_preprint":false},{"pmid":"27840026","id":"PMC_27840026","title":"CRY2 and FBXL3 Cooperatively Degrade c-MYC.","date":"2016","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/27840026","citation_count":172,"is_preprint":false},{"pmid":"28749470","id":"PMC_28749470","title":"miR-181d and c-myc-mediated inhibition of CRY2 and FBXL3 reprograms metabolism in colorectal cancer.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/28749470","citation_count":65,"is_preprint":false},{"pmid":"23616524","id":"PMC_23616524","title":"Distinct and separable roles for endogenous CRY1 and CRY2 within the circadian molecular clockwork of the suprachiasmatic nucleus, as revealed by the Fbxl3(Afh) mutation.","date":"2013","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/23616524","citation_count":51,"is_preprint":false},{"pmid":"23471982","id":"PMC_23471982","title":"Dual roles of FBXL3 in the mammalian circadian feedback loops are important for period determination and robustness of the clock.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23471982","citation_count":41,"is_preprint":false},{"pmid":"24085301","id":"PMC_24085301","title":"Substrate binding promotes formation of the Skp1-Cul1-Fbxl3 (SCF(Fbxl3)) protein complex.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24085301","citation_count":28,"is_preprint":false},{"pmid":"30655559","id":"PMC_30655559","title":"The circadian E3 ligase complex SCFFBXL3+CRY targets TLK2.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30655559","citation_count":25,"is_preprint":false},{"pmid":"30481285","id":"PMC_30481285","title":"Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature.","date":"2019","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30481285","citation_count":18,"is_preprint":false},{"pmid":"30594330","id":"PMC_30594330","title":"FBXL3 is regulated by miRNA-4735-3p and suppresses cell proliferation and migration in non-small cell lung cancer.","date":"2018","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/30594330","citation_count":15,"is_preprint":false},{"pmid":"35216494","id":"PMC_35216494","title":"A Zebrafish Model for a Rare Genetic Disease Reveals a Conserved Role for FBXL3 in the Circadian Clock System.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35216494","citation_count":8,"is_preprint":false},{"pmid":"32138500","id":"PMC_32138500","title":"lncRNA CASC2 suppresses the growth of hemangioma cells by regulating miR-18a-5p/FBXL3 axis.","date":"2020","source":"Journal of biological regulators and homeostatic agents","url":"https://pubmed.ncbi.nlm.nih.gov/32138500","citation_count":7,"is_preprint":false},{"pmid":"40413171","id":"PMC_40413171","title":"Shaking culture attenuates circadian rhythms in induced pluripotent stem cells during osteogenic differentiation through the TEAD-Fbxl3-CRY axis.","date":"2025","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/40413171","citation_count":1,"is_preprint":false},{"pmid":"39051074","id":"PMC_39051074","title":"[Tumor-associated fibroblasts promotes proliferation and migration of prostate cancer cells by suppressing FBXL3 via upregulating hsa-miR-18b-5p].","date":"2024","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/39051074","citation_count":1,"is_preprint":false},{"pmid":"41728086","id":"PMC_41728086","title":"Phosphorylation of FBXL3 mediates GLDC polyubiquitination to suppress MHC-I expression and promote cancer immune evasion.","date":"2026","source":"Cell insight","url":"https://pubmed.ncbi.nlm.nih.gov/41728086","citation_count":1,"is_preprint":false},{"pmid":"40554051","id":"PMC_40554051","title":"Fbxl3 deletion mitigates myopathy in mdx mice through upregulation of myogenin.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/40554051","citation_count":0,"is_preprint":false},{"pmid":"40755783","id":"PMC_40755783","title":"FBXL3 serves as a suppressor of regenerative myogenesis.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40755783","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.17.633578","title":"Evolution of circadian clock and light-input pathway genes in Hemiptera","date":"2025-01-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.17.633578","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10987,"output_tokens":3264,"usd":0.04096,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10726,"output_tokens":4139,"usd":0.078552,"stage2_stop_reason":"end_turn"},"total_usd":0.119512,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"FBXL3 (F-box protein with leucine-rich repeats) is required for normal mammalian circadian period determination; the Afh Cys358Ser mutation delays CRY protein degradation and attenuates circadian transcriptional/translational oscillations, establishing FBXL3 as a core regulator of CRY stability in the circadian clock.