{"gene":"CFDP1","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2014,"finding":"Drosophila YETI (ortholog of CFDP1) binds to polytene chromosomes through its conserved BCNT domain, physically interacts with histone variant H2A.V, HP1a, and the ATPase subunit Domino-A (DOM-A) of the DOM/Tip60 chromatin remodeling complex, and is required for H2A.V accumulation at chromatin sites. Loss of YETI causes lethality and severe defects in higher-order chromatin organization including impaired association of H2A.V, nucleosomal histones, and epigenetic marks with polytene chromosomes. YETI was identified as a downstream target of DOM-A.","method":"Co-immunoprecipitation, chromatin binding assays, RNAi/genetic loss-of-function, immunostaining of polytene chromosomes","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, chromatin binding, genetic LOF with defined phenotype), replicated across multiple experimental approaches in single rigorous study","pmids":["24652835"],"is_preprint":false},{"year":2017,"finding":"Human CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. RNAi-mediated depletion of CFDP1 in HeLa cells causes chromosome organization defects, impaired SMC2 condensin recruitment, and cell cycle progression defects.","method":"RNAi knockdown, Co-immunoprecipitation, chromatin fractionation, immunofluorescence, cell cycle analysis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and clean KD with multiple defined cellular phenotypes (chromosome organization, condensin recruitment, cell cycle), single lab but multiple orthogonal methods","pmids":["28367969"],"is_preprint":false},{"year":2016,"finding":"Both Drosophila YETI and human CFDP1 undergo homodimerization mediated by the BCNT domain. YETI and CFDP1 physically interact with each other to form inactive heterodimers, which underlies the dominant-negative effect of CFDP1 expression in flies.","method":"GST pull-down assays, in vivo expression in Drosophila with phenotypic analysis","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — GST pull-down (direct binding) combined with in vivo dominant-negative phenotype, single lab","pmids":["27151176"],"is_preprint":false},{"year":2003,"finding":"Drosophila YETI (CFDP1 ortholog) binds specifically to both the kinesin light chain (via tetratricopeptide repeats) and the kinesin heavy chain (amino acids 675–975) subunits of kinesin-I, as shown by yeast two-hybrid and copurification from S2 cells. YETI localizes to both nucleus and cytosol.","method":"Yeast two-hybrid screen, copurification assay from Drosophila S2 cells, immunostaining","journal":"Biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid confirmed by co-purification in a cell-based assay, single lab, two orthogonal methods","pmids":["14720462"],"is_preprint":false},{"year":2015,"finding":"Mammalian Bcnt/Cfdp1 has an acidic stretch in its disordered N-terminal region that causes anomalous gel mobility on SDS-PAGE. Ser250 in the conserved BCNT-C domain is heavily phosphorylated in vivo and is a major determinant of the protein's electrophoretic behavior. Four lysine residues including Lys268 in BCNT-C are acetylated in vivo, and Bcnt/Cfdp1 is acetylated in vitro by CREB-binding protein (CBP). Bovine and human BCNTs are phosphorylated by casein kinase II in vitro.","method":"Deletion mutant expression in E. coli and HEK cells, phosphatase treatment, Ser250 substitution mutagenesis, mass spectrometry-based phosphosite mapping, in vitro acetylation assay with CBP","journal":"Bioscience reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assays (CKII phosphorylation, CBP acetylation), active-site mutagenesis (Ser250 substitution), and multiple PTM identification methods in single study","pmids":["26182435"],"is_preprint":false},{"year":1999,"finding":"Bovine BCNT (Cfdp1 ortholog) shows partial nuclear localization as determined by subcellular fractionation and immunohistochemistry in bovine epithelial cells and brain tissue, with a significant nuclear fraction and a major cytosolic portion. Bovine BCNT is a phosphoprotein, and both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.","method":"Subcellular fractionation, immunohistochemistry, in vitro kinase assay with casein kinase II","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct fractionation plus in vitro kinase assay, two orthogonal methods, single lab","pmids":["10350657"],"is_preprint":false},{"year":2024,"finding":"CFDP1 colocalizes with heterochromatin at major and minor satellite repeats and is essential for structural stability of centromeric heterochromatin including CENPA, HP1α, and H2A.Z. Loss of CFDP1 reduces RCC1 binding to satellite repeats, decreasing RanGTP levels and impairing chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Knockdown of histone chaperone ANP32E in CFDP1-deficient cells/mice partially rescued H2A.Z levels, RanGTP, craniofacial defects, and microtubule nucleation.","method":"Co-localization imaging, ChIP, RanGTP activity assays, genetic rescue experiments (ANP32E knockdown in CFDP1 KO cells and mice), microtubule nucleation assays","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ChIP, functional GTPase assay, genetic epistasis rescue in both cells and mice), clear mechanistic pathway defined","pmids":["38630655"],"is_preprint":false},{"year":2025,"finding":"CFDP1 weakly associates with the human SRCAP complex (SRCAP-C) in a salt-concentration-dependent manner. SRCAP-C purified under high-salt conditions lacks CFDP1 and is inactive for H2A.Z dimer exchange; addition of exogenous CFDP1 restores H2A.Z deposition activity of SRCAP-C. CFDP1 stimulates the basal ATPase activity of reconstituted SRCAP-C. CFDP1 deficiency in hiPSCs causes genome-wide reduction of H2A.Z, H3K27me3, and H3K4me3 deposition and upregulation of developmental genes normally marked by these modifications.","method":"Biochemical reconstitution of SRCAP-C, in vitro H2A.Z dimer exchange assay, ATPase activity