{"gene":"CBY1","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2003,"finding":"Chibby (CBY1) was identified as a nuclear protein that directly interacts with the C-terminal region of β-catenin and inhibits β-catenin-mediated transcriptional activation by competing with Lef-1 for β-catenin binding. Epistasis experiments in Drosophila indicate chibby acts downstream of wingless and upstream of armadillo.","method":"Yeast two-hybrid screen, co-immunoprecipitation, transcriptional reporter assays, Drosophila RNAi epistasis experiments","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — direct binding demonstrated by Y2H and Co-IP, functional competition assay, in vivo epistasis in Drosophila, replicated across subsequent studies","pmids":["12712206"],"is_preprint":false},{"year":2004,"finding":"CBY1 (PIGEA-14) interacts with the C-terminus of polycystin-2 (PC2) via yeast two-hybrid, and co-expression of PIGEA-14 with PC2 redistributes both proteins to the trans-Golgi network, suggesting CBY1 regulates intracellular trafficking of polycystin-2. CBY1 also interacts with GM130, a cis-Golgi component, in a two-hybrid screen.","method":"Yeast two-hybrid screen, co-expression in LLC-PK1 and HeLa cells, immunofluorescence localization","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid and co-expression localization, single lab, two orthogonal methods but no reciprocal Co-IP or in vitro reconstitution","pmids":["15194699"],"is_preprint":false},{"year":2008,"finding":"CBY1 forms a stable tripartite complex with 14-3-3ε/ζ and β-catenin, promoting cytoplasmic sequestration of β-catenin. 14-3-3 specifically recognizes phosphorylated serine 20 of CBY1 (phosphorylated by Akt kinase), and 14-3-3 binding sequesters CBY1 into the cytoplasm.","method":"Affinity purification/mass spectrometry, co-immunoprecipitation, Akt kinase assay, subcellular fractionation, phosphomutant analysis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — AP/MS identification, reciprocal Co-IP, kinase assay identifying Akt as the writer, phosphomutant validation, multiple orthogonal methods in one study","pmids":["18573912"],"is_preprint":false},{"year":2009,"finding":"CBY1 localizes to the base of cilia, and Cby-knockout mice exhibit impaired basal body docking to the apical surface of multiciliated cells, complete absence of mucociliary transport, and a paucity of motile cilia in nasal epithelium, establishing CBY1 as required for ciliogenesis in airway epithelium.","method":"Cby-/- mouse generation, immunofluorescence localization, electron microscopy, mucociliary transport assays, bacterial clearance challenge","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with defined cellular phenotype, ultrastructural analysis, direct localization by immunofluorescence, multiple orthogonal readouts","pmids":["19364920"],"is_preprint":false},{"year":2009,"finding":"CBY1 harbors bona fide nuclear localization signal (NLS) and nuclear export signal (NES) motifs and constitutively shuttles between nucleus and cytoplasm. 14-3-3 binding promotes CBY1 interaction with CRM1 nuclear export receptor while inhibiting importin-α binding, driving cytoplasmic compartmentalization of CBY1. NLS/NES-dependent shuttling of CBY1 modulates the dynamic intracellular localization of β-catenin.","method":"NLS/NES mutagenesis, shRNA knockdown, nuclear export inhibitor (leptomycin B) treatment, co-immunoprecipitation with CRM1 and importin-α, subcellular fractionation, fluorescence microscopy","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — mutagenesis of NLS/NES with functional readouts, Co-IP with transport receptors, multiple orthogonal methods in single study, shRNA KD confirmation","pmids":["19940019"],"is_preprint":false},{"year":2009,"finding":"CBY1 forms a stable homodimer through a heptad repeat of leucine residues in its C-terminal coiled-coil motif. Alanine substitutions of two or more of four critical leucine residues abolish the CBY1-CBY1 interaction. Dimerization is not required for β-catenin binding or transcriptional repression but is required for efficient interaction with importin-α and subsequent nuclear translocation.","method":"Alanine-scanning mutagenesis, co-immunoprecipitation, gel filtration, transcriptional reporter assay, importin-α binding assay","journal":"BMC molecular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — comprehensive mutagenesis with multiple functional readouts (dimerization, β-catenin binding, transcription, nuclear import), single lab but multiple orthogonal methods","pmids":["19435523"],"is_preprint":false},{"year":2006,"finding":"TC1 (C8orf4) interacts directly with CBY1 and enhances Wnt/β-catenin signaling by relieving CBY1's antagonistic function. Upon co-expression, TC1 redistributes from nucleolus to nuclear speckles where it colocalizes with CBY1.","method":"Co-immunoprecipitation, co-localization by fluorescence microscopy, transcriptional reporter assays (TOPflash), gene expression analysis","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and reporter assay, localization, single lab, multiple methods but no in vitro reconstitution","pmids":["16424001"],"is_preprint":false},{"year":2007,"finding":"CBY1 promotes adipocyte differentiation of 3T3-L1 cells by inhibiting β-catenin signaling. CBY1 protein levels increase during adipogenic differentiation and its depletion by RNAi blocks adipogenesis in 3T3-L1 and mouse embryonic stem cells, while ectopic CBY1 expression induces spontaneous adipocyte differentiation.","method":"RNAi knockdown, overexpression, adipogenic differentiation assays, β-catenin reporter assay (TOPflash), embryonic fibroblast analysis from Cby-deficient embryos","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — both loss-of-function (RNAi, KO fibroblasts) and gain-of-function with defined molecular mechanism (β-catenin inhibition), multiple cell types","pmids":["17403895"],"is_preprint":false},{"year":2007,"finding":"TC-1 is an intrinsically disordered protein that interacts with CBY1 via three regions of high helical propensity (D44-R53, K58-A64, D73-T88) in its C-terminal portion, as demonstrated by NMR line broadening upon Cby addition.","method":"NMR spectroscopy (chemical shift analysis, relaxation measurements), structural characterization of TC-1","journal":"Protein science","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structural data identifying binding regions, single lab, no mutagenesis validation","pmids":["17905836"],"is_preprint":false},{"year":2011,"finding":"Human CBY1 is a partially disordered protein: its N-terminal portion is predominantly unstructured in solution while its C-terminal half forms a coiled-coil structure through self-association. Initial binding studies show the N-terminal unstructured region interacts with 14-3-3ζ while the C-terminal coiled-coil region is involved in TC-1 binding.","method":"NMR spectroscopy, ESI-MS, circular dichroism (CD), dynamic light scattering (DLS)","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — multiple biophysical methods in a single study, NMR + CD + DLS, single lab","pmids":["21182262"],"is_preprint":false},{"year":2012,"finding":"CBY1 localizes specifically to the distal end of the mother centriole, dependent on recruitment by Cenexin (Cnx). CBY1 physically interacts with Cenexin, and this interaction abrogates CBY1's inhibitory effect on β-catenin-mediated transcription in a dose-dependent manner. CBY1 is dispensable for Cnx localization but required for primary cilia assembly.","method":"Co-immunoprecipitation, immunofluorescence localization, centriole appendage marker co-staining, primary cilia assembly assay in quiescent cells","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP, co-localization, functional reporter assays, single lab but multiple orthogonal methods","pmids":["22911743"],"is_preprint":false},{"year":2012,"finding":"Drosophila CBY localizes to the basal body transition zone in sensory neurons and male germ cells and is essential for normal basal body structure and function (sensory transduction and spermatogenesis). Loss of CBY causes altered ciliary trafficking in neuronal cilia and irregular deposition of proteins on spermatocyte basal bodies. Notably, Drosophila cby mutant flies do not show Wingless signaling defects, suggesting the WNT-signaling role may not be conserved in Drosophila.","method":"Cby mutant Drosophila analysis, immunofluorescence, electron microscopy, sensory transduction assays, spermatogenesis analysis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with multiple orthogonal phenotypic readouts (sensory, reproductive, structural), ultrastructural EM, negative result for WNT signaling rigorously established","pmids":["22508513"],"is_preprint":false},{"year":2014,"finding":"CBY1 facilitates basal body docking to the apical cell membrane during ciliogenesis by promoting formation of ciliary vesicles at distal appendages. CBY1 is recruited to distal appendages via physical interaction with CEP164. CBY1 then associates with Rabin8 (a GEF for Rab8) to promote Rab8 recruitment and efficient assembly of ciliary vesicles.","method":"Primary cultures of mouse tracheal epithelial cells, co-immunoprecipitation, immunofluorescence, Cby-/- mouse analysis, electron microscopy, Rabin8/Rab8 recruitment assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP demonstrating CBY1-CEP164 and CBY1-Rabin8 interactions, KO mouse cells, ultrastructural analysis of ciliary vesicle formation, multiple orthogonal methods","pmids":["25313408"],"is_preprint":false},{"year":2014,"finding":"CBY1 localizes to an ~250-nm ring at the distal end of mature centrioles, as revealed by super-resolution microscopy (3D-SIM and STED). CBY1 localization to the distal centriole depends on Ofd1. CBY1 is required for efficient recruitment of Ahi1 (a Joubert syndrome protein/transition zone component) to centrioles; loss of CBY1 reduces centriole-localized Ahi1 but not Ofd1. Deletion of Cby1 results in cystic kidneys and impaired primary cilia formation.","method":"Super-resolution microscopy (3D-SIM and STED), Cby1-/- mouse analysis (kidney phenotype, primary cilia), Ahi1/Ofd1 localization analysis in KO cells, cilia recruitment assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — super-resolution structural