\",\n      \"method\": \"ENU mutagenesis screen, in vivo wheel-running assays, Per2::Luciferase tissue-slice bioluminescence, in vitro degradation assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal in vivo and in vitro methods, widely replicated across subsequent labs\",\n      \"pmids\": [\"17463252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structures of mammalian CRY2 in apo, FAD-bound, and FBXL3–SKP1-complexed forms reveal that FBXL3 captures CRY2 by inserting its conserved C-terminal tail into the FAD-binding pocket and simultaneously burying the PER-binding interface of CRY2; FAD and PER proteins can competitively disrupt this interaction, providing a mechanism for regulated CRY ubiquitination by SCF(FBXL3).\",\n      \"method\": \"X-ray crystallography of CRY2 alone and in complex with FBXL3-SKP1; FAD competition assays; structural mutagenesis\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structures with functional validation, highly cited, defining mechanistic study\",\n      \"pmids\": [\"23503662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SCF(FBXL3) complex formation is substrate-dependent in vivo: Fbxl3 does not associate substantially with Skp1/Cul1 unless its substrate CRY1 is present; a CRY1-binding-deficient Fbxl3 mutant fails to form the SCF complex; the C-terminal LRR domain of Fbxl3 autoinhibits Skp1 binding, suggesting an unknown interactor suppresses SCF assembly until CRY binding relieves inhibition.\",\n      \"method\": \"Co-immunoprecipitation in transfected mammalian cells; in vitro reconstitution with recombinant proteins; domain-swap mutagenesis\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution plus cell-based Co-IP with mutagenesis, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"24085301\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Genetic epistasis in double-mutant mice shows that FBXL3 regulates the circadian clock through two separable mechanisms: (1) ubiquitin-mediated degradation of CRY proteins (E-box loop), and (2) inactivation of the Rev-Erbα:HDAC3 corepressor complex to regulate RRE-driven transcription; deletion of Rev-erbα rescues the long-period phenotype of Fbxl3-deficient mice.\",\n      \"method\": \"Double-mutant mouse genetics (Fbxl3-KO × Rev-erbα-KO; Fbxl3 × Cry1 double mutants); circadian behavioral assays; transcriptional reporter assays\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic epistasis with multiple double-mutant combinations and behavioral readouts\",\n      \"pmids\": [\"23471982\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In the SCN, FBXL3-mediated CRY stabilization (via the Afh allele) demonstrates that CRY1 and CRY2 have distinct, non-redundant roles: CRY1 is a more potent transcriptional repressor and period-lengthening factor than CRY2; Fbxl3(Afh/Afh) has no effect on CRY1/CRY2 double-null SCN rhythms, confirming FBXL3's circadian action is exclusively CRY-dependent.\",\n      \"method\": \"SCN bioluminescence recordings in Cry-deficient mice carrying Fbxl3(Afh); wheel-running behavioral assays; genetic epistasis\",\n      \"journal\": \"Journal of Neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — rigorous genetic epistasis across multiple CRY-null backgrounds with behavioral and molecular readouts\",\n      \"pmids\": [\"23616524\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CRY2 functions as an essential cofactor within the SCF(FBXL3) E3 ligase complex to recruit T58-phosphorylated c-MYC for ubiquitylation and degradation; CRY1 cannot substitute for CRY2 in this function; loss of CRY2 or FBXL3 stabilizes c-MYC protein.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitylation assays; CRY1/CRY2 substitution experiments; siRNA knockdown with protein stability measurements\",\n      \"journal\": \"Molecular Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, ubiquitylation assays, genetic substitution experiments, widely cited\",\n      \"pmids\": [\"27840026\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Both CRY1 and CRY2 recruit the cell-cycle kinase TLK2 (when TLK2 is catalytically active) to SCF(FBXL3) for ubiquitin-mediated degradation; CRY overexpression decreases TLK2 abundance and CRY genetic deletion increases TLK2 abundance, establishing a molecular link between circadian and cell-cycle oscillators.