assay, CFDP1 KO in hiPSCs with ChIP-seq","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with enzymatic activity assay (H2A.Z exchange, ATPase), plus genome-wide functional validation in KO cells via ChIP-seq","pmids":["41278978"],"is_preprint":true},{"year":2026,"finding":"CFDP1 functions as a bipartite microtubule-associated protein (MAP): its acidic N-terminus harbors a nuclear localization signal required for dissociation of importin α from the spindle assembly factor TPX2 (thereby promoting Aurora A kinase activation and microtubule nucleation), while its basic C-terminus interacts with tubulin, co-localizes with the mitotic spindle, and promotes microtubule bundling and polymerization. Loss of CFDP1 in mice causes gastrulation defects and embryonic lethality at e8.5 associated with chromosome segregation spindle defects and loss of K-fiber stability.","method":"Mouse CFDP1 knockout (phenotypic analysis), domain dissection with N-terminal/C-terminal constructs, importin α–TPX2 dissociation assay, tubulin-binding assay, microtubule bundling/polymerization assay, co-localization with mitotic spindle","journal":"International journal of molecular sciences","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical assays (tubulin binding, microtubule polymerization), domain mutagenesis, and KO mouse phenotype with mechanistic pathway established; single lab but multiple orthogonal methods","pmids":["41683788"],"is_preprint":false},{"year":2021,"finding":"In zebrafish, loss of Cfdp1 (cfdp1 mutants) causes G2-to-M phase cell cycle delay, mitotic block before anaphase (despite normal spindle formation), increased apoptosis (via tp53-dependent pathway), and failure of neural progenitor differentiation in the cerebellum and retina, accompanied by elevated cyclin B1 expression.","method":"Zebrafish cfdp1 mutant analysis, phospho-histone H3 staining, apoptosis assays, tp53 inhibition rescue, cyclin B1 expression analysis","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined cellular phenotypes (cell cycle, apoptosis, differentiation), tp53 epistasis, single lab","pmids":["33987914"],"is_preprint":false},{"year":2023,"finding":"In zebrafish, cfdp1 loss-of-function (morpholino knockdown and CRISPR knockout) causes arrhythmic hearts with defective cardiac performance and lethality. Mechanistically, cfdp1 abrogation downregulates Wnt signaling in embryonic hearts during valve development without affecting Notch activation.","method":"Morpholino knockdown, CRISPR knockout in zebrafish, cardiac function imaging, Wnt and Notch pathway reporter/expression analysis","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic LOF with pathway epistasis (Wnt vs. Notch), two independent LOF approaches (MO + KO), single lab","pmids":["37566073"],"is_preprint":false},{"year":2022,"finding":"CFDP1 promotes hepatocellular carcinoma malignancy via NEDD4-mediated ubiquitination and degradation of PTEN, leading to activation of the PI3K/AKT signaling pathway, as demonstrated by western blotting in HCC cell lines and in vivo tumor models.","method":"Western blotting, in vitro and in vivo loss/gain-of-function experiments in HCC cells, GSEA/GeneCards pathway analysis, xenograft mouse model","journal":"Cancer medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — western blot-based pathway analysis, single lab, limited mechanistic detail on direct CFDP1–NEDD4 interaction","pmids":["35861040"],"is_preprint":false},{"year":2012,"finding":"TFII-I transcription factors (GTF2I/GTF2IRD1) are directly recruited to the promoter of CFDP1 in human neural crest progenitor cells, identifying CFDP1 as a direct transcriptional target of TFII-I.","method":"ChIP-chip (chromatin immunoprecipitation with tiling promoter arrays) in human neural crest progenitor cells","journal":"The Cleft palate-craniofacial journal","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct ChIP-chip evidence of promoter binding, single lab, single method","pmids":["23145914"],"is_preprint":false},{"year":2025,"finding":"In C2C12 myoblasts, fluorescent protein-tagged Bcnt/Cfdp1 localizes predominantly to the nucleus, preferentially in low-DAPI-density regions, and this localization persists in differentiated myotubes. However, detergent-based biochemical fractionation consistently recovers a substantial fraction in the cytoplasm, an artifact attributed to the elastic/disordered properties of Bcnt/Cfdp1 causing artifactual translocation during fractionation under macromolecular crowding conditions.","method":"Live-cell fluorescence imaging of tagged Bcnt/Cfdp1, detergent-based subcellular fractionation, digitonin-based fractionation, quantitative proteomics (LC-MS/MS) of fractions","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live imaging vs. biochemical fractionation discrepancy resolved by digitonin-based method and quantitative proteomics, single lab but multiple orthogonal methods","pmids":["bio_10.1101_2025.04.28.651124"],"is_preprint":true}],"current_model":"CFDP1 (BCNT/SWC5/Yeti/CENP-29) is an evolutionarily conserved chromatin factor that functions as a required activating subunit of the SRCAP (SWR1) chromatin remodeling complex, stimulating its ATPase activity to catalyze genome-wide deposition of histone variant H2A.Z; it also stabilizes centromeric heterochromatin to support RCC1-dependent RanGTP production and chromatin-mediated microtubule nucleation, and acts as a bipartite microtubule-associated protein that promotes Aurora A/TPX2-dependent spindle assembly by dissociating importin α from TPX2 while its C-terminus directly binds tubulin—collectively making CFDP1 essential for cell division, craniofacial development, and cardiac morphogenesis."