localization, genetic KO with multiple phenotypic readouts, epistatic ordering of Ofd1→CBY1→Ahi1 recruitment","pmids":["25103236"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the human 14-3-3ζ/CBY1 protein-peptide complex reveals a canonical binding mode; phosphorylation of S20 is essential for 14-3-3 recognition, but flanking residues also contribute to binding affinity. NMR titration experiments reveal that residues outside the conserved 14-3-3 binding cleft (flexible loop residues 203-210 of 14-3-3ζ) are also involved in binding CBY1.","method":"X-ray crystallography, NMR spectroscopy (backbone resonance assignment, NMR titration), isothermal titration calorimetry (ITC), phosphomutant binding analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure determination plus NMR plus ITC, multiple orthogonal biophysical methods validating the binding interface","pmids":["25909186"],"is_preprint":false},{"year":2015,"finding":"CBY1 is required for normal ciliary morphology and proper distribution of intraflagellar transport (IFT) particles. In Cby-/- airway cells, IFT88 (IFT-B subcomplex) accumulates in dilated ciliary tips, and IFT-B components (IFT20, IFT57) but not IFT-A or BBS proteins accumulate in distended ciliary tips.","method":"Cby-/- mouse and primary tracheal epithelial cell cultures, immunofluorescence, transmission electron microscopy, IFT protein distribution analysis","journal":"Cell cycle","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined cellular readout (IFT distribution), EM ultrastructure, selective IFT-B specificity established by co-staining multiple IFT components","pmids":["26266958"],"is_preprint":false},{"year":2016,"finding":"FAM92A and FAM92B (BAR domain-containing proteins) interact with CBY1 as novel binding partners, identified by tandem affinity purification and mass spectrometry. FAM92A colocalizes with CBY1 at centrioles/basal bodies; centriolar localization of FAM92A and FAM92B depends largely on CBY1. FAM92A/B in cooperation with CBY1 induce membrane-remodeling structures containing Rab8, and knockdown of FAM92A impairs ciliogenesis.","method":"Tandem affinity purification/mass spectrometry, co-immunoprecipitation, immunofluorescence, Cby1-/- cell localization analysis, FAM92A knockdown ciliogenesis assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — AP/MS identification confirmed by Co-IP, dependency of localization tested in KO cells, functional knockdown phenotype, Rab8 membrane-remodeling assay","pmids":["27528616"],"is_preprint":false},{"year":2010,"finding":"CBY1 interacts with NBPF1 (and other NBPF proteins) through a coiled-coil region in NBPF and the C-terminal coiled-coil domain of CBY1, as shown by yeast two-hybrid and co-immunoprecipitation. CBY1 also interacts with clusterin, and a trimolecular complex of CBY1, NBPF1, and clusterin was co-immunoprecipitated. The NBPF1-CBY1 interaction does not influence CBY1's repressor function in a TOPflash reporter assay.","method":"Yeast two-hybrid screening, co-immunoprecipitation, TOPflash reporter assay","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid plus Co-IP confirming interaction, negative functional result (no effect on reporter) rigorously established, single lab","pmids":["20096688"],"is_preprint":false},{"year":2013,"finding":"Phosphorylation of the C-terminal region of polycystin-2 (PC2) at S812 (pseudophosphorylated mutant S812D) reduces its binding affinity to CBY1 (PIGEA14) approximately twofold compared to wild-type PC2, as quantified by quartz crystal microbalance; dissociation constant is in the 10 nM range.","method":"Quartz crystal microbalance (QCM) with solid-supported membranes, kinetic binding analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biophysical measurement with defined phosphomutant, single lab, single method","pmids":["23838289"],"is_preprint":false},{"year":2016,"finding":"CBY1 is a partially disordered protein with three structural elements: a disordered N-terminal half, a C-terminal coiled-coil domain, and a C-terminal unstructured extension (~25 residues). TC-1 binding requires only the coiled-coil domain of CBY1; deletion of either disordered region retains TC-1 binding. The C-terminal half of CBY1 alone binds TC-1 with greater affinity than full-length CBY1, suggesting flanking disordered regions modulate target binding.","method":"Hydrogen/deuterium exchange mass spectrometry (HDX-MS), circular dichroism, NMR spectroscopy, isothermal titration calorimetry (ITC), truncation mutagenesis","journal":"Protein science","confidence":"High","confidence_rationale":"Tier 1 / Moderate — HDX-MS, CD, NMR, ITC all applied in same study; systematic truncation mutagenesis to map binding domains","pmids":["27082063"],"is_preprint":false},{"year":2018,"finding":"Centrosomal protein Dzip1l interacts with CBY1 (as shown by co-immunoprecipitation), colocalizes at basal body appendages, and acts upstream of CBY1 in ciliogenesis. Loss of Dzip1l arrests ciliogenesis at the stage of ciliary bud formation, with failure to remove capping protein Cp110 from distal centrioles and failure to recruit Rpgrip1l to the transition zone.","method":"Co-immunoprecipitation, immunofluorescence co-localization, Dzip1l knockout mouse analysis, epistasis (Dzip1l upstream of Cby1)","journal":"Development","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP interaction, genetic epistasis ordering Dzip1l upstream of Cby1, KO phenotype, single lab","pmids":["29487109"],"is_preprint":false},{"year":2020,"finding":"Loss-of-function variants in CBY1 in humans cause a ciliopathy with features of Joubert syndrome. Patient fibroblasts show reduced ability to ciliate, increased ciliary length, and reduced levels of ciliary proteins AHI1 and ARL13B. Depletion of Cby1 in zebrafish recapitulates ciliopathy-related phenotypes.","method":"Human genetics (biallelic LOF variants), patient fibroblast cilia analysis (immunofluorescence), zebrafish Cby1 depletion morpholino, protein detection by immunofluorescence","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 2 / Strong — human genetic evidence with cellular validation in patient fibroblasts plus zebrafish model, multiple orthogonal methods confirming ciliary protein recruitment defects","pmids":["33131181"],"is_preprint":false},{"year":2021,"finding":"DZIP1 forms a multimeric complex with CBY1 and β-catenin at the basal body of primary cilia. DZIP1 stabilizes the complex and suppresses β-catenin activities. Loss of DZIP1 interaction with CBY1 (via a specific peptide domain) reduces DZIP1 and CBY1 stability and increases β-catenin activities, upregulating MMP2 and causing myxomatous valve phenotype, establishing DZIP1 functions to restrain β-catenin signaling through a CBY1 linker during cardiac development.","method":"Co-immunoprecipitation, biochemical decoy peptide experiments, subcellular fractionation, transcriptional reporter assays, mouse cardiac valve phenotype analysis, mutation identification in MVP patients","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP, biochemical peptide competition, functional reporter assays, in vivo phenotype; single lab","pmids":["33811421"],"is_preprint":false},{"year":2021,"finding":"Loss of Cby1 in mice results in severe exocrine pancreatic atrophy with dilated ducts, reduced cilia number and length in pancreatic tissue, and defective zymogen granule (ZG) secretion with accumulation of ZGs and altered polarity in acinar cells, establishing CBY1 as required for normal ciliogenesis and secretory function in exocrine pancreas.","method":"Cby1-knockout mouse analysis, immunofluorescence, histology/electron microscopy, in vitro acini secretion assay","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — genetic KO with multiple phenotypic readouts (histology, EM, in vitro secretion), single lab but orthogonal methods","pmids":["34446743"],"is_preprint":false},{"year":2024,"finding":"The Cby-Fam92 module near the ciliary membrane and the Cep131-Cep162 module near the axoneme synergistically control basal body localization of Cep290 and initiation of ciliogenesis. Concurrent deletion of any protein from both modules causes complete loss of Cep290 from the basal body and blocks ciliogenesis initiation, demonstrating cooperative and retroactive interactions between these complexes.","method":"Drosophila genetic double mutants, epistasis analysis, immunofluorescence, electron microscopy, Cep290 localization assays","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic double-mutant epistasis with defined molecular (Cep290 localization) and cellular (ciliogenesis initiation) readouts, multiple orthogonal methods","pmids":["38442096"],"is_preprint":false},{"year":2025,"finding":"The crystal structure of FAM92A BAR domain (2.2 Å) reveals an antiparallel crescent-shaped homodimer. FAM92A BAR domain directly binds the N-terminal region of CBY1, and dimerization of FAM92A and CBY1 synergistically enhances their binding affinity. Positively charged clusters on the concave BAR surface are critical for lipid binding, and specific residues are essential for dimerization.","method":"X-ray crystallography (2.2 Å), structure-guided mutagenesis, lipid binding assays, CBY1 interaction assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with mutagenesis validation of lipid binding and dimerization, identification of CBY1 binding region, single lab but rigorous Tier 1 methods","pmids":["40484380"],"is_preprint":false},{"year":2026,"finding":"Rhotekin interacts with CBY1 and competes with β-catenin for binding to CBY1, thereby activating canonical Wnt/β-catenin signaling and promoting osteoblast differentiation. CBY1 suppresses osteoblast differentiation, an effect counteracted by Rhotekin overexpression.","method":"Co-immunoprecipitation, competition binding assay, overexpression/knockdown differentiation assays, in vivo bone marrow silencing, β-catenin target gene analysis","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP, competition assay, both in vitro and in vivo functional phenotypes, single lab","pmids":["42000008"],"is_preprint":false},{"year":2013,"finding":"In BCR-ABL1+ cells, CBY1 enforced expression promotes β-catenin cytoplasmic translocation through its two known mechanisms (Tcf/Lef competition and 14-3-3-mediated nuclear export). Cytoplasmic