{"gene":"FANCI","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2007,"finding":"FANCI is monoubiquitinated (on K523) and forms the FANCI-FANCD2 (ID) complex that localizes to chromatin in response to DNA damage; ubiquitination of each protein is required for maintenance of ubiquitin on the other, indicating a dual ubiquitin-locking mechanism.","method":"Co-immunoprecipitation, western blot, chromatin fractionation, siRNA knockdown, patient cell complementation","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, chromatin fractionation, functional complementation; independently replicated in two simultaneous papers (PMID:17412408, PMID:17460694)","pmids":["17412408","17460694"],"is_preprint":false},{"year":2007,"finding":"FANCI is an ATM/ATR kinase substrate required for resistance to mitomycin C-induced DNA interstrand crosslinks; it is a paralog of FANCD2 likely evolving from a common ancestral gene.","method":"Mass spectrometry phosphoproteomics, siRNA knockdown, MMC sensitivity assay","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — MS-based substrate identification, functional knockdown, replicated across two independent labs","pmids":["17412408"],"is_preprint":false},{"year":2008,"finding":"Multiple phosphorylation of conserved Ser/Thr-Gln (S/TQ) motifs in FANCI acts as a molecular switch to activate the FA pathway: alanine substitutions at six clustered S/TQ sites abrogate monoubiquitination and focus formation of both FANCI and FANCD2, while phosphomimetic mutations constitutively activate monoubiquitination and confer crosslink resistance.","method":"Site-directed mutagenesis (alanine and phosphomimetic substitutions), chicken DT40 cell complementation, MMC sensitivity assay, immunofluorescence","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis with multiple orthogonal functional readouts (ubiquitination, foci, cell survival), conserved mechanism validated in human cells","pmids":["18931676"],"is_preprint":false},{"year":2008,"finding":"FANCI enhances FANCD2 monoubiquitination by Ube2t-FANCL in vitro and restricts ubiquitination to the correct in vivo lysine residue on FANCD2.","method":"In vitro reconstituted ubiquitination assay with purified Ube2t, FANCL, and FANCI proteins","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified components, site-specific ubiquitination confirmed; single lab but rigorous biochemical approach","pmids":["19111657"],"is_preprint":false},{"year":2009,"finding":"FANCI directly binds DNA with a preference for branched structures; the DNA-binding domain spans approximately residues 200–1000; the FANCI-FANCD2 complex shows enhanced and preferential binding to branched DNA substrates compared to either protein alone; FANCI interacts with FANCD2 through its C-terminal region (residues 1001–1328).","method":"Purified recombinant protein DNA-binding assays (EMSA), co-immunoprecipitation with purified proteins, truncation and point mutant analysis, immunofluorescence","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro binding assays with purified proteins plus mutagenesis, confirmed by two independent papers (PMID:19561358, PMID:19589784)","pmids":["19561358","19589784"],"is_preprint":false},{"year":2009,"finding":"FANCI is monoubiquitinated specifically on Lys-523 by the UBE2T-FANCL E2-E3 pair in vitro.","method":"In vitro ubiquitination assay with purified recombinant proteins","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution identifying precise ubiquitin acceptor lysine; consistent with in vivo data from other studies","pmids":["19589784"],"is_preprint":false},{"year":2010,"finding":"The monoubiquitinated FANCI-FANCD2 (ID) complex recruits the downstream nuclease FAN1 to sites of DNA damage to facilitate ICL repair; FAN1 accumulation is strictly dependent on ID complex monoubiquitination.","method":"Co-immunoprecipitation, siRNA knockdown, immunofluorescence foci assay, ICL sensitivity assay","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, epistatic knockdown with defined phenotype, multiple orthogonal methods","pmids":["20671156"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of the ~300 kDa FANCI-FANCD2 (ID) complex at 3.4 Å reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface; electron density maps of FANCI-DNA crystals show binding sites for both single- and double-stranded DNA, suggesting the ID complex recognizes DNA structures formed at replication fork-ICL encounters.","method":"X-ray crystallography (3.4 Å crystal structure of ID complex; 7.8 Å electron density of FANCI-DNA), in vitro DNA binding assays","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation; landmark structural study","pmids":["21764741"],"is_preprint":false},{"year":2012,"finding":"FANCI stimulates FANCD2-mediated