},"narrative":{"mechanistic_narrative":"CFDP1 (BCNT/Yeti) is an evolutionarily conserved chromatin factor that links histone variant deposition to chromosome organization and mitotic spindle assembly [PMID:24652835, PMID:28367969, PMID:38630655]. It is a required activating subunit of the SRCAP (SWR1-class) chromatin remodeling complex: CFDP1 associates with SRCAP-C in a salt-sensitive manner, stimulates the complex's basal ATPase activity, and is necessary to restore genome-wide deposition of histone variant H2A.Z, with its loss reducing H2A.Z, H3K27me3, and H3K4me3 and derepressing developmental genes [PMID:41278978, PMID:28367969]. The conserved BCNT domain mediates chromatin binding and homodimerization [PMID:24652835, PMID:27151176]. At centromeric heterochromatin, CFDP1 colocalizes with satellite repeats and is required for the structural stability of CENPA, HP1α, and H2A.Z; this stabilization supports RCC1 binding, RanGTP production, and chromatin-mediated microtubule nucleation, a defect partially rescued by depleting the H2A.Z chaperone ANP32E [PMID:38630655]. Independently, CFDP1 acts as a bipartite microtubule-associated protein in which the acidic N-terminus dissociates importin α from TPX2 to promote Aurora A activation while the basic C-terminus binds tubulin and drives microtubule bundling and polymerization [PMID:41683788]. Consistent with these roles in cell division, CFDP1 loss causes cell-cycle and chromosome-segregation defects across HeLa cells, zebrafish, and mice, with embryonic lethality, gastrulation and spindle defects in mouse knockouts and cardiac and craniofacial defects in lower vertebrates [PMID:41683788, PMID:33987914, PMID:38630655, PMID:37566073]. CFDP1 is regulated by phosphorylation (CKII, Ser250) and acetylation (CBP, including Lys268), and is a direct transcriptional target of TFII-I in neural crest progenitors [PMID:26182435, PMID:23145914].","teleology":[{"year":1999,"claim":"Established the basic biochemical character of CFDP1/BCNT, showing it is a nuclear-and-cytosolic phosphoprotein, the first clue that it is a regulated, post-translationally modified factor.","evidence":"Subcellular fractionation, immunohistochemistry, and in vitro casein kinase II assay on bovine/human BCNT","pmids":["10350657"],"confidence":"Medium","gaps":["No functional role assigned","Physiological kinase and consequence of phosphorylation unknown"]},{"year":2003,"claim":"Tested whether CFDP1 has a cytoskeletal/transport role, linking the Drosophila ortholog YETI directly to kinesin-I motor subunits and hinting at a non-chromatin function.","evidence":"Yeast two-hybrid and copurification from Drosophila S2 cells, immunostaining","pmids":["14720462"],"confidence":"Medium","gaps":["Functional significance of kinesin binding not established","Not validated in mammalian cells"]},{"year":2014,"claim":"Identified CFDP1's core chromatin function by showing the YETI ortholog binds chromatin through its BCNT domain and is required for H2A.V deposition via interaction with the DOM/Tip60 remodeling machinery.","evidence":"Co-IP, chromatin binding assays, RNAi loss-of-function and polytene immunostaining in Drosophila","pmids":["24652835"],"confidence":"High","gaps":["Mechanism of H2A.V deposition stimulation not defined","Whether mammalian CFDP1 acts identically not shown"]},{"year":2015,"claim":"Mapped the post-translational modification landscape of CFDP1, defining Ser250 phosphorylation and lysine acetylation by CBP within the conserved BCNT-C domain.","evidence":"Deletion/substitution mutagenesis, mass spectrometry phosphosite mapping, in vitro acetylation with CBP","pmids":["26182435"],"confidence":"High","gaps":["Functional consequence of each PTM on chromatin activity unknown","In vivo enzymes for acetylation not confirmed"]},{"year":2016,"claim":"Showed that CFDP1 homodimerizes via the BCNT domain and that YETI/CFDP1 heterodimers are inactive, explaining the dominant-negative behavior and implicating dimerization in regulation.","evidence":"GST pull-down and in vivo dominant-negative expression in Drosophila","pmids":["27151176"],"confidence":"Medium","gaps":["Structural basis of dimerization not resolved","Whether dimerization gates complex assembly unknown"]},{"year":2017,"claim":"Translated the chromatin role to human cells, linking CFDP1 to the SRCAP complex and showing depletion disrupts chromosome organization, condensin recruitment, and cell cycle progression.","evidence":"RNAi, reciprocal Co-IP, chromatin fractionation, immunofluorescence and cell cycle analysis in HeLa cells","pmids":["28367969"],"confidence":"High","gaps":["Whether CFDP1 is a stable vs. transient SRCAP subunit not resolved","Mechanism connecting H2A.Z to condensin loading unknown"]},{"year":2021,"claim":"Defined the developmental consequence of CFDP1 loss, showing G2/M delay, p53-dependent apoptosis, and failed neural progenitor differentiation in zebrafish.","evidence":"Zebrafish cfdp1 mutant analysis with pH3 staining, apoptosis assays, tp53 rescue","pmids":["33987914"],"confidence":"Medium","gaps":["Molecular cause of mitotic block not pinpointed","Link to chromatin defect not directly tested"]},{"year":2023,"claim":"Extended CFDP1 function to organogenesis by showing its loss causes cardiac arrhythmia and valve defects through downregulation of Wnt (but not Notch) signaling.","evidence":"Morpholino and CRISPR loss-of-function in zebrafish with cardiac imaging and pathway reporters","pmids":["37566073"],"confidence":"Medium","gaps":["How CFDP1 chromatin activity feeds into Wnt regulation unknown","Direct vs. indirect effect on Wnt genes not distinguished"]},{"year":2024,"claim":"Connected CFDP1's chromatin role to spindle assembly, showing it stabilizes centromeric heterochromatin to enable RCC1/RanGTP-driven microtubule nucleation, with ANP32E depletion rescuing the H2A.Z and developmental defects.","evidence":"Colocalization imaging, ChIP, RanGTP assays, microtubule nucleation assays, ANP32E epistasis rescue in cells and mice","pmids":["38630655"],"confidence":"High","gaps":["Direct vs. H2A.Z-mediated effect on RCC1 binding not fully separated","Whether SRCAP activity is required at centromeres not