accumulation of β-catenin activates the unfolded protein response (UPR), leading to induction of BIM and activation of ER-resident caspase-12, contributing to apoptosis.","method":"CBY1 overexpression in K562 cells, subcellular fractionation, β-catenin target gene analysis, UPR pathway markers, caspase-12 activation, BIM induction assays","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — overexpression with defined signaling readouts, linking CBY1-driven cytoplasmic β-catenin to UPR activation, single lab","pmids":["23707389"],"is_preprint":false},{"year":2015,"finding":"CBY1 protein stability in BCR-ABL1+ CML cells is reduced through binding to 14-3-3σ (mediated by Akt phosphorylation of CBY1 at serine 20), leading to proteasome-dependent degradation via enhanced SUMOylation. c-Jun N-terminal kinase (JNK) phosphorylation of 14-3-3σ at serine 186 promotes dissociation of CBY1 from 14-3-3σ, providing a mechanism to modulate CBY1 stability.","method":"Co-immunoprecipitation, phosphomutant analysis, proteasome inhibition assays, SUMOylation assays, JNK kinase analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — Co-IP with phosphomutants, biochemical pathway analysis identifying Akt/JNK/SUMOylation as regulators, single lab","pmids":["26147002"],"is_preprint":false}],"current_model":"CBY1 (Chibby1) is a conserved, partially disordered coiled-coil protein that (1) directly binds the C-terminal activation domain of β-catenin to compete with Tcf/Lef transcription factors and repress Wnt/β-catenin target gene expression; (2) upon Akt-mediated phosphorylation at serine 20, recruits 14-3-3 proteins to form a tripartite complex with β-catenin, facilitating CRM1-dependent nuclear export of both CBY1 and β-catenin; (3) localizes to the distal appendages of mature centrioles via CEP164 and Cenexin interactions, where it recruits Rabin8 and Rab8 to drive ciliary vesicle formation and basal body docking during ciliogenesis; and (4) acts within a DZIP1-CBY1-FAM92 complex at the centriole-to-cilium interface to maintain transition zone integrity, recruit Ahi1, and enable proper IFT-B distribution, with loss of CBY1 in mice and humans causing ciliopathies including airway disease, cystic kidneys, pancreatic degeneration, and Joubert syndrome."},"narrative":{"mechanistic_narrative":"CBY1 (Chibby1) is a conserved, partially disordered coiled-coil protein with dual roles as an antagonist of Wnt/β-catenin signaling and as a structural organizer at the centriole-to-cilium interface [PMID:12712206, PMID:19364920]. In the nucleus it directly binds the C-terminal activation domain of β-catenin and represses β-catenin/Tcf-Lef-driven transcription by competing with Lef-1 for β-catenin binding [PMID:12712206]. This repressive output is tuned by partners that bind CBY1 to relieve or redirect its activity, and by Akt-mediated phosphorylation of serine 20, which creates a 14-3-3 docking site; 14-3-3 binding assembles a tripartite CBY1–β-catenin complex, biases CBY1 toward CRM1-dependent nuclear export over importin-α import, and drives cytoplasmic sequestration of both proteins [PMID:18573912, PMID:19940019, PMID:25909186]. Structurally, CBY1 comprises a disordered N-terminal half that engages 14-3-3 and a C-terminal coiled-coil that mediates homodimerization and binds the disordered partner TC-1, with dimerization required for efficient nuclear import [PMID:19435523, PMID:21182262, PMID:27082063]. At the cilium, CBY1 localizes as a ring at the distal end of the mature mother centriole, recruited there via CEP164 and Cenexin, and drives basal body docking and ciliary vesicle formation by recruiting the Rabin8–Rab8 module [PMID:19364920, PMID:22911743, PMID:25313408, PMID:25103236]. Within a DZIP1L/DZIP1-CBY1-FAM92 module at the centriole-to-cilium interface, CBY1 maintains transition zone integrity, recruits Ahi1, and ensures proper IFT-B distribution, with the FAM92A BAR domain binding the CBY1 N-terminus to remodel ciliary membrane [PMID:25103236, PMID:26266958, PMID:27528616, PMID:29487109, PMID:40484380]. Loss of CBY1 in mice produces ciliopathy phenotypes including impaired mucociliary airway clearance, cystic kidneys, and exocrine pancreatic degeneration, and biallelic loss-of-function variants in humans cause a Joubert syndrome-spectrum ciliopathy [PMID:19364920, PMID:25103236, PMID:33131181, PMID:34446743].","teleology":[{"year":2003,"claim":"Established CBY1's founding molecular function: the unknown was what restrains β-catenin transcriptional output, and CBY1 was shown to directly bind β-catenin's C-terminus and compete with Lef-1 to repress Wnt target genes.","evidence":"Yeast two-hybrid, Co-IP, transcriptional reporter assays, and Drosophila RNAi epistasis","pmids":["12712206"],"confidence":"High","gaps":["Did not resolve how CBY1 is itself regulated","Did not address any non-nuclear function"]},{"year":2004,"claim":"First link to membrane trafficking: CBY1 (PIGEA-14) was shown to bind the polycystin-2 C-terminus and GM130 and redistribute PC2 to the trans-Golgi, hinting at a role beyond transcription.","evidence":"Yeast two-hybrid and co-expression localization in LLC-PK1 and HeLa cells","pmids":["15194699"],"confidence":"Medium","gaps":["No reciprocal Co-IP or in vitro reconstitution","Physiological significance of PC2 trafficking role unestablished"]},{"year":2006,"claim":"Defined a positive regulator of Wnt acting through CBY1: TC1/C8orf4 binds CBY1 and relieves its antagonism, showing CBY1 repression is a regulatable node.","evidence":"Co-IP, fluorescence colocalization, and TOPflash reporter assays","pmids":["16424001"],"confidence":"Medium","gaps":["Binding interface not mapped at residue level","No in vitro reconstitution"]},{"year":2007,"claim":"Connected CBY1's β-catenin antagonism to a developmental output: CBY1 promotes adipocyte differentiation by inhibiting β-catenin signaling.","evidence":"RNAi, overexpression, and adipogenic differentiation assays in 3T3-L1 and ES cells plus Cby-deficient embryo fibroblasts","pmids":["17403895"],"confidence":"High","gaps":["Did not address ciliary functions","Mechanism of CBY1 induction during adipogenesis unknown"]},{"year":2008,"claim":"Revealed the switch controlling CBY1 compartmentalization: Akt phosphorylates CBY1 at S20, creating a 14-3-3 binding site that assembles a CBY1–14-3-3–β-catenin complex and sequesters β-catenin in the cytoplasm.","evidence":"AP/MS, reciprocal Co-IP, Akt kinase assay, subcellular fractionation, and phosphomutant analysis","pmids":["18573912"],"confidence":"High","gaps":["Did not define the export machinery involved","Upstream signals controlling Akt activity in this context not addressed"]},{"year":2009,"claim":"Mechanism of compartmentalization resolved: CBY1 shuttles via NLS/NES motifs, and 14-3-3 binding promotes CRM1 association while blocking importin-α, driving CRM1-dependent nuclear export of CBY1 and β-catenin.","evidence":"NLS/NES mutagenesis, leptomycin B treatment, Co-IP with CRM1 and importin-α, shRNA knockdown, and fractionation","pmids":["19940019"],"confidence":"High","gaps":["Quantitative coupling between shuttling rate and β-catenin output not measured"]},{"year":2009,"claim":"Defined the structural basis of CBY1 oligomerization: a C-terminal coiled-coil heptad mediates homodimerization, which is dispensable for β-catenin binding/repression but required for importin-α binding and nuclear import.","evidence":"Alanine-scanning mutagenesis, Co-IP, gel filtration, reporter assay, and importin-α binding assay","pmids":["19435523"],"confidence":"High","gaps":["Higher-order assembly state in vivo not determined"]},{"year":2009,"claim":"Established CBY1 as a ciliogenesis factor in vivo: CBY1 localizes to the base of cilia, and Cby-/- mice show failed basal body docking, absent mucociliary transport, and motile cilia paucity in airway epithelium.","evidence":"Cby-/- mouse generation, immunofluorescence, electron microscopy, and mucociliary/bacterial clearance assays","pmids":["19364920"],"confidence":"High","gaps":["Molecular recruitment partners at the basal body not yet identified","Relationship between ciliary and Wnt roles unresolved"]},{"year":2012,"claim":"Mapped CBY1 to a specific centriolar substructure and tied it to β-catenin control: Cenexin recruits CBY1 to the distal mother centriole, and this interaction abrogates CBY1's repression of β-catenin transcription.","evidence":"Co-IP, immunofluorescence with centriole appendage markers, and primary cilia assembly assays in quiescent cells","pmids":["22911743"],"confidence":"Medium","gaps":["Single lab; reciprocal validation limited","Direct competition mechanism between centriolar tethering and β-catenin binding not structurally defined"]},{"year":2012,"claim":"Tested conservation of CBY1's two roles: Drosophila CBY localizes to the transition zone and is essential for basal body function in sensory neurons and germ cells, but cby mutants show no Wingless defect, indicating the Wnt role may not be conserved.","evidence":"Cby mutant Drosophila analysis, immunofluorescence, EM, and sensory/spermatogenesis assays","pmids":["22508513"],"confidence":"High","gaps":["Why the ciliary role is conserved while the Wnt role diverged unexplained"]},{"year":2014,"claim":"Defined the ciliary vesicle pathway: CBY1 is recruited to distal appendages by CEP164 and then engages Rabin8 to recruit Rab8 and assemble ciliary vesicles during basal body docking.","evidence":"Mouse tracheal epithelial cells, Co-IP, immunofluorescence, Cby-/- analysis, EM, and Rabin8/Rab8 recruitment assays","pmids":["25313408"],"confidence":"High","gaps":["Stoichiometry and order of CEP164 vs Cenexin recruitment not fully reconciled"]},{"year":2014,"claim":"Resolved CBY1's centriolar architecture and downstream recruitment: super-resolution imaging placed CBY1 in a ~250-nm distal ring downstream of Ofd1, and CBY1 is required to recruit the Joubert protein Ahi1; Cby1-/- mice develop cystic kidneys.","evidence":"3D-SIM/STED microscopy, Cby1-/- mouse kidney/cilia phenotyping, and Ahi1/Ofd1 localization analysis","pmids":["25103236"],"confidence":"High","gaps":["Mechanism by which CBY1 recruits Ahi1 not defined at the molecular level"]},{"year":2015,"claim":"Provided atomic detail of the regulatory switch: the 14-3-3ζ/CBY1 crystal structure