{"gene":"FAAP20","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2012,"finding":"FAAP20 is an integral component of the FA nuclear core complex; it physically interacts with FANCA through a defined region on FANCA, and FANCA regulates the stability of FAAP20.","method":"Co-immunoprecipitation, interaction mapping, protein stability assays","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — replicated independently in two simultaneous publications (PMID:22343915 and PMID:22396592) using reciprocal co-IP and functional assays","pmids":["22343915","22396592"],"is_preprint":false},{"year":2012,"finding":"FAAP20 contains a conserved ubiquitin-binding zinc-finger (UBZ) domain that binds K63-linked ubiquitin chains in vitro; the UBZ domain is not required for interaction with FANCA but is required for DNA-damage-induced chromatin loading of FANCA and functional integrity of the FA pathway.","method":"In vitro ubiquitin-binding assay, domain mutagenesis, chromatin fractionation","journal":"Blood","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro binding assay with domain mutagenesis, independently replicated across multiple labs (PMID:22343915, PMID:22396592, PMID:22705371)","pmids":["22343915","22396592","22705371"],"is_preprint":false},{"year":2012,"finding":"Loss of FAAP20 results in hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination, establishing FAAP20 as required for FA core complex ubiquitin ligase function.","method":"Somatic knockout cell lines, FANCD2 monoubiquitination assay, clonogenic survival assay, cytogenetics","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout with multiple orthogonal phenotypic readouts, independently replicated across labs","pmids":["22396592","22343915","22705371"],"is_preprint":false},{"year":2012,"finding":"FAAP20 preferentially binds the K63-linked ubiquitin product of the RNF8-UBC13 E3/E2 pair, and this ubiquitin-binding activity and RNF8-UBC13 are both required for recruitment of FAAP20 (and the FA core complex) to interstrand crosslink sites; RNF8 and FAAP20 are needed for efficient FANCD2 monoubiquitination.","method":"Co-immunoprecipitation, ubiquitin-binding assays, immunofluorescence foci, epistasis analysis with RNF8/RNF168 knockdown","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, epistasis with genetic knockdown, multiple orthogonal methods in single study","pmids":["22705371"],"is_preprint":false},{"year":2014,"finding":"Ubiquitin binding by FAAP20 extends beyond the canonical ββα UBZ module: a disordered C-terminal tail folds into a rigid extended β-loop upon ubiquitin binding, with an invariant C-terminal tryptophan contacting I44 of ubiquitin; substitution of this tryptophan abolishes ubiquitin binding in vitro and causes hypersensitivity to ICL lesions in vivo.","method":"NMR/structural analysis, in vitro binding assay, site-directed mutagenesis, cellular ICL sensitivity assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — structural characterization combined with mutagenesis and in vitro binding plus cellular validation in one study","pmids":["25414354"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of FAAP20-UBZ in complex with K63-linked diubiquitin at 1.9 Å resolution showed that FAAP20-UBZ contacts only one ubiquitin moiety; surface plasmon resonance demonstrated similar affinities for mono-ubiquitin and M1-, K48-, and K63-linked diubiquitin chains; key interacting residues (Ala168, Trp180, Asp164) were identified and their mutation abolished ubiquitin binding in vitro and FAAP20 accumulation at damage sites in vivo.","method":"X-ray crystallography (1.9 Å), surface plasmon resonance, site-directed mutagenesis, live-cell damage-site accumulation assay","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with SPR and mutagenesis with cellular validation in one study","pmids":["25799058"],"is_preprint":false},{"year":2015,"finding":"FAAP20-UBZ4 domain binds Rev1-BRCT domain through a distinct binding surface from its ubiquitin-binding surface; ubiquitin binding to FAAP20-UBZ4 enhances binding affinity between FAAP20-UBZ4 and Rev1-BRCT, suggesting a mechanism for FA core complex-mediated recruitment of Rev1 to DNA lesions.","method":"NMR chemical shift perturbation mapping, biophysical interaction assays","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structure-function, single lab, single study","pmids":["26318859"],"is_preprint":false},{"year":2015,"finding":"Deletion of Faap20 in mice causes a mild FA-like phenotype including defects in hematopoietic stem and progenitor cell reconstitution and susceptibility to MMC-induced pancytopenia; double-knockout with Fanca revealed a dominant effect of FANCA in the FAAP20-FANCA interaction in vivo.","method":"Faap20 knockout mouse model, bone marrow transplantation, MMC treatment, flow cytometry, double-knockout epistasis","journal":"Stem cells (Dayton, Ohio)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean mouse knockout with multiple hematopoietic phenotypic readouts and epistasis with Fanca