tested"]},{"year":2025,"claim":"Provided the biochemical mechanism for CFDP1 in chromatin remodeling, reconstituting SRCAP-C and showing CFDP1 is required to stimulate its ATPase activity and H2A.Z dimer exchange, with genome-wide consequences for H2A.Z and developmental gene marks.","evidence":"In vitro SRCAP-C reconstitution, H2A.Z exchange and ATPase assays, CFDP1 KO hiPSC ChIP-seq (preprint)","pmids":["41278978"],"confidence":"High","gaps":["Structural basis of ATPase stimulation not solved","Stoichiometry and regulation of CFDP1 within SRCAP-C unclear"]},{"year":2025,"claim":"Resolved a long-standing localization ambiguity, demonstrating by live imaging that CFDP1 is predominantly nuclear and that the cytoplasmic fraction recovered biochemically is a fractionation artifact of its disordered properties.","evidence":"Live-cell fluorescence imaging, detergent vs. digitonin fractionation, quantitative LC-MS/MS in C2C12 cells (preprint)","pmids":["bio_10.1101_2025.04.28.651124"],"confidence":"Medium","gaps":["Reconciliation with reported cytosolic spindle/tubulin functions unaddressed","Single cell-line context"]},{"year":2026,"claim":"Defined CFDP1 as a bipartite microtubule-associated protein, separating an N-terminal importin α/TPX2-dissociating activity that promotes Aurora A activation from a C-terminal tubulin-binding, microtubule-bundling activity, and tied loss to gastrulation defects and embryonic lethality in mice.","evidence":"Mouse knockout phenotyping, domain dissection, importin α–TPX2 dissociation assay, tubulin binding and microtubule polymerization assays","pmids":["41683788"],"confidence":"High","gaps":["How chromatin and cytoplasmic MAP functions are coordinated unknown","Regulation of N- vs C-terminal activities during the cell cycle unclear"]},{"year":null,"claim":"It remains unresolved how CFDP1's chromatin-remodeling role within SRCAP, its centromeric heterochromatin stabilization, and its direct microtubule-associated activity are mechanistically integrated within a single cell cycle.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of CFDP1 within SRCAP-C","Spatial/temporal partitioning between nuclear and spindle pools undefined","Direct CFDP1–NEDD4/PTEN mechanism in cancer not validated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7,1]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[8]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,6]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,6,13]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0,1,6]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[7,1,0]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,6,8,9]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[6,10,8]}],"complexes":["SRCAP complex"],"partners":["SRCAP","TPX2","H2A.Z","HP1A","RCC1","ANP32E","TUBULIN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UEE9","full_name":"Heterochromatin-stabilizing protein CFDP1","aliases":["Bucentaur","Craniofacial development protein 1"],"length_aa":299,"mass_kda":33.6,"function":"Required for the structural stability of pericentromeric heterochromatin (PubMed:28367969). Regulates heterochromatin state by stabilizing CBX5/HP1alpha and H3K9me3 at major satellites and CENPA at minor satellites and is required for incorporation of histone H2AZ1/H2AZ into chromatin (By similarity). Maintenance of chromatin structure promotes binding of guanine-nucleotide releasing factor RCC1 to minor and major satellite repeats (By similarity). Chromatin-bound RCC1 maintains high levels of GTP-bound RAN near the centromeric heterochromatin, facilitating RAN-mediated microtubule nucleation during mitosis (By similarity). Plays a role in craniofacial development (By similarity). Required to maintain normal cell function in embryonic development (By similarity)","subcellular_location":"Chromosome, centromere, kinetochore; Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q9UEE9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CFDP1","classification":"Common Essential","n_dependent_lines":539,"n_total_lines":1208,"dependency_fraction":0.4461920529801324},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"H2AFZ","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"RIOK1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CFDP1","total_profiled":1310},"omim":[{"mim_id":"611162","title":"MALARIA, SUSCEPTIBILITY TO","url":"https://www.omim.org/entry/611162"},{"mim_id":"608108","title":"CRANIOFACIAL DEVELOPMENT PROTEIN 1; CFDP1","url":"https://www.omim.org/entry/608108"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CFDP1"},"hgnc":{"alias_symbol":["BCNT","p97","CP27","SWC5","Yeti","CENP-29"],"prev_symbol":[]},"alphafold":{"accession":"Q9UEE9","domains":[{"cath_id":"-","chopping":"164-195_241-256","consensus_level":"medium","plddt":76.8652,"start":164,"end":256},{"cath_id":"1.20.5","chopping":"259-299","consensus_level":"medium","plddt":90.7376,"start":259,"end":299}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UEE9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UEE9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UEE9-F1-predicted_aligned_error_v6.png","plddt_mean":63.78},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CFDP1","jax_strain_url":"https://www.jax.org/strain/search?query=CFDP1"},"sequence":{"accession":"Q9UEE9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UEE9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UEE9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UEE9"}},"corpus_meta":[{"pmid":"23152477","id":"PMC_23152477","title":"Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk.","date":"2012","source":"Circulation. 