\",\n      \"method\": \"Affinity purification mass spectrometry (APMS); Co-immunoprecipitation; CRY1/CRY2 overexpression and genetic deletion with TLK2 protein quantification; kinase-dead TLK2 mutant\",\n      \"journal\": \"Scientific Reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — APMS plus Co-IP and genetic KO, single lab\",\n      \"pmids\": [\"30655559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Loss of fbxl3a function in zebrafish disrupts circadian rhythms of clock gene promoter activity, mRNA expression, and locomotor/sleep-wake cycles, confirming an evolutionarily conserved role for FBXL3 in vertebrate circadian timekeeping via CRY protein degradation.\",\n      \"method\": \"Zebrafish fbxl3a loss-of-function (exome-identified mutation); circadian promoter-activity and mRNA oscillation assays; locomotor and sleep-wake behavioral assays\",\n      \"journal\": \"International Journal of Molecular Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean loss-of-function in vertebrate model with multiple circadian readouts, single lab\",\n      \"pmids\": [\"35216494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FBXL3 promotes ubiquitination and proteasomal degradation of TCF12 in muscle satellite cells, suppressing MEF2C-driven myogenin expression; Fbxl3 deletion activates MyoD and myogenin via TCF12–MEF2C axis, augmenting myogenic differentiation and regeneration.\",\n      \"method\": \"Satellite cell-specific Fbxl3 knockout (Pax7-CreER); RNA-seq + GSEA; ChIP-PCR; dual-luciferase reporter assay; ubiquitination assays; AAV-mediated FBXL3 silencing\",\n      \"journal\": \"Frontiers in Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with multiple orthogonal molecular methods (ChIP, luciferase, ubiquitination), single lab\",\n      \"pmids\": [\"40755783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Satellite cell-specific deletion of FBXL3 in mdx mice improves muscle pathology, increases myogenin expression, and enhances regenerative activity, identifying FBXL3 as a negative regulator of muscle repair acting through repression of myogenin.\",\n      \"method\": \"Satellite cell-specific Fbxl3 deletion in mdx mice; grip strength and endurance tests; histological analysis of centrally nucleated fibers; AAV-mediated FBXL3 silencing in gastrocnemius\",\n      \"journal\": \"Biochemical and Biophysical Research Communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional KO with functional and histological readouts, single lab\",\n      \"pmids\": [\"40554051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"YAP-TEAD transcriptional cascade directly targets the Fbxl3 promoter in response to mechanical/shaking stimuli; upregulated FBXL3 enhances CRY protein degradation, thereby suppressing circadian clock gene oscillations in iPSC embryoid bodies undergoing osteogenic differentiation.\",\n      \"method\": \"ATAC-seq; chromatin immunoprecipitation (ChIP) assay; RNA-seq; verteporfin (YAP-TEAD inhibitor) treatment; circadian bioluminescence assays\",\n      \"journal\": \"Cell Death Discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and ATAC-seq with functional inhibitor rescue, single lab\",\n      \"pmids\": [\"40413171\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"EGFR activation triggers SRC-mediated phosphorylation of FBXL3 at Y306, enabling FBXL3 interaction with GLDC in the nucleus; FBXL3 then targets GLDC for K63-linked polyubiquitination at K636, promoting GLDC interaction with SMARCE1/DMAP1 to inhibit STAT1-driven MHC-I gene transcription and enable tumor immune evasion.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assays (K63-linkage specific); site-directed mutagenesis (Y306F FBXL3, K636R GLDC); SRC inhibitor treatment; CD8+ T cell functional assays\",\n      \"journal\": \"Cell Insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with mutagenesis and linkage-specific ubiquitination assays, single lab\",\n      \"pmids\": [\"41728086\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FBXL3 is the substrate-recognition subunit of the SCF(FBXL3) E3 ubiquitin ligase complex that targets CRY1 and CRY2 for ubiquitination and proteasomal degradation by inserting its C-terminal tail into the CRY FAD-binding pocket (competitively regulated by FAD and PER proteins), thereby driving circadian clock oscillations with ~24 h period; beyond the clock, FBXL3 uses CRY2 as a cofactor to ubiquitinate c-MYC (T58-phosphorylated) and TLK2, promotes K63-linked ubiquitination of GLDC following SRC-mediated Y306 phosphorylation to suppress MHC-I expression, and negatively regulates myogenic regeneration by promoting degradation of the transcription factor TCF12, collectively