confirmed phospho-S20 as essential for recognition, with flanking and noncanonical 14-3-3 loop residues contributing affinity.","evidence":"X-ray crystallography, NMR titration, ITC, and phosphomutant binding analysis","pmids":["25909186"],"confidence":"High","gaps":["Structure of full-length CBY1 or the tripartite β-catenin complex not solved"]},{"year":2015,"claim":"Defined CBY1's role in ciliary transport: Cby-/- airway cilia accumulate IFT-B components (IFT88, IFT20, IFT57) but not IFT-A or BBS proteins at dilated tips, establishing a selective IFT-B distribution defect.","evidence":"Cby-/- tracheal epithelial cells, immunofluorescence, TEM, and IFT component co-staining","pmids":["26266958"],"confidence":"High","gaps":["Direct interaction between CBY1 and IFT machinery not demonstrated"]},{"year":2016,"claim":"Identified the membrane-remodeling partner: FAM92A/B BAR-domain proteins bind CBY1, depend on it for centriolar localization, and cooperate with CBY1 to generate Rab8-containing membrane structures required for ciliogenesis.","evidence":"Tandem AP/MS, Co-IP, immunofluorescence, Cby1-/- localization analysis, and FAM92A knockdown ciliogenesis assay","pmids":["27528616"],"confidence":"High","gaps":["Lipid specificity and geometry of the membrane-remodeling event addressed only later"]},{"year":2018,"claim":"Placed CBY1 in an ordered ciliogenesis cascade: Dzip1l binds CBY1 and acts upstream, with Dzip1l loss arresting at ciliary bud formation, CP110 removal failure, and Rpgrip1l recruitment failure.","evidence":"Co-IP, colocalization at basal body appendages, Dzip1l knockout mouse analysis, and epistasis","pmids":["29487109"],"confidence":"Medium","gaps":["Single lab; biochemical directness of the CBY1–Dzip1l interaction not fully reconstituted"]},{"year":2016,"claim":"Dissected the modular binding determinants of CBY1: HDX-MS and truncation analysis showed three structural elements, with TC-1 binding requiring only the coiled-coil and flanking disordered regions modulating affinity.","evidence":"HDX-MS, CD, NMR, ITC, and truncation mutagenesis","pmids":["27082063"],"confidence":"High","gaps":["Functional consequence of disorder-mediated affinity tuning in cells not tested"]},{"year":2020,"claim":"Established human disease causation: biallelic loss-of-function CBY1 variants cause a Joubert-spectrum ciliopathy, with patient fibroblasts showing ciliation defects and reduced ciliary AHI1 and ARL13B.","evidence":"Human genetics, patient fibroblast cilia analysis, and zebrafish Cby1 morpholino depletion","pmids":["33131181"],"confidence":"High","gaps":["Genotype-phenotype correlation across the variant spectrum not detailed"]},{"year":2021,"claim":"Linked the basal body CBY1–β-catenin complex to organ development: DZIP1 stabilizes a DZIP1-CBY1-β-catenin complex at the basal body and restrains β-catenin/MMP2 signaling during cardiac valve development.","evidence":"Co-IP, decoy peptide competition, fractionation, reporter assays, mouse cardiac valve phenotyping, and MVP patient mutation analysis","pmids":["33811421"],"confidence":"Medium","gaps":["Single lab","Whether basal body localization is required for β-catenin restraint not isolated"]},{"year":2021,"claim":"Extended the in vivo ciliopathy phenotype to a new organ: Cby1 loss causes exocrine pancreatic atrophy, reduced/short cilia, and defective zymogen granule secretion with altered acinar polarity.","evidence":"Cby1 knockout mouse histology, EM, immunofluorescence, and in vitro acini secretion assay","pmids":["34446743"],"confidence":"High","gaps":["Mechanistic link between ciliary defect and secretory polarity loss unresolved"]},{"year":2024,"claim":"Defined cooperative module logic for ciliogenesis initiation: the Cby-Fam92 module and a Cep131-Cep162 module synergistically control basal body Cep290 localization, with concurrent disruption abolishing Cep290 and blocking ciliogenesis.","evidence":"Drosophila genetic double mutants, epistasis, immunofluorescence, EM, and Cep290 localization assays","pmids":["38442096"],"confidence":"High","gaps":["Molecular basis of retroactive interaction between modules not biochemically defined"]},{"year":2025,"claim":"Provided structural basis for CBY1-mediated membrane remodeling: the FAM92A BAR domain crystal structure shows a crescent homodimer that binds the CBY1 N-terminus, with synergistic dimerization enhancing affinity and a positively charged concave surface for lipid binding.","evidence":"X-ray crystallography at 2.2 Å, structure-guided mutagenesis, lipid binding, and CBY1 interaction assays","pmids":["40484380"],"confidence":"High","gaps":["Curvature of the membrane shaped in vivo not directly measured","How CBY1 dimerization couples to BAR-domain function structurally undefined"]},{"year":null,"claim":"It remains unresolved how the nuclear Wnt-antagonist function and the centriolar ciliogenesis function of CBY1 are coordinated within a single cell, and whether the two roles are mechanistically coupled or independent.","evidence":"","pmids":[],"confidence":"High","gaps":["No study integrates the β-catenin and ciliary functions in one experimental system","Whether centriolar tethering is the primary regulator of CBY1's nuclear pool is untested","Structure of full-length CBY1 in any complex is unavailable"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,6,26]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,12,16]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2,4]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[10,12,13]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[3,11,13,15]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2,7]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,12,13,16]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[7,21,22,23]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[21]}],"complexes":["CBY1-14-3-3-β-catenin tripartite complex","DZIP1-CBY1-FAM92 ciliary module","CBY1 homodimer"],"partners":["CTNNB1","YWHAE","CEP164","CEP290","FAM92A","DZIP1L","TC1","RAB8A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y3M2","full_name":"Protein chibby homolog 1","aliases":["ARPP-binding protein","Cytosolic leucine-rich protein","PIGEA-14","PKD2 interactor, Golgi and endoplasmic reticulum-associated 1"],"length_aa":126,"mass_kda":14.5,"function":"Inhibits the Wnt/Wingless pathway by binding to CTNNB1/beta-catenin and inhibiting beta-catenin-mediated transcriptional activation through competition with TCF/LEF transcription factors (PubMed:12712206, PubMed:19435523). Has also been shown to play a role in regulating the intracellular trafficking of polycystin-2/PKD2 and possibly of other intracellular proteins (PubMed:15194699). Promotes adipocyte and cardiomyocyte differentiation (By similarity)","subcellular_location":"Nucleus speckle; Cytoplasm, cytoskeleton, cilium basal body; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole; Golgi apparatus; Golgi apparatus, trans-Golgi network; Cell projection, cilium, flagellum; Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y3M2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CBY1","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CBY1","total_profiled":1310},"omim":[{"mim_id":"620892","title":"CHIBBY FAMILY, MEMBER 3; CBY3","url":"https://www.omim.org/entry/620892"},{"mim_id":"617274","title":"CBY1-INTERACTING BAR DOMAIN-CONTAINING PROTEIN 2; CIBAR2","url":"https://www.omim.org/entry/617274"},{"mim_id":"617273","title":"CBY1-INTERACTING BAR DOMAIN-CONTAINING PROTEIN 1; CIBAR1","url":"https://www.omim.org/entry/617273"},{"mim_id":"607757","title":"CHIBBY FAMILY, MEMBER 1, BETA-CATENIN ANTAGONIST; CBY1","url":"https://www.omim.org/entry/607757"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CBY1"},"hgnc":{"alias_symbol":["PIGEA14","PIGEA-14","Chibby","Cby","Chibby1"],"prev_symbol":["C22orf2","PGEA1"]},"alphafold":{"accession":"Q9Y3M2","domains":[{"cath_id":"-","chopping":"30-62","consensus_level":"medium","plddt":84.2648,"start":30,"end":62},{"cath_id":"1.10.287","chopping":"77-126","consensus_level":"medium","plddt":95.9764,"start":77,"end":126}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3M2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3M2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3M2-F1-predicted_aligned_error_v6.png","plddt_mean":85.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CBY1","jax_strain_url":"https://www.jax.org/strain/search?query=CBY1"},"sequence":{"accession":"Q9Y3M2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y3M2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y3M2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3M2"}},"corpus_meta":[{"pmid":"12712206","id":"PMC_12712206","title":"Chibby, 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cell carcinoma.","date":"2015","source":"Tumori","url":"https://pubmed.ncbi.nlm.nih.gov/25838250","citation_count":4,"is_preprint":false},{"pmid":"25175341","id":"PMC_25175341","title":"Downregulated Chibby in laryngeal squamous cell carcinoma with increased expression in laryngeal carcinoma Hep-2 cells.","date":"2014","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/25175341","citation_count":3,"is_preprint":false},{"pmid":"29552214","id":"PMC_29552214","title":"Anti-oncogenic activity of Chibby in the development of human nasopharyngeal carcinoma.","date":"2018","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/29552214","citation_count":3,"is_preprint":false},{"pmid":"38733656","id":"PMC_38733656","title":"Identification of a novel mutation in chibby family member 2 in a non-obstructive azoospermic patient.","date":"2024","source":"Reproductive biology","url":"https://pubmed.ncbi.nlm.nih.gov/38733656","citation_count":3,"is_preprint":false},{"pmid":"30063079","id":"PMC_30063079","title":"Chibby is a weak regulator of β-catenin activity in gastric epithelium.