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Part B, Resources","url":"https://pubmed.ncbi.nlm.nih.gov/33473745","citation_count":5,"is_preprint":false},{"pmid":"33320380","id":"PMC_33320380","title":"Influence of sequence length and charged residues on Swc5 binding with histone H2A-H2B.","date":"2020","source":"Proteins","url":"https://pubmed.ncbi.nlm.nih.gov/33320380","citation_count":4,"is_preprint":false},{"pmid":"37566073","id":"PMC_37566073","title":"Cfdp1 Is Essential for Cardiac Development and Function.","date":"2023","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/37566073","citation_count":3,"is_preprint":false},{"pmid":"38630655","id":"PMC_38630655","title":"CFDP1 regulates the stability of pericentric heterochromatin thereby affecting RAN GTPase activity and mitotic spindle formation.","date":"2024","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/38630655","citation_count":3,"is_preprint":false},{"pmid":"32432658","id":"PMC_32432658","title":"Overcoming off-targets: assessing Western blot signals for Bcnt/Cfdp1, a tentative component of the chromatin remodeling complex.","date":"2020","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/32432658","citation_count":2,"is_preprint":false},{"pmid":"41683788","id":"PMC_41683788","title":"The Chromatin Protein CFDP1 Activates TPX2 and Promotes Chromosomal Microtubule Nucleation and Spindle Assembly.","date":"2026","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41683788","citation_count":1,"is_preprint":false},{"pmid":"41040403","id":"PMC_41040403","title":"The Chromatin Protein CFDP1 Activates TPX2 and Promotes Chromosomal Microtubule Nucleation and Spindle Assembly.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41040403","citation_count":0,"is_preprint":false},{"pmid":"41278978","id":"PMC_41278978","title":"CFDP1 is required for histone variant H2A.Z deposition by the human SRCAP chromatin remodeling complex.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41278978","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.04.28.651124","title":"Macromolecular Crowding-Affected Mobility of Bcnt/Cfdp1, a Disordered Component of the Srcap Complex, from the Nucleus to Cytosol in Subcellular Fractionation","date":"2025-04-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.28.651124","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17025,"output_tokens":4029,"usd":0.055755,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11802,"output_tokens":4208,"usd":0.082105,"stage2_stop_reason":"end_turn"},"total_usd":0.13786,"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\": 2014,\n      \"finding\": \"Drosophila YETI (ortholog of CFDP1) binds to polytene chromosomes through its conserved BCNT domain, physically interacts with histone variant H2A.V, HP1a, and the ATPase subunit Domino-A (DOM-A) of the DOM/Tip60 chromatin remodeling complex, and is required for H2A.V accumulation at chromatin sites. Loss of YETI causes lethality and severe defects in higher-order chromatin organization including impaired association of H2A.V, nucleosomal histones, and epigenetic marks with polytene chromosomes. YETI was identified as a downstream target of DOM-A.\",\n      \"method\": \"Co-immunoprecipitation, chromatin binding assays, RNAi/genetic loss-of-function, immunostaining of polytene chromosomes\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, chromatin binding, genetic LOF with defined phenotype), replicated across multiple experimental approaches in single rigorous study\",\n      \"pmids\": [\"24652835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Human CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. RNAi-mediated depletion of CFDP1 in HeLa cells causes chromosome organization defects, impaired SMC2 condensin recruitment, and cell cycle progression defects.\",\n      \"method\": \"RNAi knockdown, Co-immunoprecipitation, chromatin fractionation, immunofluorescence, cell cycle analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and clean KD with multiple defined cellular phenotypes (chromosome organization, condensin recruitment, cell cycle), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28367969\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Both Drosophila YETI and human CFDP1 undergo homodimerization mediated by the BCNT domain. YETI and CFDP1 physically interact with each other to form inactive heterodimers, which underlies the dominant-negative effect of CFDP1 expression in flies.\",\n      \"method\": \"GST pull-down assays, in vivo expression in Drosophila with phenotypic analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — GST pull-down (direct binding) combined with in vivo dominant-negative phenotype, single lab\",\n      \"pmids\": [\"27151176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Drosophila YETI (CFDP1 ortholog) binds specifically to both the kinesin light chain (via tetratricopeptide repeats) and the kinesin heavy chain (amino acids 675–975) subunits of kinesin-I, as shown by yeast two-hybrid and copurification from S2 cells. YETI localizes to both nucleus and cytosol.\",\n      \"method\": \"Yeast two-hybrid screen, copurification assay from Drosophila S2 cells, immunostaining\",\n      \"journal\": \"Biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid confirmed by co-purification in a cell-based assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"14720462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Mammalian Bcnt/Cfdp1 has an acidic stretch in its disordered N-terminal region that causes anomalous gel mobility on SDS-PAGE. Ser250 in the conserved BCNT-C domain is heavily phosphorylated in vivo and is a major determinant of the protein's electrophoretic behavior. Four lysine residues including Lys268 in BCNT-C are acetylated in vivo, and Bcnt/Cfdp1 is acetylated in vitro by CREB-binding protein (CBP). Bovine and human BCNTs are phosphorylated by casein kinase II in vitro.