KO, single lab","pmids":["25917546"],"is_preprint":false},{"year":2016,"finding":"FAAP20 is phosphorylated at a degron motif by GSK3β, which enables recognition and polyubiquitination by the SCF-FBW7 E3 ligase, leading to proteasomal degradation of FAAP20; expression of non-phosphorylatable FAAP20 deregulates FANCA turnover at chromatin during ICL repair and compromises the FA pathway.","method":"In vitro kinase assay (GSK3β), ubiquitination assay, proteasome inhibitor treatment, phosphomimetic/non-phosphorylatable mutant analysis, chromatin fractionation","journal":"Oncotarget","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro kinase assay plus mutagenesis plus cellular pathway readout (FANCD2 monoubiquitination, chromatin loading), single lab but multiple orthogonal methods","pmids":["27232758"],"is_preprint":false},{"year":2019,"finding":"PIN1 phosphorylation-specific prolyl isomerase catalyzes cis-trans isomerization of the FAAP20 pSer48-Pro49 motif, promoting FAAP20 stability by enhancing its interaction with PP2A phosphatase, thereby counteracting SCF-FBW7-dependent proteolysis at the phosphodegron; PIN1 deficiency impairs FANCD2 activation and ICL repair.","method":"Prolyl isomerization assay, co-immunoprecipitation (PIN1-FAAP20, FAAP20-PP2A), phosphomutant analysis, FANCD2 monoubiquitination assay, ICL sensitivity assay","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP of multiple interactions with functional readouts and mechanistic mutants, single lab","pmids":["30789902"],"is_preprint":false},{"year":2020,"finding":"FAAP20 is acetylated by the acetyltransferase p300/CBP on lysine 152; acetylation of K152 prevents polyubiquitination at this residue, stabilizing FAAP20 against proteasomal degradation; disruption of this acetylation pathway impairs FANCD2 monoubiquitination, revealing a competition between ubiquitination and acetylation at K152 for FAAP20 stability.","method":"In vitro acetylation assay, ubiquitination assay, acetylation-mimetic/lysine mutant analysis, proteasome inhibitor treatment, FANCD2 monoubiquitination assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro acetyltransferase assay with mutagenesis and pathway readout, single lab","pmids":["32763975"],"is_preprint":false},{"year":2023,"finding":"FAAP20 plays a role in homologous recombination (HR) at DNA double-strand breaks independently of FANCA; FAAP20 also stimulates FANCA's strand annealing biochemical activity in vitro and participates in single-strand annealing (SSA) repair in a FANCA-dependent manner; FAAP20 loss reduces nuclear RAD51 IRIF and sensitizes cells to ionizing radiation and PARP inhibition.","method":"HR reporter assay, SSA reporter assay, in vitro biochemical stimulation assay (FANCA strand annealing), RAD51 foci immunofluorescence, clonogenic survival with IR and PARP inhibitor","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple repair pathway reporter assays and in vitro biochemical assay plus cellular readouts, single lab","pmids":["37620397"],"is_preprint":false}],"current_model":"FAAP20 is an integral structural and regulatory component of the FA nuclear core complex that binds FANCA (which stabilizes it), uses its UBZ domain and C-terminal tail to recognize ubiquitinated chromatin (particularly K63-Ub generated by RNF8-UBC13) to recruit the FA core complex to interstrand crosslink sites, facilitates FANCD2 monoubiquitination and ICL repair, recruits the translesion polymerase Rev1 via a distinct UBZ surface, and participates in homologous recombination and single-strand annealing at DSBs; its abundance is tightly controlled by GSK3β phosphorylation of a degron followed by SCF-FBW7-mediated polyubiquitination and proteasomal degradation, a process counteracted by PIN1-catalyzed prolyl isomerization (which promotes PP2A-mediated dephosphorylation) and by p300/CBP-mediated acetylation of the same lysine targeted for polyubiquitination."},"narrative":{"mechanistic_narrative":"FAAP20 is an integral subunit of the Fanconi anemia (FA) nuclear core complex that couples ubiquitin signaling at damaged chromatin to FA-pathway activation and DNA interstrand crosslink (ICL) repair [PMID:22343915, PMID:22396592, PMID:22705371]. It binds FANCA through a defined interaction that reciprocally stabilizes FAAP20, and its loss produces hallmark FA defects—crosslinker hypersensitivity, chromosome aberrations, and reduced FANCD2 monoubiquitination [PMID:22343915, PMID:22396592, PMID:22705371]. FAAP20 recognizes ubiquitinated chromatin through a ubiquitin-binding zinc-finger (UBZ) module whose binding surface is extended by a C-terminal tail that folds into a rigid β-loop on ubiquitin engagement, with an invariant C-terminal tryptophan contacting the ubiquitin I44 patch; this activity is dispensable for FANCA binding but required for DNA-damage-induced chromatin loading of FANCA [PMID:22343915, PMID:22396592, PMID:22705371, PMID:25414354, PMID:25799058]. FAAP20 preferentially reads the K63-linked ubiquitin product generated by the RNF8–UBC13 pair, and