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30063079","citation_count":2,"is_preprint":false},{"pmid":"23645032","id":"PMC_23645032","title":"No important role for genetic variation in the Chibby gene in monogenic and complex obesity.","date":"2013","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/23645032","citation_count":2,"is_preprint":false},{"pmid":"10369925","id":"PMC_10369925","title":"The H-mshi antigen is conserved among standard BALB/cBy, C57BL/6J, and wild-derived CAST/Ei and SPRET/Ei inbred strains of mice.","date":"1999","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/10369925","citation_count":2,"is_preprint":false},{"pmid":"36637515","id":"PMC_36637515","title":"Elimination of 4T1 Mammary Tumor Cells by BALB/cBy UBC-GFP Transgenics following Stable Inheritance of the H-2b MHC Allele.","date":"2023","source":"ImmunoHorizons","url":"https://pubmed.ncbi.nlm.nih.gov/36637515","citation_count":2,"is_preprint":false},{"pmid":"37986347","id":"PMC_37986347","title":"Upregulated TC1 and downregulated Chibby were correlated with the aberrant β-catenin expression in laryngeal squamous cell carcinoma.","date":"2023","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37986347","citation_count":1,"is_preprint":false},{"pmid":"29181101","id":"PMC_29181101","title":"Downregulation of nuclear and cytoplasmic Chibby is associated with advanced cervical cancer.","date":"2017","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/29181101","citation_count":1,"is_preprint":false},{"pmid":"35947191","id":"PMC_35947191","title":"Defective bone repletion in aged Balb/cBy mice was caused by impaired osteoblastic differentiation.","date":"2022","source":"Journal of bone and mineral metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/35947191","citation_count":1,"is_preprint":false},{"pmid":"40484380","id":"PMC_40484380","title":"Dimerization of the BAR domain-containing protein FAM92A modulates lipid binding and interaction with CBY1.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40484380","citation_count":0,"is_preprint":false},{"pmid":"42000008","id":"PMC_42000008","title":"Rhotekin contributes to osteoblast differentiation and bone homeostasis by interacting with Chibby 1.","date":"2026","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/42000008","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":33923,"output_tokens":7909,"usd":0.110202,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":17362,"output_tokens":6774,"usd":0.12808,"stage2_stop_reason":"end_turn"},"total_usd":0.238282,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"Chibby (CBY1) was identified as a nuclear protein that directly interacts with the C-terminal region of β-catenin and inhibits β-catenin-mediated transcriptional activation by competing with Lef-1 for β-catenin binding. Epistasis experiments in Drosophila indicate chibby acts downstream of wingless and upstream of armadillo.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, transcriptional reporter assays, Drosophila RNAi epistasis experiments\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — direct binding demonstrated by Y2H and Co-IP, functional competition assay, in vivo epistasis in Drosophila, replicated across subsequent studies\",\n      \"pmids\": [\"12712206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CBY1 (PIGEA-14) interacts with the C-terminus of polycystin-2 (PC2) via yeast two-hybrid, and co-expression of PIGEA-14 with PC2 redistributes both proteins to the trans-Golgi network, suggesting CBY1 regulates intracellular trafficking of polycystin-2. CBY1 also interacts with GM130, a cis-Golgi component, in a two-hybrid screen.\",\n      \"method\": \"Yeast two-hybrid screen, co-expression in LLC-PK1 and HeLa cells, immunofluorescence localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid and co-expression localization, single lab, two orthogonal methods but no reciprocal Co-IP or in vitro reconstitution\",\n      \"pmids\": [\"15194699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CBY1 forms a stable tripartite complex with 14-3-3ε/ζ and β-catenin, promoting cytoplasmic sequestration of β-catenin. 14-3-3 specifically recognizes phosphorylated serine 20 of CBY1 (phosphorylated by Akt kinase), and 14-3-3 binding sequesters CBY1 into the cytoplasm.\",\n      \"method\": \"Affinity purification/mass spectrometry, co-immunoprecipitation, Akt kinase assay, subcellular fractionation, phosphomutant analysis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — AP/MS identification, reciprocal Co-IP, kinase assay identifying Akt as the writer, phosphomutant validation, multiple orthogonal methods in one study\",\n      \"pmids\": [\"18573912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CBY1 localizes to the base of cilia, and Cby-knockout mice exhibit impaired basal body docking to the apical surface of multiciliated cells, complete absence of mucociliary transport, and a paucity of motile cilia in nasal epithelium, establishing CBY1 as required for ciliogenesis in airway epithelium.\",\n      \"method\": \"Cby-/- mouse generation, immunofluorescence localization, electron microscopy, mucociliary transport assays, bacterial clearance challenge\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with defined cellular phenotype, ultrastructural analysis, direct localization by immunofluorescence, multiple orthogonal readouts\",\n      \"pmids\": [\"19364920\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CBY1 harbors bona fide nuclear localization signal (NLS) and nuclear export signal (NES) motifs and constitutively shuttles between nucleus and cytoplasm. 14-3-3 binding promotes CBY1 interaction with CRM1 nuclear export receptor while inhibiting importin-α binding, driving cytoplasmic compartmentalization of CBY1. NLS/NES-dependent shuttling of CBY1 modulates the dynamic intracellular localization of β-catenin.\",\n      \"method\": \"NLS/NES mutagenesis, shRNA knockdown, nuclear export inhibitor (leptomycin B) treatment, co-immunoprecipitation with CRM1 and importin-α, subcellular fractionation, fluorescence microscopy\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mutagenesis of NLS/NES with functional readouts, Co-IP with transport receptors, multiple orthogonal methods in single study, shRNA KD confirmation\",\n      \"pmids\": [\"19940019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CBY1 forms a stable homodimer through a heptad repeat of leucine residues in its C-terminal coiled-coil motif. Alanine substitutions of two or more of four critical leucine residues abolish the CBY1-CBY1 interaction. Dimerization is not required for β-catenin binding or transcriptional repression but is required for efficient interaction with importin-α and subsequent nuclear translocation.\",\n      \"method\": \"Alanine-scanning mutagenesis, co-immunoprecipitation, gel filtration, transcriptional reporter assay, importin-α binding assay\",\n      \"journal\": \"BMC molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — comprehensive mutagenesis with multiple functional readouts (dimerization, β-catenin binding, transcription, nuclear import), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"19435523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TC1 (C8orf4) interacts directly with CBY1 and enhances Wnt/β-catenin signaling by relieving CBY1's antagonistic function. Upon co-expression, TC1 redistributes from nucleolus to nuclear speckles where it colocalizes with CBY1.\",\n      \"method\": \"Co-immunoprecipitation, co-localization by fluorescence microscopy, transcriptional reporter assays (TOPflash), gene expression analysis\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and reporter assay, localization, single lab, multiple methods but no in vitro reconstitution\",\n      \"pmids\": [\"16424001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CBY1 promotes adipocyte differentiation of 3T3-L1 cells by inhibiting β-catenin signaling. CBY1 protein levels increase during adipogenic differentiation and its depletion by RNAi blocks adipogenesis in 3T3-L1 and mouse embryonic stem cells, while ectopic CBY1 expression induces spontaneous adipocyte differentiation.\",\n      \"method\": \"RNAi knockdown, overexpression, adipogenic differentiation assays, β-catenin reporter assay (TOPflash), embryonic fibroblast analysis from Cby-deficient embryos\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — both loss-of-function (RNAi, KO fibroblasts) and gain-of-function with defined molecular mechanism (β-catenin inhibition), multiple cell types\",\n      \"pmids\": [\"17403895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"TC-1 is an intrinsically disordered protein that interacts with CBY1 via three regions of high helical propensity (D44-R53, K58-A64, D73-T88) in its C-terminal portion, as demonstrated by NMR line broadening upon Cby addition.\",\n      \"method\": \"NMR spectroscopy (chemical shift analysis, relaxation measurements), structural characterization of TC-1\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structural data identifying binding regions, single lab, no mutagenesis validation\",\n      \"pmids\": [\"17905836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Human CBY1 is a partially disordered protein: its N-terminal portion is predominantly unstructured in solution while its C-terminal half forms a coiled-coil structure through self-association. Initial binding studies show the N-terminal unstructured region interacts with 14-3-3ζ while the C-terminal coiled-coil region is involved in TC-1 binding.\",\n      \"method\": \"NMR spectroscopy, ESI-MS, circular dichroism (CD), dynamic light scattering (DLS)\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple biophysical methods in a single study, NMR + CD + DLS, single lab\",\n      \"pmids\": [\"21182262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CBY1 localizes specifically to the distal end of the mother centriole, dependent on recruitment by Cenexin (Cnx). CBY1 physically interacts with Cenexin, and this interaction abrogates CBY1's inhibitory effect on β-catenin-mediated transcription in a dose-dependent manner. CBY1 is dispensable for Cnx localization but required for primary cilia assembly.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence localization, centriole appendage marker co-staining, primary cilia assembly assay in quiescent cells\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP, co-localization, functional reporter assays, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"22911743\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Drosophila CBY localizes to the basal body transition zone in sensory neurons and male germ cells and is essential for normal basal body structure and function (sensory transduction and spermatogenesis). Loss of CBY causes altered ciliary trafficking in neuronal cilia and irregular deposition of proteins on spermatocyte basal bodies. Notably, Drosophila cby mutant flies do not show Wingless signaling defects, suggesting the WNT-signaling role may not be conserved in Drosophila.