\",\n      \"method\": \"Deletion mutant expression in E. coli and HEK cells, phosphatase treatment, Ser250 substitution mutagenesis, mass spectrometry-based phosphosite mapping, in vitro acetylation assay with CBP\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assays (CKII phosphorylation, CBP acetylation), active-site mutagenesis (Ser250 substitution), and multiple PTM identification methods in single study\",\n      \"pmids\": [\"26182435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Bovine BCNT (Cfdp1 ortholog) shows partial nuclear localization as determined by subcellular fractionation and immunohistochemistry in bovine epithelial cells and brain tissue, with a significant nuclear fraction and a major cytosolic portion. Bovine BCNT is a phosphoprotein, and both bovine and human BCNTs are phosphorylated by casein kinase II in vitro.\",\n      \"method\": \"Subcellular fractionation, immunohistochemistry, in vitro kinase assay with casein kinase II\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct fractionation plus in vitro kinase assay, two orthogonal methods, single lab\",\n      \"pmids\": [\"10350657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CFDP1 colocalizes with heterochromatin at major and minor satellite repeats and is essential for structural stability of centromeric heterochromatin including CENPA, HP1α, and H2A.Z. Loss of CFDP1 reduces RCC1 binding to satellite repeats, decreasing RanGTP levels and impairing chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Knockdown of histone chaperone ANP32E in CFDP1-deficient cells/mice partially rescued H2A.Z levels, RanGTP, craniofacial defects, and microtubule nucleation.\",\n      \"method\": \"Co-localization imaging, ChIP, RanGTP activity assays, genetic rescue experiments (ANP32E knockdown in CFDP1 KO cells and mice), microtubule nucleation assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ChIP, functional GTPase assay, genetic epistasis rescue in both cells and mice), clear mechanistic pathway defined\",\n      \"pmids\": [\"38630655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CFDP1 weakly associates with the human SRCAP complex (SRCAP-C) in a salt-concentration-dependent manner. SRCAP-C purified under high-salt conditions lacks CFDP1 and is inactive for H2A.Z dimer exchange; addition of exogenous CFDP1 restores H2A.Z deposition activity of SRCAP-C. CFDP1 stimulates the basal ATPase activity of reconstituted SRCAP-C. CFDP1 deficiency in hiPSCs causes genome-wide reduction of H2A.Z, H3K27me3, and H3K4me3 deposition and upregulation of developmental genes normally marked by these modifications.\",\n      \"method\": \"Biochemical reconstitution of SRCAP-C, in vitro H2A.Z dimer exchange assay, ATPase activity assay, CFDP1 KO in hiPSCs with ChIP-seq\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with enzymatic activity assay (H2A.Z exchange, ATPase), plus genome-wide functional validation in KO cells via ChIP-seq\",\n      \"pmids\": [\"41278978\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CFDP1 functions as a bipartite microtubule-associated protein (MAP): its acidic N-terminus harbors a nuclear localization signal required for dissociation of importin α from the spindle assembly factor TPX2 (thereby promoting Aurora A kinase activation and microtubule nucleation), while its basic C-terminus interacts with tubulin, co-localizes with the mitotic spindle, and promotes microtubule bundling and polymerization. Loss of CFDP1 in mice causes gastrulation defects and embryonic lethality at e8.5 associated with chromosome segregation spindle defects and loss of K-fiber stability.\",\n      \"method\": \"Mouse CFDP1 knockout (phenotypic analysis), domain dissection with N-terminal/C-terminal constructs, importin α–TPX2 dissociation assay, tubulin-binding assay, microtubule bundling/polymerization assay, co-localization with mitotic spindle\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical assays (tubulin binding, microtubule polymerization), domain mutagenesis, and KO mouse phenotype with mechanistic pathway established; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"41683788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In zebrafish, loss of Cfdp1 (cfdp1 mutants) causes G2-to-M phase cell cycle delay, mitotic block before anaphase (despite normal spindle formation), increased apoptosis (via tp53-dependent pathway), and failure of neural progenitor differentiation in the cerebellum and retina, accompanied by elevated cyclin B1 expression.\",\n      \"method\": \"Zebrafish cfdp1 mutant analysis, phospho-histone H3 staining, apoptosis assays, tp53 inhibition rescue, cyclin B1 expression analysis\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined cellular phenotypes (cell cycle, apoptosis, differentiation), tp53 epistasis, single lab\",\n      \"pmids\": [\"33987914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In zebrafish, cfdp1 loss-of-function (morpholino knockdown and CRISPR knockout) causes arrhythmic hearts with defective cardiac performance and lethality. Mechanistically, cfdp1 abrogation downregulates Wnt signaling in embryonic hearts during valve development without affecting Notch activation.\",\n      \"method\": \"Morpholino knockdown, CRISPR knockout in zebrafish, cardiac function imaging, Wnt and Notch pathway reporter/expression analysis\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic LOF with pathway epistasis (Wnt vs. Notch), two independent LOF approaches (MO + KO), single lab\",\n      \"pmids\": [\"37566073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CFDP1 promotes hepatocellular carcinoma malignancy via NEDD4-mediated ubiquitination and degradation of PTEN, leading to activation of the PI3K/AKT signaling pathway, as demonstrated by western blotting in HCC cell lines and in vivo tumor models.\",\n      \"method\": \"Western blotting, in vitro and in vivo loss/gain-of-function experiments in HCC cells, GSEA/GeneCards pathway analysis, xenograft mouse model\",\n      \"journal\": \"Cancer medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — western blot-based pathway analysis, single lab, limited mechanistic detail on direct CFDP1–NEDD4 interaction\",\n      \"pmids\": [\"35861040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TFII-I transcription factors (GTF2I/GTF2IRD1) are directly recruited to the promoter of CFDP1 in human neural crest progenitor cells, identifying CFDP1 as a direct transcriptional target of TFII-I.