both this E3/E2 activity and FAAP20 ubiquitin binding are required to recruit the FA core complex to ICL sites [PMID:22705371]. A distinct UBZ surface engages the Rev1 BRCT domain, and ubiquitin binding enhances this interaction, linking FAAP20 to translesion-polymerase recruitment [PMID:26318859]. Beyond ICL repair, FAAP20 acts in double-strand-break repair: it stimulates FANCA strand-annealing activity in vitro, supports single-strand annealing in a FANCA-dependent manner, and promotes homologous recombination and RAD51 focus formation, with its loss sensitizing cells to ionizing radiation and PARP inhibition [PMID:37620397]. FAAP20 abundance is tightly regulated by a phosphodegron: GSK3β phosphorylation licenses SCF-FBW7-mediated polyubiquitination and proteasomal turnover [PMID:27232758], which is opposed by PIN1-catalyzed prolyl isomerization that recruits PP2A to reverse the phosphorylation [PMID:30789902] and by p300/CBP acetylation of K152 that competes with ubiquitination at the same lysine [PMID:32763975]. Knockout mice display a mild FA-like phenotype with hematopoietic reconstitution defects and MMC-induced pancytopenia [PMID:25917546].","teleology":[{"year":2012,"claim":"Establishing FAAP20 as a bona fide FA core complex subunit answered whether this factor operates within the canonical FA machinery and identified FANCA as its stabilizing anchor.","evidence":"Co-IP, FANCA interaction mapping, and protein stability assays in human cells","pmids":["22343915","22396592"],"confidence":"High","gaps":["Did not define the structural basis of the FAAP20-FANCA interface","Mechanism by which FANCA stabilizes FAAP20 not resolved"]},{"year":2012,"claim":"Discovery of the UBZ domain and its K63-ubiquitin binding showed how FAAP20 reads damaged chromatin and separated its ubiquitin-recognition role from FANCA binding.","evidence":"In vitro ubiquitin-binding assay, domain mutagenesis, and chromatin fractionation","pmids":["22343915","22396592","22705371"],"confidence":"High","gaps":["Did not identify the in vivo source of the K63 chains at that point","Atomic-level recognition mode not yet defined"]},{"year":2012,"claim":"Loss-of-function studies established FAAP20 as functionally required for FA core complex ubiquitin ligase output, linking it to FANCD2 monoubiquitination and ICL resistance.","evidence":"Somatic knockouts with FANCD2 monoubiquitination, clonogenic survival, and cytogenetics","pmids":["22396592","22343915","22705371"],"confidence":"High","gaps":["Did not distinguish chromatin-recruitment defect from catalytic defect","Non-ICL repair roles unexamined"]},{"year":2012,"claim":"Identifying RNF8–UBC13 as the upstream K63 source and showing its requirement for FAAP20 recruitment placed FAAP20 in a defined signaling cascade at crosslink sites.","evidence":"Co-IP, ubiquitin-binding assays, immunofluorescence foci, and RNF8/RNF168 knockdown epistasis","pmids":["22705371"],"confidence":"High","gaps":["Did not establish the chromatin substrate ubiquitinated by RNF8 in this context","Quantitative kinetics of recruitment unresolved"]},{"year":2015,"claim":"Structural studies of the UBZ–ubiquitin interaction defined the molecular recognition mechanism, revealing a C-terminal tail extension and key residues whose mutation abolishes binding and damage-site accumulation.","evidence":"NMR and 1.9 Å crystal structure of UBZ with diubiquitin, SPR, mutagenesis, and cellular damage-site assays","pmids":["25414354","25799058"],"confidence":"High","gaps":["SPR showed similar affinity across M1/K48/K63 linkages, leaving in vivo linkage selectivity to be explained by context","Did not capture full-length FAAP20 conformation"]},{"year":2015,"claim":"Mapping a distinct UBZ surface for Rev1-BRCT binding extended FAAP20's role beyond core-complex recruitment to coordinating translesion polymerase delivery.","evidence":"NMR chemical shift perturbation mapping and biophysical interaction assays","pmids":["26318859"],"confidence":"Medium","gaps":["Single lab, single study without in vivo Rev1 recruitment validation","Functional consequence for translesion synthesis not tested"]},{"year":2015,"claim":"An in vivo mouse knockout established the organismal consequence of FAAP20 loss and the dominance of FANCA within the FAAP20-FANCA axis.","evidence":"Faap20 knockout mice with bone marrow transplantation, MMC treatment, and Fanca double-knockout epistasis","pmids":["25917546"],"confidence":"Medium","gaps":["Phenotype milder than core FA components, leaving relative pathway weight uncertain","Single lab"]},{"year":2016,"claim":"Identifying the GSK3β/SCF-FBW7 phosphodegron explained how FAAP20 levels are downregulated and showed that turnover control is itself required for proper FANCA dynamics during ICL repair.","evidence":"In vitro GSK3β kinase assay, ubiquitination assay, proteasome inhibition, and phosphomutant chromatin fractionation","pmids":["27232758"],"confidence":"High","gaps":["Did not identify upstream signals activating GSK3β toward FAAP20","Single