establishing FBXL3 as a multifunctional SCF ubiquitin ligase that integrates circadian timing, cell proliferation, immune evasion, and muscle differentiation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FBXL3 is the substrate-recognition subunit of an SCF (SKP1–CUL1–F-box) E3 ubiquitin ligase whose central, conserved role is to set the period of the mammalian circadian clock by driving ubiquitin-mediated degradation of the cryptochrome repressors CRY1 and CRY2 [#0, #7]. Structurally, FBXL3 captures CRY by inserting its C-terminal tail into the cryptochrome FAD-binding pocket while burying the PER-binding surface, so that FAD and PER proteins competitively oppose FBXL3 engagement and thereby gate the timing of CRY turnover [#1]. SCF(FBXL3) assembly is itself substrate-driven: the C-terminal LRR domain autoinhibits SKP1 binding until CRY binding relieves this inhibition, so the ligase forms productively only in the presence of its substrate [#2]. Beyond promoting CRY degradation through the E-box loop, FBXL3 also acts genetically through inactivation of the REV-ERBα:HDAC3 corepressor complex on RRE-driven transcription, the two arms together accounting for its long-period phenotype [#3]. FBXL3 additionally repurposes cryptochromes as substrate-recruiting cofactors for non-clock targets: CRY2 is an essential cofactor for ubiquitylation of T58-phosphorylated c-MYC [#5], and CRY1/CRY2 recruit the active cell-cycle kinase TLK2 for degradation, linking the clock to proliferation [#6]. In muscle satellite cells FBXL3 degrades the transcription factor TCF12 to suppress the MEF2C–myogenin axis, acting as a negative regulator of myogenic differentiation and muscle repair [#8, #9]. In a distinct nuclear, non-degradative role downstream of EGFR/SRC signaling, SRC-mediated phosphorylation of FBXL3 at Y306 enables K63-linked polyubiquitination of GLDC, promoting GLDC-driven repression of MHC-I transcription and tumor immune evasion [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that a previously uncharacterized F-box protein governs circadian period, defining FBXL3 as a core clock component by controlling CRY protein stability.\",\n      \"evidence\": \"ENU mutagenesis screen with the Afh (Cys358Ser) allele, in vivo wheel-running, Per2::Luciferase tissue bioluminescence, and in vitro degradation assays in mouse\",\n      \"pmids\": [\"17463252\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of CRY recognition\", \"Did not address non-clock substrates\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved how FBXL3 recognizes its substrate and how that recognition is regulated, showing tail insertion into the CRY FAD pocket and competition by FAD and PER.\",\n      \"evidence\": \"X-ray crystallography of CRY2 apo, FAD-bound, and FBXL3–SKP1-complexed forms, plus FAD competition and structural mutagenesis\",\n      \"pmids\": [\"23503662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not quantify in-cell competition kinetics between FAD/PER and FBXL3\", \"Structure of the full SCF holocomplex on CRY not determined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed that SCF(FBXL3) assembly is substrate-gated, with LRR autoinhibition of SKP1 binding relieved by CRY engagement — explaining how ligase activity is coupled to substrate availability.\",\n      \"evidence\": \"Co-IP in transfected cells, in vitro reconstitution with recombinant proteins, and domain-swap mutagenesis\",\n      \"pmids\": [\"24085301\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The inferred autoinhibition-relieving interactor was not identified\", \"Single-lab biochemistry\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Separated FBXL3's clock action into two genetically distinct arms — CRY degradation and REV-ERBα:HDAC3 inactivation — broadening its role beyond the E-box loop.\",\n      \"evidence\": \"Double-mutant mouse genetics (Fbxl3-KO × Rev-erbα-KO; Fbxl3 × Cry1) with circadian behavioral and reporter assays\",\n      \"pmids\": [\"23471982\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which FBXL3 inactivates REV-ERBα:HDAC3 not defined\", \"Whether the RRE arm involves direct FBXL3 substrate ubiquitination unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Confirmed that FBXL3's circadian function is exclusively CRY-dependent and that CRY1 and CRY2 are non-redundant period determinants.\",\n      \"evidence\": \"SCN bioluminescence and wheel-running in Cry-deficient mice carrying Fbxl3(Afh); genetic epistasis\",\n      \"pmids\": [\"23616524\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address tissue-specific CRY targeting outside the SCN\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed a non-clock function in which CRY2 serves as a cofactor enabling FBXL3 to degrade oncogenic c-MYC, connecting the ligase to growth control.