\",\n      \"method\": \"ChIP-chip (chromatin immunoprecipitation with tiling promoter arrays) in human neural crest progenitor cells\",\n      \"journal\": \"The Cleft palate-craniofacial journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct ChIP-chip evidence of promoter binding, single lab, single method\",\n      \"pmids\": [\"23145914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In C2C12 myoblasts, fluorescent protein-tagged Bcnt/Cfdp1 localizes predominantly to the nucleus, preferentially in low-DAPI-density regions, and this localization persists in differentiated myotubes. However, detergent-based biochemical fractionation consistently recovers a substantial fraction in the cytoplasm, an artifact attributed to the elastic/disordered properties of Bcnt/Cfdp1 causing artifactual translocation during fractionation under macromolecular crowding conditions.\",\n      \"method\": \"Live-cell fluorescence imaging of tagged Bcnt/Cfdp1, detergent-based subcellular fractionation, digitonin-based fractionation, quantitative proteomics (LC-MS/MS) of fractions\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live imaging vs. biochemical fractionation discrepancy resolved by digitonin-based method and quantitative proteomics, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"bio_10.1101_2025.04.28.651124\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"CFDP1 (BCNT/SWC5/Yeti/CENP-29) is an evolutionarily conserved chromatin factor that functions as a required activating subunit of the SRCAP (SWR1) chromatin remodeling complex, stimulating its ATPase activity to catalyze genome-wide deposition of histone variant H2A.Z; it also stabilizes centromeric heterochromatin to support RCC1-dependent RanGTP production and chromatin-mediated microtubule nucleation, and acts as a bipartite microtubule-associated protein that promotes Aurora A/TPX2-dependent spindle assembly by dissociating importin α from TPX2 while its C-terminus directly binds tubulin—collectively making CFDP1 essential for cell division, craniofacial development, and cardiac morphogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CFDP1 (BCNT/Yeti) is an evolutionarily conserved chromatin factor that links histone variant deposition to chromosome organization and mitotic spindle assembly [#0, #1, #6]. It is a required activating subunit of the SRCAP (SWR1-class) chromatin remodeling complex: CFDP1 associates with SRCAP-C in a salt-sensitive manner, stimulates the complex's basal ATPase activity, and is necessary to restore genome-wide deposition of histone variant H2A.Z, with its loss reducing H2A.Z, H3K27me3, and H3K4me3 and derepressing developmental genes [#7, #1]. The conserved BCNT domain mediates chromatin binding and homodimerization [#0, #2]. At centromeric heterochromatin, CFDP1 colocalizes with satellite repeats and is required for the structural stability of CENPA, HP1\\u03b1, and H2A.Z; this stabilization supports RCC1 binding, RanGTP production, and chromatin-mediated microtubule nucleation, a defect partially rescued by depleting the H2A.Z chaperone ANP32E [#6]. Independently, CFDP1 acts as a bipartite microtubule-associated protein in which the acidic N-terminus dissociates importin \\u03b1 from TPX2 to promote Aurora A activation while the basic C-terminus binds tubulin and drives microtubule bundling and polymerization [#8]. Consistent with these roles in cell division, CFDP1 loss causes cell-cycle and chromosome-segregation defects across HeLa cells, zebrafish, and mice, with embryonic lethality, gastrulation and spindle defects in mouse knockouts and cardiac and craniofacial defects in lower vertebrates [#8, #9, #6, #10]. CFDP1 is regulated by phosphorylation (CKII, Ser250) and acetylation (CBP, including Lys268), and is a direct transcriptional target of TFII-I in neural crest progenitors [#4, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established the basic biochemical character of CFDP1/BCNT, showing it is a nuclear-and-cytosolic phosphoprotein, the first clue that it is a regulated, post-translationally modified factor.\",\n      \"evidence\": \"Subcellular fractionation, immunohistochemistry, and in vitro casein kinase II assay on bovine/human BCNT\",\n      \"pmids\": [\"10350657\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional role assigned\", \"Physiological kinase and consequence of phosphorylation unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Tested whether CFDP1 has a cytoskeletal/transport role, linking the Drosophila ortholog YETI directly to kinesin-I motor subunits and hinting at a non-chromatin function.\",\n      \"evidence\": \"Yeast two-hybrid and copurification from Drosophila S2 cells, immunostaining\",\n      \"pmids\": [\"14720462\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional significance of kinesin binding not established\", \"Not validated in mammalian cells\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified CFDP1's core chromatin function by showing the YETI ortholog binds chromatin through its BCNT domain and is required for H2A.V deposition via interaction with the DOM/Tip60 remodeling machinery.\",\n      \"evidence\": \"Co-IP, chromatin binding assays, RNAi loss-of-function and polytene immunostaining in Drosophila\",\n      \"pmids\": [\"24652835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of H2A.V deposition stimulation not defined\", \"Whether mammalian CFDP1 acts identically not shown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapped the post-translational modification landscape of CFDP1, defining Ser250 phosphorylation and lysine acetylation by CBP within the conserved BCNT-C domain.