\",\n      \"method\": \"Cby mutant Drosophila analysis, immunofluorescence, electron microscopy, sensory transduction assays, spermatogenesis analysis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with multiple orthogonal phenotypic readouts (sensory, reproductive, structural), ultrastructural EM, negative result for WNT signaling rigorously established\",\n      \"pmids\": [\"22508513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CBY1 facilitates basal body docking to the apical cell membrane during ciliogenesis by promoting formation of ciliary vesicles at distal appendages. CBY1 is recruited to distal appendages via physical interaction with CEP164. CBY1 then associates with Rabin8 (a GEF for Rab8) to promote Rab8 recruitment and efficient assembly of ciliary vesicles.\",\n      \"method\": \"Primary cultures of mouse tracheal epithelial cells, co-immunoprecipitation, immunofluorescence, Cby-/- mouse analysis, electron microscopy, Rabin8/Rab8 recruitment assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP demonstrating CBY1-CEP164 and CBY1-Rabin8 interactions, KO mouse cells, ultrastructural analysis of ciliary vesicle formation, multiple orthogonal methods\",\n      \"pmids\": [\"25313408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CBY1 localizes to an ~250-nm ring at the distal end of mature centrioles, as revealed by super-resolution microscopy (3D-SIM and STED). CBY1 localization to the distal centriole depends on Ofd1. CBY1 is required for efficient recruitment of Ahi1 (a Joubert syndrome protein/transition zone component) to centrioles; loss of CBY1 reduces centriole-localized Ahi1 but not Ofd1. Deletion of Cby1 results in cystic kidneys and impaired primary cilia formation.\",\n      \"method\": \"Super-resolution microscopy (3D-SIM and STED), Cby1-/- mouse analysis (kidney phenotype, primary cilia), Ahi1/Ofd1 localization analysis in KO cells, cilia recruitment assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — super-resolution structural localization, genetic KO with multiple phenotypic readouts, epistatic ordering of Ofd1→CBY1→Ahi1 recruitment\",\n      \"pmids\": [\"25103236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the human 14-3-3ζ/CBY1 protein-peptide complex reveals a canonical binding mode; phosphorylation of S20 is essential for 14-3-3 recognition, but flanking residues also contribute to binding affinity. NMR titration experiments reveal that residues outside the conserved 14-3-3 binding cleft (flexible loop residues 203-210 of 14-3-3ζ) are also involved in binding CBY1.\",\n      \"method\": \"X-ray crystallography, NMR spectroscopy (backbone resonance assignment, NMR titration), isothermal titration calorimetry (ITC), phosphomutant binding analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure determination plus NMR plus ITC, multiple orthogonal biophysical methods validating the binding interface\",\n      \"pmids\": [\"25909186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CBY1 is required for normal ciliary morphology and proper distribution of intraflagellar transport (IFT) particles. In Cby-/- airway cells, IFT88 (IFT-B subcomplex) accumulates in dilated ciliary tips, and IFT-B components (IFT20, IFT57) but not IFT-A or BBS proteins accumulate in distended ciliary tips.\",\n      \"method\": \"Cby-/- mouse and primary tracheal epithelial cell cultures, immunofluorescence, transmission electron microscopy, IFT protein distribution analysis\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined cellular readout (IFT distribution), EM ultrastructure, selective IFT-B specificity established by co-staining multiple IFT components\",\n      \"pmids\": [\"26266958\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"FAM92A and FAM92B (BAR domain-containing proteins) interact with CBY1 as novel binding partners, identified by tandem affinity purification and mass spectrometry. FAM92A colocalizes with CBY1 at centrioles/basal bodies; centriolar localization of FAM92A and FAM92B depends largely on CBY1. FAM92A/B in cooperation with CBY1 induce membrane-remodeling structures containing Rab8, and knockdown of FAM92A impairs ciliogenesis.\",\n      \"method\": \"Tandem affinity purification/mass spectrometry, co-immunoprecipitation, immunofluorescence, Cby1-/- cell localization analysis, FAM92A knockdown ciliogenesis assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — AP/MS identification confirmed by Co-IP, dependency of localization tested in KO cells, functional knockdown phenotype, Rab8 membrane-remodeling assay\",\n      \"pmids\": [\"27528616\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"CBY1 interacts with NBPF1 (and other NBPF proteins) through a coiled-coil region in NBPF and the C-terminal coiled-coil domain of CBY1, as shown by yeast two-hybrid and co-immunoprecipitation. CBY1 also interacts with clusterin, and a trimolecular complex of CBY1, NBPF1, and clusterin was co-immunoprecipitated. The NBPF1-CBY1 interaction does not influence CBY1's repressor function in a TOPflash reporter assay.\",\n      \"method\": \"Yeast two-hybrid screening, co-immunoprecipitation, TOPflash reporter assay\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid plus Co-IP confirming interaction, negative functional result (no effect on reporter) rigorously established, single lab\",\n      \"pmids\": [\"20096688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Phosphorylation of the C-terminal region of polycystin-2 (PC2) at S812 (pseudophosphorylated mutant S812D) reduces its binding affinity to CBY1 (PIGEA14) approximately twofold compared to wild-type PC2, as quantified by quartz crystal microbalance; dissociation constant is in the 10 nM range.\",\n      \"method\": \"Quartz crystal microbalance (QCM) with solid-supported membranes, kinetic binding analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biophysical measurement with defined phosphomutant, single lab, single method\",\n      \"pmids\": [\"23838289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CBY1 is a partially disordered protein with three structural elements: a disordered N-terminal half, a C-terminal coiled-coil domain, and a C-terminal unstructured extension (~25 residues). TC-1 binding requires only the coiled-coil domain of CBY1; deletion of either disordered region retains TC-1 binding. The C-terminal half of CBY1 alone binds TC-1 with greater affinity than full-length CBY1, suggesting flanking disordered regions modulate target binding.\",\n      \"method\": \"Hydrogen/deuterium exchange mass spectrometry (HDX-MS), circular dichroism, NMR spectroscopy, isothermal titration calorimetry (ITC), truncation mutagenesis\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — HDX-MS, CD, NMR, ITC all applied in same study; systematic truncation mutagenesis to map binding domains\",\n      \"pmids\": [\"27082063\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Centrosomal protein Dzip1l interacts with CBY1 (as shown by co-immunoprecipitation), colocalizes at basal body appendages, and acts upstream of CBY1 in ciliogenesis. Loss of Dzip1l arrests ciliogenesis at the stage of ciliary bud formation, with failure to remove capping protein Cp110 from distal centrioles and failure to recruit Rpgrip1l to the transition zone.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence co-localization, Dzip1l knockout mouse analysis, epistasis (Dzip1l upstream of Cby1)\",\n      \"journal\": \"Development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP interaction, genetic epistasis ordering Dzip1l upstream of Cby1, KO phenotype, single lab\",\n      \"pmids\": [\"29487109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss-of-function variants in CBY1 in humans cause a ciliopathy with features of Joubert syndrome. Patient fibroblasts show reduced ability to ciliate, increased ciliary length, and reduced levels of ciliary proteins AHI1 and ARL13B. Depletion of Cby1 in zebrafish recapitulates ciliopathy-related phenotypes.\",\n      \"method\": \"Human genetics (biallelic LOF variants), patient fibroblast cilia analysis (immunofluorescence), zebrafish Cby1 depletion morpholino, protein detection by immunofluorescence\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — human genetic evidence with cellular validation in patient fibroblasts plus zebrafish model, multiple orthogonal methods confirming ciliary protein recruitment defects\",\n      \"pmids\": [\"33131181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DZIP1 forms a multimeric complex with CBY1 and β-catenin at the basal body of primary cilia. DZIP1 stabilizes the complex and suppresses β-catenin activities. Loss of DZIP1 interaction with CBY1 (via a specific peptide domain) reduces DZIP1 and CBY1 stability and increases β-catenin activities, upregulating MMP2 and causing myxomatous valve phenotype, establishing DZIP1 functions to restrain β-catenin signaling through a CBY1 linker during cardiac development.\",\n      \"method\": \"Co-immunoprecipitation, biochemical decoy peptide experiments, subcellular fractionation, transcriptional reporter assays, mouse cardiac valve phenotype analysis, mutation identification in MVP patients\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP, biochemical peptide competition, functional reporter assays, in vivo phenotype; single lab\",\n      \"pmids\": [\"33811421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Loss of Cby1 in mice results in severe exocrine pancreatic atrophy with dilated ducts, reduced cilia number and length in pancreatic tissue, and defective zymogen granule (ZG) secretion with accumulation of ZGs and altered polarity in acinar cells, establishing CBY1 as required for normal ciliogenesis and secretory function in exocrine pancreas.