lab"]},{"year":2019,"claim":"PIN1-catalyzed prolyl isomerization was shown to counteract the phosphodegron by recruiting PP2A, adding a stabilizing arm to FAAP20 abundance control.","evidence":"Prolyl isomerization assay, PIN1-FAAP20 and FAAP20-PP2A co-IPs, phosphomutant analysis, and ICL/FANCD2 readouts","pmids":["30789902"],"confidence":"Medium","gaps":["Single lab without independent confirmation","Stoichiometry and dynamics relative to FBW7 not quantified"]},{"year":2020,"claim":"Discovery of p300/CBP acetylation at K152 competing with ubiquitination at the same lysine revealed a second stabilizing mechanism and a direct switch governing FAAP20 fate.","evidence":"In vitro acetylation and ubiquitination assays, acetyl-mimetic/lysine mutants, proteasome inhibition, and FANCD2 monoubiquitination assay","pmids":["32763975"],"confidence":"Medium","gaps":["Single lab","Signals controlling the acetylation/ubiquitination balance in vivo unknown"]},{"year":2023,"claim":"Demonstrating FAAP20 roles in HR and SSA, including stimulation of FANCA strand annealing, broadened its function beyond ICL repair to double-strand-break processing and PARP-inhibitor sensitivity.","evidence":"HR and SSA reporter assays, in vitro FANCA strand-annealing stimulation, RAD51 foci, and IR/PARP-inhibitor survival","pmids":["37620397"],"confidence":"Medium","gaps":["Single lab","Mechanism distinguishing FANCA-independent HR role from FANCA-dependent SSA role not fully defined"]},{"year":null,"claim":"How the multiple stability inputs (GSK3β/FBW7, PIN1/PP2A, p300/CBP acetylation) are integrated with upstream DNA-damage signaling to time FAAP20 levels during repair remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking abundance control to repair-pathway choice","Direct disease-causing FAAP20 mutations not established in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,11]}],"localization":[{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,11]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[2,3,11]}],"complexes":["FA nuclear core complex"],"partners":["FANCA","RNF8","UBC13","REV1","PIN1","PP2A","FBXW7"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6NZ36","full_name":"Fanconi anemia core complex-associated protein 20","aliases":["FANCA-associated protein of 20 kDa","Fanconi anemia-associated protein of 20 kDa"],"length_aa":180,"mass_kda":19.9,"function":"Component of the Fanconi anemia (FA) complex required to recruit the FA complex to DNA interstrand cross-links (ICLs) and promote ICLs repair. Following DNA damage recognizes and binds 'Lys-63'-linked ubiquitin generated by RNF8 at ICLs and recruits other components of the FA complex. Promotes translesion synthesis via interaction with REV1","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q6NZ36/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FAAP20","classification":"Not Classified","n_dependent_lines":199,"n_total_lines":1208,"dependency_fraction":0.16473509933774835},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FAAP20","total_profiled":1310},"omim":[{"mim_id":"615183","title":"FA CORE COMPLEX-ASSOCIATED PROTEIN 20; FAAP20","url":"https://www.omim.org/entry/615183"},{"mim_id":"611685","title":"RING FINGER PROTEIN 8; RNF8","url":"https://www.omim.org/entry/611685"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"},{"location":"Cell Junctions","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FAAP20"},"hgnc":{"alias_symbol":["FLJ31031"],"prev_symbol":["C1orf86"]},"alphafold":{"accession":"Q6NZ36","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6NZ36","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6NZ36-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6NZ36-F1-predicted_aligned_error_v6.png","plddt_mean":65.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FAAP20","jax_strain_url":"https://www.jax.org/strain/search?query=FAAP20"},"sequence":{"accession":"Q6NZ36","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6NZ36.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6NZ36/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6NZ36"}},"corpus_meta":[{"pmid":"22343915","id":"PMC_22343915","title":"FAAP20: a novel ubiquitin-binding FA nuclear core-complex protein required for functional integrity of the FA-BRCA DNA repair pathway.","date":"2012","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/22343915","citation_count":73,"is_preprint":false},{"pmid":"22396592","id":"PMC_22396592","title":"Fanconi anemia (FA) binding protein FAAP20 stabilizes FA complementation group A (FANCA) and participates in interstrand cross-link repair.","date":"2012","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/22396592","citation_count":70,"is_preprint":false},{"pmid":"22705371","id":"PMC_22705371","title":"A ubiquitin-binding protein, FAAP20, links RNF8-mediated ubiquitination to the Fanconi anemia DNA repair network.","date":"2012","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/22705371","citation_count":59,"is_preprint":false},{"pmid":"27232758","id":"PMC_27232758","title":"FBW7 regulates DNA interstrand cross-link repair by modulating FAAP20 degradation.