\",\n      \"evidence\": \"Deletion/substitution mutagenesis, mass spectrometry phosphosite mapping, in vitro acetylation with CBP\",\n      \"pmids\": [\"26182435\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of each PTM on chromatin activity unknown\", \"In vivo enzymes for acetylation not confirmed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed that CFDP1 homodimerizes via the BCNT domain and that YETI/CFDP1 heterodimers are inactive, explaining the dominant-negative behavior and implicating dimerization in regulation.\",\n      \"evidence\": \"GST pull-down and in vivo dominant-negative expression in Drosophila\",\n      \"pmids\": [\"27151176\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of dimerization not resolved\", \"Whether dimerization gates complex assembly unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Translated the chromatin role to human cells, linking CFDP1 to the SRCAP complex and showing depletion disrupts chromosome organization, condensin recruitment, and cell cycle progression.\",\n      \"evidence\": \"RNAi, reciprocal Co-IP, chromatin fractionation, immunofluorescence and cell cycle analysis in HeLa cells\",\n      \"pmids\": [\"28367969\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether CFDP1 is a stable vs. transient SRCAP subunit not resolved\", \"Mechanism connecting H2A.Z to condensin loading unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the developmental consequence of CFDP1 loss, showing G2/M delay, p53-dependent apoptosis, and failed neural progenitor differentiation in zebrafish.\",\n      \"evidence\": \"Zebrafish cfdp1 mutant analysis with pH3 staining, apoptosis assays, tp53 rescue\",\n      \"pmids\": [\"33987914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular cause of mitotic block not pinpointed\", \"Link to chromatin defect not directly tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended CFDP1 function to organogenesis by showing its loss causes cardiac arrhythmia and valve defects through downregulation of Wnt (but not Notch) signaling.\",\n      \"evidence\": \"Morpholino and CRISPR loss-of-function in zebrafish with cardiac imaging and pathway reporters\",\n      \"pmids\": [\"37566073\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How CFDP1 chromatin activity feeds into Wnt regulation unknown\", \"Direct vs. indirect effect on Wnt genes not distinguished\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected CFDP1's chromatin role to spindle assembly, showing it stabilizes centromeric heterochromatin to enable RCC1/RanGTP-driven microtubule nucleation, with ANP32E depletion rescuing the H2A.Z and developmental defects.\",\n      \"evidence\": \"Colocalization imaging, ChIP, RanGTP assays, microtubule nucleation assays, ANP32E epistasis rescue in cells and mice\",\n      \"pmids\": [\"38630655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs. H2A.Z-mediated effect on RCC1 binding not fully separated\", \"Whether SRCAP activity is required at centromeres not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided the biochemical mechanism for CFDP1 in chromatin remodeling, reconstituting SRCAP-C and showing CFDP1 is required to stimulate its ATPase activity and H2A.Z dimer exchange, with genome-wide consequences for H2A.Z and developmental gene marks.\",\n      \"evidence\": \"In vitro SRCAP-C reconstitution, H2A.Z exchange and ATPase assays, CFDP1 KO hiPSC ChIP-seq (preprint)\",\n      \"pmids\": [\"41278978\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ATPase stimulation not solved\", \"Stoichiometry and regulation of CFDP1 within SRCAP-C unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved a long-standing localization ambiguity, demonstrating by live imaging that CFDP1 is predominantly nuclear and that the cytoplasmic fraction recovered biochemically is a fractionation artifact of its disordered properties.\",\n      \"evidence\": \"Live-cell fluorescence imaging, detergent vs. digitonin fractionation, quantitative LC-MS/MS in C2C12 cells (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.04.28.651124\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reconciliation with reported cytosolic spindle/tubulin functions unaddressed\", \"Single cell-line context\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined CFDP1 as a bipartite microtubule-associated protein, separating an N-terminal importin \\u03b1/TPX2-dissociating activity that promotes Aurora A activation from a C-terminal tubulin-binding, microtubule-bundling activity, and tied loss to gastrulation defects and embryonic lethality in mice.\",\n      \"evidence\": \"Mouse knockout phenotyping, domain dissection, importin \\u03b1\\u2013TPX2 dissociation assay, tubulin binding and microtubule polymerization assays\",\n      \"pmids\": [\"41683788\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How chromatin and cytoplasmic MAP functions are coordinated unknown\", \"Regulation of N- vs C-terminal activities during the cell cycle unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how CFDP1's chromatin-remodeling role within SRCAP, its centromeric heterochromatin stabilization, and its direct microtubule-associated activity are mechanistically integrated within a single cell cycle.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of CFDP1 within SRCAP-C\", \"Spatial/temporal partitioning between nuclear and spindle pools undefined\", \"Direct CFDP1\\u2013NEDD4/PTEN mechanism in cancer not validated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7, 1]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 6, 13]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [7, 1, 0]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 6, 8, 9]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [6, 10, 8]}\n    ],\n    \"complexes\": [\"SRCAP complex\"],\n    \"partners\": [\"SRCAP\", \"TPX2\", \"H2A.Z\", \"HP1a\", \"RCC1\", \"ANP32E\", \"tubulin\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}