nucleosome assembly (histone chaperone activity) in vitro, although FANCI alone lacks nucleosome-assembly activity; this activity is required for DNA crosslink repair.","method":"In vitro nucleosome assembly assay, histone H3 mobility assay in FANCD2-knockdown cells, cisplatin survival assay with assembly-defective FANCD2 mutants","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution plus cell-based functional assay, but FANCI's role is stimulatory rather than direct","pmids":["22828868"],"is_preprint":false},{"year":2012,"finding":"Various forms of DNA (ssDNA, dsDNA, branched DNA) robustly stimulate FANCD2 monoubiquitination in vitro in a manner strictly requiring FANCI; a FANCI mutant defective in DNA binding is also defective in stimulating FANCD2 monoubiquitination.","method":"In vitro reconstituted ubiquitination assay with purified components and defined DNA substrates; FANCI DNA-binding mutants","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified proteins, mutagenesis, multiple DNA substrates tested; consistent with PMID:24623813","pmids":["22287633"],"is_preprint":false},{"year":2012,"finding":"FANCI phosphorylation (at S/TQ sites) is the molecular trigger for FANCD2-FANCI dissociation: phosphodead FANCI fails to dissociate from FANCD2, while phosphomimetic FANCI cannot interact with FANCD2; FANCD2-FANCI complex represents the inactive form and dissociates upon DNA damage-induced FA pathway activation.","method":"Co-immunoprecipitation, phosphomimetic and phosphodead FANCI mutant expression, chromatin fractionation, flow cytometry cell-cycle analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with phosphomutants and chromatin fractionation; single lab","pmids":["22753026"],"is_preprint":false},{"year":2014,"finding":"FANCI DNA-binding activity is required for DNA-stimulated FANCD2 monoubiquitination within the ID2 complex; duplex or branched DNA strongly stimulates FANCD2 monoubiquitination in the ID2 complex via FANCL interaction, but in the absence of FANCD2, DNA stimulates FANCI monoubiquitination in a FANCL-independent manner.","method":"In vitro reconstituted ubiquitination assay with purified human FANCD2, FANCI, UBE2T, FANCL and defined DNA substrates; FANCI DNA-binding mutants","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with multiple DNA substrates and mutagenesis; single lab but rigorous biochemistry","pmids":["24623813"],"is_preprint":false},{"year":2015,"finding":"ATR-mediated phosphorylation of FANCI inhibits dormant origin firing while promoting replication fork restart/DNA repair; FANCI co-localizes with MCM-bound chromatin under replication stress; cells lacking FANCI have reduced origins and increased inter-origin distances.","method":"Super-resolution microscopy (STORM), DNA fiber assay, phosphomimetic/phosphodead FANCI mutants, siRNA knockdown","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (fiber assay, super-resolution imaging, phosphomutants), novel function clearly defined","pmids":["25843623"],"is_preprint":false},{"year":2015,"finding":"FANCI, but not its partner FANCD2, is required for efficient FA core complex recruitment to sites of DNA damage (nuclear foci formation); FANCI deubiquitination by USP1 is required for this function; monoubiquitination and ATR-dependent phosphorylation of FANCI are not required for core complex recruitment.","method":"Immunofluorescence foci assay, ATR inhibition, USP1 depletion, FANCI mutant complementation in isogenic cell lines","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — foci assay with multiple genetic perturbations; single lab but epistatic evidence places FANCI upstream of core complex","pmids":["26430909"],"is_preprint":false},{"year":2016,"finding":"The FANCI-FANCD2 (I-D) complex directly binds RAD51 and stabilizes RAD51-DNA filaments; DNA binding activity of FANCI (but not FANCD2) is required for this stabilization; the stabilized RAD51 filament protects DNA ends from FAN1 nucleolytic degradation.","method":"Pulldown assay with purified proteins, RAD51-DNA filament stabilization assay, nuclease protection assay, FANCI DNA-binding mutants","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro biochemical reconstitution with purified proteins, mutagenesis, and nuclease assay; multiple orthogonal methods","pmids":["27694619"],"is_preprint":false},{"year":2016,"finding":"The FA core complex contains a homo-dimeric catalytic module (FANCB-FANCL-FAAP100 dimer of trimers) with two FANCL molecules positioned to ubiquitinate both FANCI and FANCD2; FANCC-FANCE-FANCF bridges the catalytic module to FANCI-FANCD2 and stabilizes the dimerization interface.","method":"Structural electron microscopy combined with crosslink-coupled mass spectrometry","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structural