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27232758","citation_count":16,"is_preprint":false},{"pmid":"25799058","id":"PMC_25799058","title":"Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP20.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25799058","citation_count":13,"is_preprint":false},{"pmid":"30789902","id":"PMC_30789902","title":"Prolyl isomerization of FAAP20 catalyzed by PIN1 regulates the Fanconi anemia pathway.","date":"2019","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30789902","citation_count":12,"is_preprint":false},{"pmid":"25414354","id":"PMC_25414354","title":"Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain.","date":"2014","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/25414354","citation_count":12,"is_preprint":false},{"pmid":"25917546","id":"PMC_25917546","title":"Loss of Faap20 Causes Hematopoietic Stem and Progenitor Cell Depletion in Mice Under Genotoxic Stress.","date":"2015","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/25917546","citation_count":8,"is_preprint":false},{"pmid":"32763975","id":"PMC_32763975","title":"Acetylation modulates the Fanconi anemia pathway by protecting FAAP20 from ubiquitin-mediated proteasomal degradation.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32763975","citation_count":7,"is_preprint":false},{"pmid":"37620397","id":"PMC_37620397","title":"Fanconi anemia associated protein 20 (FAAP20) plays an essential role in homology-directed repair of DNA double-strand breaks.","date":"2023","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/37620397","citation_count":6,"is_preprint":false},{"pmid":"26318859","id":"PMC_26318859","title":"Biophysical characterization of the interaction between FAAP20-UBZ4 domain and Rev1-BRCT domain.","date":"2015","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/26318859","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7197,"output_tokens":3190,"usd":0.034721,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10637,"output_tokens":3858,"usd":0.074817,"stage2_stop_reason":"end_turn"},"total_usd":0.109538,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"FAAP20 is an integral component of the FA nuclear core complex; it physically interacts with FANCA through a defined region on FANCA, and FANCA regulates the stability of FAAP20.\",\n      \"method\": \"Co-immunoprecipitation, interaction mapping, protein stability assays\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — replicated independently in two simultaneous publications (PMID:22343915 and PMID:22396592) using reciprocal co-IP and functional assays\",\n      \"pmids\": [\"22343915\", \"22396592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FAAP20 contains a conserved ubiquitin-binding zinc-finger (UBZ) domain that binds K63-linked ubiquitin chains in vitro; the UBZ domain is not required for interaction with FANCA but is required for DNA-damage-induced chromatin loading of FANCA and functional integrity of the FA pathway.\",\n      \"method\": \"In vitro ubiquitin-binding assay, domain mutagenesis, chromatin fractionation\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro binding assay with domain mutagenesis, independently replicated across multiple labs (PMID:22343915, PMID:22396592, PMID:22705371)\",\n      \"pmids\": [\"22343915\", \"22396592\", \"22705371\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Loss of FAAP20 results in hypersensitivity to DNA cross-linking agents, chromosome aberrations, and reduced FANCD2 monoubiquitination, establishing FAAP20 as required for FA core complex ubiquitin ligase function.\",\n      \"method\": \"Somatic knockout cell lines, FANCD2 monoubiquitination assay, clonogenic survival assay, cytogenetics\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout with multiple orthogonal phenotypic readouts, independently replicated across labs\",\n      \"pmids\": [\"22396592\", \"22343915\", \"22705371\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FAAP20 preferentially binds the K63-linked ubiquitin product of the RNF8-UBC13 E3/E2 pair, and this ubiquitin-binding activity and RNF8-UBC13 are both required for recruitment of FAAP20 (and the FA core complex) to interstrand crosslink sites; RNF8 and FAAP20 are needed for efficient FANCD2 monoubiquitination.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitin-binding assays, immunofluorescence foci, epistasis analysis with RNF8/RNF168 knockdown\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, epistasis with genetic knockdown, multiple orthogonal methods in single study\",\n      \"pmids\": [\"22705371\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Ubiquitin binding by FAAP20 extends beyond the canonical ββα UBZ module: a disordered C-terminal tail folds into a rigid extended β-loop upon ubiquitin binding, with an invariant C-terminal tryptophan contacting I44 of ubiquitin; substitution of this tryptophan abolishes ubiquitin binding in vitro and causes hypersensitivity to ICL lesions in vivo.