\",\n      \"evidence\": \"Reciprocal Co-IP, ubiquitylation assays, CRY1/CRY2 substitution, and siRNA knockdown with protein stability measurements\",\n      \"pmids\": [\"27840026\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo tumor relevance of c-MYC targeting not established\", \"Basis of CRY2-specific (vs CRY1) cofactor function not structurally defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended the cofactor model to TLK2, linking circadian and cell-cycle oscillators through CRY-dependent FBXL3 substrate recruitment.\",\n      \"evidence\": \"APMS, Co-IP, CRY overexpression/deletion with TLK2 quantification, and kinase-dead TLK2 mutant\",\n      \"pmids\": [\"30655559\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological consequences of TLK2 turnover not characterized\", \"Single-lab data\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated evolutionary conservation of FBXL3's circadian role in a non-mammalian vertebrate.\",\n      \"evidence\": \"Zebrafish fbxl3a loss-of-function with circadian promoter, mRNA oscillation, and sleep-wake behavioral assays\",\n      \"pmids\": [\"35216494\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not test non-clock substrates in fish\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified TCF12 as an FBXL3 degradation target in satellite cells, defining FBXL3 as a negative regulator of myogenic differentiation via the MEF2C–myogenin axis.\",\n      \"evidence\": \"Satellite-cell-specific Fbxl3 KO, RNA-seq/GSEA, ChIP-PCR, dual-luciferase, ubiquitination assays, and AAV silencing\",\n      \"pmids\": [\"40755783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether TCF12 targeting requires a CRY cofactor not tested\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed the muscle-repair relevance of FBXL3 loss in a dystrophic model, supporting it as a brake on regeneration.\",\n      \"evidence\": \"Satellite-cell-specific Fbxl3 deletion in mdx mice with grip/endurance tests, histology, and AAV silencing\",\n      \"pmids\": [\"40554051\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Long-term therapeutic durability not assessed\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed Fbxl3 as a transcriptional output of YAP-TEAD mechanotransduction that feeds back to suppress clock oscillations.\",\n      \"evidence\": \"ATAC-seq, ChIP, RNA-seq, verteporfin inhibition, and circadian bioluminescence in iPSC embryoid bodies\",\n      \"pmids\": [\"40413171\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct YAP-TEAD binding at the Fbxl3 promoter in vivo not fully resolved\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Uncovered a non-degradative, phosphorylation-gated nuclear function in which FBXL3 mediates K63-linked GLDC ubiquitination to repress MHC-I and drive immune evasion.\",\n      \"evidence\": \"Co-IP, K63-linkage-specific ubiquitination assays, Y306F/K636R mutagenesis, SRC inhibition, and CD8+ T cell assays\",\n      \"pmids\": [\"41728086\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether this requires SCF holocomplex or a CRY cofactor not addressed\", \"In vivo tumor immunity validation limited\", \"Single-lab study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how FBXL3 selects between its degradative clock/cell-cycle substrates and its non-degradative K63-ubiquitination nuclear targets, and what governs cofactor-dependent versus cofactor-independent substrate recruitment across tissues.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating CRY-cofactor recruitment with phospho-gated targeting\", \"The autoinhibition-relieving interactor of the LRR domain is unidentified\", \"Mechanism of REV-ERBα:HDAC3 inactivation undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 5, 8, 11]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 5, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 2, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9909396\", \"supporting_discovery_ids\": [0, 1, 3, 7, 10]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 5, 8, 11]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [\n      \"SCF(FBXL3) (SKP1-CUL1-FBXL3) E3 ubiquitin ligase\"\n    ],\n    \"partners\": [\n      \"CRY1\",\n      \"CRY2\",\n      \"SKP1\",\n      \"CUL1\",\n      \"TLK2\",\n      \"TCF12\",\n      \"GLDC\",\n      \"SRC\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}