\",\n      \"method\": \"Cby1-knockout mouse analysis, immunofluorescence, histology/electron microscopy, in vitro acini secretion assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with multiple phenotypic readouts (histology, EM, in vitro secretion), single lab but orthogonal methods\",\n      \"pmids\": [\"34446743\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The Cby-Fam92 module near the ciliary membrane and the Cep131-Cep162 module near the axoneme synergistically control basal body localization of Cep290 and initiation of ciliogenesis. Concurrent deletion of any protein from both modules causes complete loss of Cep290 from the basal body and blocks ciliogenesis initiation, demonstrating cooperative and retroactive interactions between these complexes.\",\n      \"method\": \"Drosophila genetic double mutants, epistasis analysis, immunofluorescence, electron microscopy, Cep290 localization assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic double-mutant epistasis with defined molecular (Cep290 localization) and cellular (ciliogenesis initiation) readouts, multiple orthogonal methods\",\n      \"pmids\": [\"38442096\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The crystal structure of FAM92A BAR domain (2.2 Å) reveals an antiparallel crescent-shaped homodimer. FAM92A BAR domain directly binds the N-terminal region of CBY1, and dimerization of FAM92A and CBY1 synergistically enhances their binding affinity. Positively charged clusters on the concave BAR surface are critical for lipid binding, and specific residues are essential for dimerization.\",\n      \"method\": \"X-ray crystallography (2.2 Å), structure-guided mutagenesis, lipid binding assays, CBY1 interaction assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with mutagenesis validation of lipid binding and dimerization, identification of CBY1 binding region, single lab but rigorous Tier 1 methods\",\n      \"pmids\": [\"40484380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Rhotekin interacts with CBY1 and competes with β-catenin for binding to CBY1, thereby activating canonical Wnt/β-catenin signaling and promoting osteoblast differentiation. CBY1 suppresses osteoblast differentiation, an effect counteracted by Rhotekin overexpression.\",\n      \"method\": \"Co-immunoprecipitation, competition binding assay, overexpression/knockdown differentiation assays, in vivo bone marrow silencing, β-catenin target gene analysis\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP, competition assay, both in vitro and in vivo functional phenotypes, single lab\",\n      \"pmids\": [\"42000008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In BCR-ABL1+ cells, CBY1 enforced expression promotes β-catenin cytoplasmic translocation through its two known mechanisms (Tcf/Lef competition and 14-3-3-mediated nuclear export). Cytoplasmic accumulation of β-catenin activates the unfolded protein response (UPR), leading to induction of BIM and activation of ER-resident caspase-12, contributing to apoptosis.\",\n      \"method\": \"CBY1 overexpression in K562 cells, subcellular fractionation, β-catenin target gene analysis, UPR pathway markers, caspase-12 activation, BIM induction assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — overexpression with defined signaling readouts, linking CBY1-driven cytoplasmic β-catenin to UPR activation, single lab\",\n      \"pmids\": [\"23707389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CBY1 protein stability in BCR-ABL1+ CML cells is reduced through binding to 14-3-3σ (mediated by Akt phosphorylation of CBY1 at serine 20), leading to proteasome-dependent degradation via enhanced SUMOylation. c-Jun N-terminal kinase (JNK) phosphorylation of 14-3-3σ at serine 186 promotes dissociation of CBY1 from 14-3-3σ, providing a mechanism to modulate CBY1 stability.\",\n      \"method\": \"Co-immunoprecipitation, phosphomutant analysis, proteasome inhibition assays, SUMOylation assays, JNK kinase analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — Co-IP with phosphomutants, biochemical pathway analysis identifying Akt/JNK/SUMOylation as regulators, single lab\",\n      \"pmids\": [\"26147002\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CBY1 (Chibby1) is a conserved, partially disordered coiled-coil protein that (1) directly binds the C-terminal activation domain of β-catenin to compete with Tcf/Lef transcription factors and repress Wnt/β-catenin target gene expression; (2) upon Akt-mediated phosphorylation at serine 20, recruits 14-3-3 proteins to form a tripartite complex with β-catenin, facilitating CRM1-dependent nuclear export of both CBY1 and β-catenin; (3) localizes to the distal appendages of mature centrioles via CEP164 and Cenexin interactions, where it recruits Rabin8 and Rab8 to drive ciliary vesicle formation and basal body docking during ciliogenesis; and (4) acts within a DZIP1-CBY1-FAM92 complex at the centriole-to-cilium interface to maintain transition zone integrity, recruit Ahi1, and enable proper IFT-B distribution, with loss of CBY1 in mice and humans causing ciliopathies including airway disease, cystic kidneys, pancreatic degeneration, and Joubert syndrome.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CBY1 (Chibby1) is a conserved, partially disordered coiled-coil protein with dual roles as an antagonist of Wnt/\\u03b2-catenin signaling and as a structural organizer at the centriole-to-cilium interface [#0, #3]. In the nucleus it directly binds the C-terminal activation domain of \\u03b2-catenin and represses \\u03b2-catenin/Tcf-Lef-driven transcription by competing with Lef-1 for \\u03b2-catenin binding [#0]. This repressive output is tuned by partners that bind CBY1 to relieve or redirect its activity, and by Akt-mediated phosphorylation of serine 20, which creates a 14-3-3 docking site; 14-3-3 binding assembles a tripartite CBY1\\u2013\\u03b2-catenin complex, biases CBY1 toward CRM1-dependent nuclear export over importin-\\u03b1 import, and drives cytoplasmic sequestration of both proteins [#2, #4, #14]. Structurally, CBY1 comprises a disordered N-terminal half that engages 14-3-3 and a C-terminal coiled-coil that mediates homodimerization and binds the disordered partner TC-1, with dimerization required for efficient nuclear import [#5, #9, #19]. At the cilium, CBY1 localizes as a ring at the distal end of the mature mother centriole, recruited there via CEP164 and Cenexin, and drives basal body docking and ciliary vesicle formation by recruiting the Rabin8\\u2013Rab8 module [#3, #10, #12, #13]. Within a DZIP1L/DZIP1-CBY1-FAM92 module at the centriole-to-cilium interface, CBY1 maintains transition zone integrity, recruits Ahi1, and ensures proper IFT-B distribution, with the FAM92A BAR domain binding the CBY1 N-terminus to remodel ciliary membrane [#13, #15, #16, #20, #25]. Loss of CBY1 in mice produces ciliopathy phenotypes including impaired mucociliary airway clearance, cystic kidneys, and exocrine pancreatic degeneration, and biallelic loss-of-function variants in humans cause a Joubert syndrome-spectrum ciliopathy [#3, #13, #21, #23].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established CBY1's founding molecular function: the unknown was what restrains \\u03b2-catenin transcriptional output, and CBY1 was shown to directly bind \\u03b2-catenin's C-terminus and compete with Lef-1 to repress Wnt target genes.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, transcriptional reporter assays, and Drosophila RNAi epistasis\",\n      \"pmids\": [\"12712206\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how CBY1 is itself regulated\", \"Did not address any non-nuclear function\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"First link to membrane trafficking: CBY1 (PIGEA-14) was shown to bind the polycystin-2 C-terminus and GM130 and redistribute PC2 to the trans-Golgi, hinting at a role beyond transcription.\",\n      \"evidence\": \"Yeast two-hybrid and co-expression localization in LLC-PK1 and HeLa cells\",\n      \"pmids\": [\"15194699\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reciprocal Co-IP or in vitro reconstitution\", \"Physiological significance of PC2 trafficking role unestablished\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Defined a positive regulator of Wnt acting through CBY1: TC1/C8orf4 binds CBY1 and relieves its antagonism, showing CBY1 repression is a regulatable node.\",\n      \"evidence\": \"Co-IP, fluorescence colocalization, and TOPflash reporter assays\",\n      \"pmids\": [\"16424001\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface not mapped at residue level\", \"No in vitro reconstitution\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Connected CBY1's \\u03b2-catenin antagonism to a developmental output: CBY1 promotes adipocyte differentiation by inhibiting \\u03b2-catenin signaling.\",\n      \"evidence\": \"RNAi, overexpression, and adipogenic differentiation assays in 3T3-L1 and ES cells plus Cby-deficient embryo fibroblasts\",\n      \"pmids\": [\"17403895\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address ciliary functions\", \"Mechanism of CBY1 induction during adipogenesis unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Revealed the switch controlling CBY1 compartmentalization: Akt phosphorylates CBY1 at S20, creating a 14-3-3 binding site that assembles a CBY1\\u201314-3-3\\u2013\\u03b2-catenin complex and sequesters \\u03b2-catenin in the cytoplasm.\",\n      \"evidence\": \"AP/MS, reciprocal Co-IP, Akt kinase assay, subcellular fractionation, and phosphomutant analysis\",\n      \"pmids\": [\"18573912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the export machinery involved\", \"Upstream signals controlling Akt activity in this context not addressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Mechanism of compartmentalization resolved: CBY1 shuttles via NLS/NES motifs, and 14-3-3 binding promotes CRM1 association while blocking importin-\\u03b1, driving CRM1-dependent nuclear export of CBY1 and \\u03b2-catenin.\",\n      \"evidence\": \"NLS/NES mutagenesis, leptomycin B treatment, Co-IP with CRM1 and importin-\\u03b1, shRNA knockdown, and fractionation\",\n      \"pmids\": [\"19940019\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative coupling between shuttling rate and \\u03b2-catenin output not measured\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined the structural basis of CBY1 oligomerization: a C-terminal coiled-coil heptad mediates homodimerization, which is dispensable for \\u03b2-catenin binding/repression but required for importin-\\u03b1 binding and nuclear import.