\",\n      \"method\": \"NMR/structural analysis, in vitro binding assay, site-directed mutagenesis, cellular ICL sensitivity assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — structural characterization combined with mutagenesis and in vitro binding plus cellular validation in one study\",\n      \"pmids\": [\"25414354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of FAAP20-UBZ in complex with K63-linked diubiquitin at 1.9 Å resolution showed that FAAP20-UBZ contacts only one ubiquitin moiety; surface plasmon resonance demonstrated similar affinities for mono-ubiquitin and M1-, K48-, and K63-linked diubiquitin chains; key interacting residues (Ala168, Trp180, Asp164) were identified and their mutation abolished ubiquitin binding in vitro and FAAP20 accumulation at damage sites in vivo.\",\n      \"method\": \"X-ray crystallography (1.9 Å), surface plasmon resonance, site-directed mutagenesis, live-cell damage-site accumulation assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with SPR and mutagenesis with cellular validation in one study\",\n      \"pmids\": [\"25799058\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FAAP20-UBZ4 domain binds Rev1-BRCT domain through a distinct binding surface from its ubiquitin-binding surface; ubiquitin binding to FAAP20-UBZ4 enhances binding affinity between FAAP20-UBZ4 and Rev1-BRCT, suggesting a mechanism for FA core complex-mediated recruitment of Rev1 to DNA lesions.\",\n      \"method\": \"NMR chemical shift perturbation mapping, biophysical interaction assays\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structure-function, single lab, single study\",\n      \"pmids\": [\"26318859\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Deletion of Faap20 in mice causes a mild FA-like phenotype including defects in hematopoietic stem and progenitor cell reconstitution and susceptibility to MMC-induced pancytopenia; double-knockout with Fanca revealed a dominant effect of FANCA in the FAAP20-FANCA interaction in vivo.\",\n      \"method\": \"Faap20 knockout mouse model, bone marrow transplantation, MMC treatment, flow cytometry, double-knockout epistasis\",\n      \"journal\": \"Stem cells (Dayton, Ohio)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean mouse knockout with multiple hematopoietic phenotypic readouts and epistasis with Fanca KO, single lab\",\n      \"pmids\": [\"25917546\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"FAAP20 is phosphorylated at a degron motif by GSK3β, which enables recognition and polyubiquitination by the SCF-FBW7 E3 ligase, leading to proteasomal degradation of FAAP20; expression of non-phosphorylatable FAAP20 deregulates FANCA turnover at chromatin during ICL repair and compromises the FA pathway.\",\n      \"method\": \"In vitro kinase assay (GSK3β), ubiquitination assay, proteasome inhibitor treatment, phosphomimetic/non-phosphorylatable mutant analysis, chromatin fractionation\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro kinase assay plus mutagenesis plus cellular pathway readout (FANCD2 monoubiquitination, chromatin loading), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"27232758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PIN1 phosphorylation-specific prolyl isomerase catalyzes cis-trans isomerization of the FAAP20 pSer48-Pro49 motif, promoting FAAP20 stability by enhancing its interaction with PP2A phosphatase, thereby counteracting SCF-FBW7-dependent proteolysis at the phosphodegron; PIN1 deficiency impairs FANCD2 activation and ICL repair.\",\n      \"method\": \"Prolyl isomerization assay, co-immunoprecipitation (PIN1-FAAP20, FAAP20-PP2A), phosphomutant analysis, FANCD2 monoubiquitination assay, ICL sensitivity assay\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP of multiple interactions with functional readouts and mechanistic mutants, single lab\",\n      \"pmids\": [\"30789902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAAP20 is acetylated by the acetyltransferase p300/CBP on lysine 152; acetylation of K152 prevents polyubiquitination at this residue, stabilizing FAAP20 against proteasomal degradation; disruption of this acetylation pathway impairs FANCD2 monoubiquitination, revealing a competition between ubiquitination and acetylation at K152 for FAAP20 stability.\",\n      \"method\": \"In vitro acetylation assay, ubiquitination assay, acetylation-mimetic/lysine mutant analysis, proteasome inhibitor treatment, FANCD2 monoubiquitination assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro acetyltransferase assay with mutagenesis and pathway readout, single lab\",\n      \"pmids\": [\"32763975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FAAP20 plays a role in homologous recombination (HR) at DNA double-strand breaks independently of FANCA; FAAP20 also stimulates FANCA's strand annealing biochemical activity in vitro and participates in single-strand annealing (SSA) repair in a FANCA-dependent manner; FAAP20 loss reduces nuclear RAD51 IRIF and sensitizes cells to ionizing radiation and PARP inhibition.