EM with crosslink-MS; single study, no mutagenesis validation reported in abstract","pmids":["27986592"],"is_preprint":false},{"year":2016,"finding":"FANCI acts as a negative regulator of Akt activation: depletion of FANCI (but not FANCD2 or USP1) results in increased Akt phosphorylation/activation due to reduced PHLPP1-Akt interaction; FANCI forms a complex with Akt, PHLPP1, PHLPP2, FANCD2, USP1, and UAF1.","method":"Co-immunoprecipitation, siRNA knockdown, phospho-Akt western blot, apoptosis assay","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — Co-IP and knockdown with defined signaling readout; single lab, single method type","pmids":["27097374"],"is_preprint":false},{"year":2016,"finding":"Cryo-EM structure of the human FANCD2-FANCI complex reveals an inner cavity large enough to accommodate dsDNA and a protruding Tower domain; the complex is recruited to a stalled replication fork before monoubiquitination, and this recruitment triggers the activating monoubiquitination event; disease-causing mutations in the Tower domain impair this function.","method":"Cryo-EM structure determination, recruitment assay at defined ICL substrates, patient mutation analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with functional epistasis establishing recruitment precedes ubiquitination; multiple orthogonal approaches","pmids":["27405460"],"is_preprint":false},{"year":2017,"finding":"FANCI phosphorylation at S/TQ sites occurs in two temporally distinct phases: serine 556 is phosphorylated upstream of monoubiquitination (ubiquitination-independent), while serines 559 and 565 are phosphorylated downstream (ubiquitination-linked); ubiquitination-linked phosphorylation inhibits FANCD2 deubiquitination by USP1 and is required for effective ICL repair.","method":"Phospho-specific antibodies against S556, S559, S565; USP1 depletion; phosphomimetic/phosphodead mutant complementation; ICL repair assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phospho-specific antibodies with multiple mutants and functional readout; single lab","pmids":["28636932"],"is_preprint":false},{"year":2017,"finding":"FANCI and FANCD2 associate with spliceosomal protein SF3B1 (U2 snRNP); replication stress induces ATR-dependent release of SF3B1 from nuclear speckles requiring FANCI; chromatin-bound FANCI and FANCD2 prevent accumulation of post-catalytic intron lariats and contribute to eviction of splicing factors.","method":"Co-immunoprecipitation, immunofluorescence, chromatin fractionation, proximity ligation assay, siRNA knockdown","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP and multiple localization/functional assays; single lab","pmids":["29030393"],"is_preprint":false},{"year":2019,"finding":"FANCI localizes to the nucleolus and functions in pre-rRNA transcription and large ribosomal subunit pre-rRNA processing independently of FANCD2; in the nucleolus FANCI is predominantly in the deubiquitinated state, requiring both nucleoplasmic deubiquitinase USP1 and nucleolar deubiquitinase USP36.","method":"Immunofluorescence (nucleolar localization), RNA metabolic labeling (pre-rRNA processing), siRNA knockdown, USP1/USP36 inhibition/knockdown","journal":"Proceedings of the National Academy of Sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment tied to functional consequence (rRNA processing), multiple orthogonal methods; single lab","pmids":["30692263"],"is_preprint":false},{"year":2019,"finding":"Purified human FANCI-FANCD2 (ID2) complex binds single-stranded RNA (ssRNA) and R-loop substrates with high affinity, preferring guanine-rich sequences; R-loop binding is via the displaced ssDNA and ssRNA but not the RNA:DNA hybrid; RNA and R-loop substrates strongly stimulate ID2 monoubiquitination in vitro.","method":"Electrophoretic mobility shift assay (EMSA), in vitro ubiquitination assay with purified components, R-loop immunofluorescence (DART assay)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemistry with purified proteins, defined substrates, and functional ubiquitination readout; multiple orthogonal methods","pmids":["30650351"],"is_preprint":false},{"year":2020,"finding":"Cryo-EM structures show that monoubiquitinated FANCD2-FANCI adopts a closed conformation that encircles dsDNA; ubiquitin at the FANCD2-FANCI interface acts as a covalent molecular pin to trap the complex on DNA; unmodified isolated FANCD2 forms a homodimer unable to bind DNA, suggesting an autoinhibitory mechanism.","method":"Cryo-EM structure determination of recombinant chicken FANCD2-FANCI complexes, DNA binding assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structures with biochemical validation; replicated by multiple labs (PMID:32066963, PMID:32167469)","pmids":["32066963"],"is_preprint":false},{"year":2020,"finding":"Monoubiquitination