\",\n      \"evidence\": \"Alanine-scanning mutagenesis, Co-IP, gel filtration, reporter assay, and importin-\\u03b1 binding assay\",\n      \"pmids\": [\"19435523\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Higher-order assembly state in vivo not determined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Established CBY1 as a ciliogenesis factor in vivo: CBY1 localizes to the base of cilia, and Cby-/- mice show failed basal body docking, absent mucociliary transport, and motile cilia paucity in airway epithelium.\",\n      \"evidence\": \"Cby-/- mouse generation, immunofluorescence, electron microscopy, and mucociliary/bacterial clearance assays\",\n      \"pmids\": [\"19364920\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular recruitment partners at the basal body not yet identified\", \"Relationship between ciliary and Wnt roles unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Mapped CBY1 to a specific centriolar substructure and tied it to \\u03b2-catenin control: Cenexin recruits CBY1 to the distal mother centriole, and this interaction abrogates CBY1's repression of \\u03b2-catenin transcription.\",\n      \"evidence\": \"Co-IP, immunofluorescence with centriole appendage markers, and primary cilia assembly assays in quiescent cells\",\n      \"pmids\": [\"22911743\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; reciprocal validation limited\", \"Direct competition mechanism between centriolar tethering and \\u03b2-catenin binding not structurally defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Tested conservation of CBY1's two roles: Drosophila CBY localizes to the transition zone and is essential for basal body function in sensory neurons and germ cells, but cby mutants show no Wingless defect, indicating the Wnt role may not be conserved.\",\n      \"evidence\": \"Cby mutant Drosophila analysis, immunofluorescence, EM, and sensory/spermatogenesis assays\",\n      \"pmids\": [\"22508513\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why the ciliary role is conserved while the Wnt role diverged unexplained\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined the ciliary vesicle pathway: CBY1 is recruited to distal appendages by CEP164 and then engages Rabin8 to recruit Rab8 and assemble ciliary vesicles during basal body docking.\",\n      \"evidence\": \"Mouse tracheal epithelial cells, Co-IP, immunofluorescence, Cby-/- analysis, EM, and Rabin8/Rab8 recruitment assays\",\n      \"pmids\": [\"25313408\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and order of CEP164 vs Cenexin recruitment not fully reconciled\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved CBY1's centriolar architecture and downstream recruitment: super-resolution imaging placed CBY1 in a ~250-nm distal ring downstream of Ofd1, and CBY1 is required to recruit the Joubert protein Ahi1; Cby1-/- mice develop cystic kidneys.\",\n      \"evidence\": \"3D-SIM/STED microscopy, Cby1-/- mouse kidney/cilia phenotyping, and Ahi1/Ofd1 localization analysis\",\n      \"pmids\": [\"25103236\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which CBY1 recruits Ahi1 not defined at the molecular level\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided atomic detail of the regulatory switch: the 14-3-3\\u03b6/CBY1 crystal structure confirmed phospho-S20 as essential for recognition, with flanking and noncanonical 14-3-3 loop residues contributing affinity.\",\n      \"evidence\": \"X-ray crystallography, NMR titration, ITC, and phosphomutant binding analysis\",\n      \"pmids\": [\"25909186\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of full-length CBY1 or the tripartite \\u03b2-catenin complex not solved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined CBY1's role in ciliary transport: Cby-/- airway cilia accumulate IFT-B components (IFT88, IFT20, IFT57) but not IFT-A or BBS proteins at dilated tips, establishing a selective IFT-B distribution defect.\",\n      \"evidence\": \"Cby-/- tracheal epithelial cells, immunofluorescence, TEM, and IFT component co-staining\",\n      \"pmids\": [\"26266958\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct interaction between CBY1 and IFT machinery not demonstrated\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified the membrane-remodeling partner: FAM92A/B BAR-domain proteins bind CBY1, depend on it for centriolar localization, and cooperate with CBY1 to generate Rab8-containing membrane structures required for ciliogenesis.\",\n      \"evidence\": \"Tandem AP/MS, Co-IP, immunofluorescence, Cby1-/- localization analysis, and FAM92A knockdown ciliogenesis assay\",\n      \"pmids\": [\"27528616\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Lipid specificity and geometry of the membrane-remodeling event addressed only later\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placed CBY1 in an ordered ciliogenesis cascade: Dzip1l binds CBY1 and acts upstream, with Dzip1l loss arresting at ciliary bud formation, CP110 removal failure, and Rpgrip1l recruitment failure.\",\n      \"evidence\": \"Co-IP, colocalization at basal body appendages, Dzip1l knockout mouse analysis, and epistasis\",\n      \"pmids\": [\"29487109\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; biochemical directness of the CBY1\\u2013Dzip1l interaction not fully reconstituted\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Dissected the modular binding determinants of CBY1: HDX-MS and truncation analysis showed three structural elements, with TC-1 binding requiring only the coiled-coil and flanking disordered regions modulating affinity.\",\n      \"evidence\": \"HDX-MS, CD, NMR, ITC, and truncation mutagenesis\",\n      \"pmids\": [\"27082063\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of disorder-mediated affinity tuning in cells not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established human disease causation: biallelic loss-of-function CBY1 variants cause a Joubert-spectrum ciliopathy, with patient fibroblasts showing ciliation defects and reduced ciliary AHI1 and ARL13B.\",\n      \"evidence\": \"Human genetics, patient fibroblast cilia analysis, and zebrafish Cby1 morpholino depletion\",\n      \"pmids\": [\"33131181\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genotype-phenotype correlation across the variant spectrum not detailed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked the basal body CBY1\\u2013\\u03b2-catenin complex to organ development: DZIP1 stabilizes a DZIP1-CBY1-\\u03b2-catenin complex at the basal body and restrains \\u03b2-catenin/MMP2 signaling during cardiac valve development.\",\n      \"evidence\": \"Co-IP, decoy peptide competition, fractionation, reporter assays, mouse cardiac valve phenotyping, and MVP patient mutation analysis\",\n      \"pmids\": [\"33811421\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Whether basal body localization is required for \\u03b2-catenin restraint not isolated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended the in vivo ciliopathy phenotype to a new organ: Cby1 loss causes exocrine pancreatic atrophy, reduced/short cilia, and defective zymogen granule secretion with altered acinar polarity.\",\n      \"evidence\": \"Cby1 knockout mouse histology, EM, immunofluorescence, and in vitro acini secretion assay\",\n      \"pmids\": [\"34446743\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between ciliary defect and secretory polarity loss unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined cooperative module logic for ciliogenesis initiation: the Cby-Fam92 module and a Cep131-Cep162 module synergistically control basal body Cep290 localization, with concurrent disruption abolishing Cep290 and blocking ciliogenesis.\",\n      \"evidence\": \"Drosophila genetic double mutants, epistasis, immunofluorescence, EM, and Cep290 localization assays\",\n      \"pmids\": [\"38442096\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of retroactive interaction between modules not biochemically defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided structural basis for CBY1-mediated membrane remodeling: the FAM92A BAR domain crystal structure shows a crescent homodimer that binds the CBY1 N-terminus, with synergistic dimerization enhancing affinity and a positively charged concave surface for lipid binding.\",\n      \"evidence\": \"X-ray crystallography at 2.2 \\u00c5, structure-guided mutagenesis, lipid binding, and CBY1 interaction assays\",\n      \"pmids\": [\"40484380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Curvature of the membrane shaped in vivo not directly measured\", \"How CBY1 dimerization couples to BAR-domain function structurally undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how the nuclear Wnt-antagonist function and the centriolar ciliogenesis function of CBY1 are coordinated within a single cell, and whether the two roles are mechanistically coupled or independent.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No study integrates the \\u03b2-catenin and ciliary functions in one experimental system\", \"Whether centriolar tethering is the primary regulator of CBY1's nuclear pool is untested\", \"Structure of full-length CBY1 in any complex is unavailable\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 6, 26]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 12, 16]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [10, 12, 13]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [3, 11, 13, 15]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2, 7]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 12, 13, 16]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [7, 21, 22, 23]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [21]}\n    ],\n    \"complexes\": [\n      \"CBY1-14-3-3-\\u03b2-catenin tripartite complex\",\n      \"DZIP1-CBY1-FAM92 ciliary module\",\n      \"CBY1 homodimer\"\n    ],\n    \"partners\": [\n      \"CTNNB1\",\n      \"YWHAE\",\n      \"CEP164\",\n      \"CEP290\",\n      \"FAM92A\",\n      \"DZIP1L\",\n      \"TC1\",\n      \"RAB8A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}