\",\n      \"method\": \"HR reporter assay, SSA reporter assay, in vitro biochemical stimulation assay (FANCA strand annealing), RAD51 foci immunofluorescence, clonogenic survival with IR and PARP inhibitor\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple repair pathway reporter assays and in vitro biochemical assay plus cellular readouts, single lab\",\n      \"pmids\": [\"37620397\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FAAP20 is an integral structural and regulatory component of the FA nuclear core complex that binds FANCA (which stabilizes it), uses its UBZ domain and C-terminal tail to recognize ubiquitinated chromatin (particularly K63-Ub generated by RNF8-UBC13) to recruit the FA core complex to interstrand crosslink sites, facilitates FANCD2 monoubiquitination and ICL repair, recruits the translesion polymerase Rev1 via a distinct UBZ surface, and participates in homologous recombination and single-strand annealing at DSBs; its abundance is tightly controlled by GSK3β phosphorylation of a degron followed by SCF-FBW7-mediated polyubiquitination and proteasomal degradation, a process counteracted by PIN1-catalyzed prolyl isomerization (which promotes PP2A-mediated dephosphorylation) and by p300/CBP-mediated acetylation of the same lysine targeted for polyubiquitination.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FAAP20 is an integral subunit of the Fanconi anemia (FA) nuclear core complex that couples ubiquitin signaling at damaged chromatin to FA-pathway activation and DNA interstrand crosslink (ICL) repair [#0, #2]. It binds FANCA through a defined interaction that reciprocally stabilizes FAAP20, and its loss produces hallmark FA defects—crosslinker hypersensitivity, chromosome aberrations, and reduced FANCD2 monoubiquitination [#0, #2]. FAAP20 recognizes ubiquitinated chromatin through a ubiquitin-binding zinc-finger (UBZ) module whose binding surface is extended by a C-terminal tail that folds into a rigid β-loop on ubiquitin engagement, with an invariant C-terminal tryptophan contacting the ubiquitin I44 patch; this activity is dispensable for FANCA binding but required for DNA-damage-induced chromatin loading of FANCA [#1, #4, #5]. FAAP20 preferentially reads the K63-linked ubiquitin product generated by the RNF8–UBC13 pair, and both this E3/E2 activity and FAAP20 ubiquitin binding are required to recruit the FA core complex to ICL sites [#3]. A distinct UBZ surface engages the Rev1 BRCT domain, and ubiquitin binding enhances this interaction, linking FAAP20 to translesion-polymerase recruitment [#6]. Beyond ICL repair, FAAP20 acts in double-strand-break repair: it stimulates FANCA strand-annealing activity in vitro, supports single-strand annealing in a FANCA-dependent manner, and promotes homologous recombination and RAD51 focus formation, with its loss sensitizing cells to ionizing radiation and PARP inhibition [#11]. FAAP20 abundance is tightly regulated by a phosphodegron: GSK3β phosphorylation licenses SCF-FBW7-mediated polyubiquitination and proteasomal turnover [#8], which is opposed by PIN1-catalyzed prolyl isomerization that recruits PP2A to reverse the phosphorylation [#9] and by p300/CBP acetylation of K152 that competes with ubiquitination at the same lysine [#10]. Knockout mice display a mild FA-like phenotype with hematopoietic reconstitution defects and MMC-induced pancytopenia [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing FAAP20 as a bona fide FA core complex subunit answered whether this factor operates within the canonical FA machinery and identified FANCA as its stabilizing anchor.\",\n      \"evidence\": \"Co-IP, FANCA interaction mapping, and protein stability assays in human cells\",\n      \"pmids\": [\"22343915\", \"22396592\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis of the FAAP20-FANCA interface\", \"Mechanism by which FANCA stabilizes FAAP20 not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Discovery of the UBZ domain and its K63-ubiquitin binding showed how FAAP20 reads damaged chromatin and separated its ubiquitin-recognition role from FANCA binding.\",\n      \"evidence\": \"In vitro ubiquitin-binding assay, domain mutagenesis, and chromatin fractionation\",\n      \"pmids\": [\"22343915\", \"22396592\", \"22705371\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the in vivo source of the K63 chains at that point\", \"Atomic-level recognition mode not yet defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Loss-of-function studies established FAAP20 as functionally required for FA core complex ubiquitin ligase output, linking it to FANCD2 monoubiquitination and ICL resistance.\",\n      \"evidence\": \"Somatic knockouts with FANCD2 monoubiquitination, clonogenic survival, and cytogenetics\",\n      \"pmids\": [\"22396592\", \"22343915\", \"22705371\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not distinguish chromatin-recruitment defect from catalytic defect\", \"Non-ICL repair roles unexamined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying RNF8–UBC13 as the upstream K63 source and showing its requirement for FAAP20 recruitment placed FAAP20 in a defined signaling cascade at crosslink sites.\",\n      \"evidence\": \"Co-IP, ubiquitin-binding assays, immunofluorescence foci, and RNF8/RNF168 knockdown epistasis\",\n      \"pmids\": [\"22705371\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish the chromatin substrate ubiquitinated by RNF8 in this context\", \"Quantitative kinetics of recruitment unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Structural studies of the UBZ–ubiquitin interaction defined the molecular recognition mechanism, revealing a C-terminal tail extension and key residues whose mutation abolishes binding and damage-site accumulation.\",\n      \"evidence\": \"NMR and 1.9 Å crystal structure of UBZ with diubiquitin, SPR, mutagenesis, and cellular damage-site assays\",\n      \"pmids\": [\"25414354\", \"25799058\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"SPR showed similar affinity across M1/K48/K63 linkages, leaving in vivo linkage selectivity to be explained by context\", \"Did not capture full-length FAAP20 conformation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapping a distinct UBZ surface for Rev1-BRCT binding extended FAAP20's role beyond core-complex recruitment to coordinating translesion polymerase delivery.\",\n      \"evidence\": \"NMR chemical shift perturbation mapping and biophysical interaction assays\",\n      \"pmids\": [\"26318859\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, single study without in vivo Rev1 recruitment validation\", \"Functional consequence for translesion synthesis not tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"An in vivo mouse knockout established the organismal consequence of FAAP20 loss and the dominance of FANCA within the FAAP20-FANCA axis.\",\n      \"evidence\": \"Faap20 knockout mice with bone marrow transplantation, MMC treatment, and Fanca double-knockout epistasis\",\n      \"pmids\": [\"25917546\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phenotype milder than core FA components, leaving relative pathway weight uncertain\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identifying the GSK3β/SCF-FBW7 phosphodegron explained how FAAP20 levels are downregulated and showed that turnover control is itself required for proper FANCA dynamics during ICL repair.\",\n      \"evidence\": \"In vitro GSK3β kinase assay, ubiquitination assay, proteasome inhibition, and phosphomutant chromatin fractionation\",\n      \"pmids\": [\"27232758\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify upstream signals activating GSK3β toward FAAP20\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"PIN1-catalyzed prolyl isomerization was shown to counteract the phosphodegron by recruiting PP2A, adding a stabilizing arm to FAAP20 abundance control.\",\n      \"evidence\": \"Prolyl isomerization assay, PIN1-FAAP20 and FAAP20-PP2A co-IPs, phosphomutant analysis, and ICL/FANCD2 readouts\",\n      \"pmids\": [\"30789902\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab without independent confirmation\", \"Stoichiometry and dynamics relative to FBW7 not quantified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discovery of p300/CBP acetylation at K152 competing with ubiquitination at the same lysine revealed a second stabilizing mechanism and a direct switch governing FAAP20 fate.\",\n      \"evidence\": \"In vitro acetylation and ubiquitination assays, acetyl-mimetic/lysine mutants, proteasome inhibition, and FANCD2 monoubiquitination assay\",\n      \"pmids\": [\"32763975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Signals controlling the acetylation/ubiquitination balance in vivo unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating FAAP20 roles in HR and SSA, including stimulation of FANCA strand annealing, broadened its function beyond ICL repair to double-strand-break processing and PARP-inhibitor sensitivity.\",\n      \"evidence\": \"HR and SSA reporter assays, in vitro FANCA strand-annealing stimulation, RAD51 foci, and IR/PARP-inhibitor survival\",\n      \"pmids\": [\"37620397\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanism distinguishing FANCA-independent HR role from FANCA-dependent SSA role not fully defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple stability inputs (GSK3β/FBW7, PIN1/PP2A, p300/CBP acetylation) are integrated with upstream DNA-damage signaling to time FAAP20 levels during repair remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking abundance control to repair-pathway choice\", \"Direct disease-causing FAAP20 mutations not established in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [2, 3, 11]}\n    ],\n    \"complexes\": [\"FA nuclear core complex\"],\n    \"partners\": [\"FANCA\", \"RNF8\", \"UBC13\", \"REV1\", \"PIN1\", \"PP2A\", \"FBXW7\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}