of FANCI:FANCD2 clamps the heterodimer onto dsDNA, forming filament-like arrays on long dsDNA; clamping requires monoubiquitination of only the FANCD2 subunit; monoubiquitination does not promote specific exogenous protein-protein interactions.","method":"In vitro reconstitution of FA pathway with purified components, electron microscopy of FANCI:FANCD2-DNA complexes, EMSA","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with EM visualization, multiple orthogonal methods; replicates and extends PMID:32066963","pmids":["32167469"],"is_preprint":false},{"year":2020,"finding":"Ubiquitination of FANCD2 promotes a large-scale conformational change in the ID2 complex that increases affinity for dsDNA by forming a secondary 'Arm' interface that encircles DNA; ubiquitination of FANCI protects the ubiquitin on FANCD2 from USP1-UAF1 deubiquitination via key hydrophobic residues on FANCI's ubiquitin.","method":"Cryo-EM, biochemical ubiquitination/deubiquitination assays, mutagenesis of ubiquitin hydrophobic surface","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structural evidence plus biochemical reconstitution with mutagenesis; single lab","pmids":["32510829"],"is_preprint":false},{"year":2020,"finding":"ATR directly phosphorylates FANCI on serines 556, 559, and 565 to stabilize its association with DNA and FANCD2; this phosphorylation stimulates ubiquitin conjugation to both FANCI and FANCD2 and inhibits deubiquitination by USP1:UAF1; S559 and S565 are particularly important for protecting the complex from USP1:UAF1.","method":"In vitro reconstitution with recombinant ATR, FANCI phosphomimetic/phosphodead mutants, deubiquitination assay with USP1:UAF1","journal":"Frontiers in cell and developmental biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution with recombinant proteins and site-specific mutants; multiple orthogonal readouts","pmids":["32117957"],"is_preprint":false},{"year":2021,"finding":"FANCI switches between two mutually exclusive binding partners depending on ICL repair status: it binds FANCD2 for repair, or alternatively binds PIDD1 to enable PIDDosome (PIDD1-RAIDD-caspase-2) formation and apoptosis when ICL repair fails; monoubiquitination and deubiquitination at K523 regulate interactor selection.","method":"Co-immunoprecipitation, caspase-2 activation assay, genetic epistasis with endonuclease deletions, ubiquitination-resistant FANCI mutants","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, genetic epistasis, multiple loss-of-function combinations with defined apoptosis readout; single lab","pmids":["34256011"],"is_preprint":false},{"year":2021,"finding":"FANCI is essential for spermatogenesis in mice: FANCI deletion causes massive germ cell apoptosis, loss of undifferentiated spermatogonia, and impairs FANCD2 foci formation; FANCI is required for H3K4 and H3K9 methylation on meiotic sex chromosomes.","method":"Fanci knockout mouse model, immunofluorescence, histone methylation analysis, germ cell apoptosis assay","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO mouse with defined meiotic phenotypes and epigenetic readout; single lab","pmids":["34373449"],"is_preprint":false},{"year":2019,"finding":"FANCI interacts with RAD51 and stimulates D-loop formation (homologous recombination) independently of FANCD2; FANCI co-localizes with RPA along meiotic chromosomes; Fanci knockout mice display severe hypogonadism and meiotic phenotype.","method":"Fanci conditional knockout mouse, D-loop assay with purified proteins, immunofluorescence on meiotic chromosomes, co-immunoprecipitation","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro D-loop assay plus KO mouse phenotype; single lab","pmids":["31219578"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structures of phosphomimetic FANCI-FANCD2 show that phosphorylation destabilizes the open state of the complex and promotes closure around DNA independent of the FA core complex; phosphomimetic mutations do not substantially alter DNA binding affinity but alter conformational dynamics to prime the complex for ubiquitination.","method":"Cryo-EM structure determination of phosphomimetic FANCI-FANCD2, biochemical ubiquitination assays, EMSA","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structures with biochemical reconstitution showing mechanistic basis of phosphorylation activation; single lab","pmids":["36050501"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structure of the FANCI-ubiquitinated/FANCD2-unmodified (IUbD2) complex shows the complex in the closed DNA-clamping conformation; FANCD2 target lysine K561 becomes fully exposed (primed for ubiquitination) in IUbD2-DNA, while FANCI's K523 is primed for ubiquitination in ID2Ub-DNA; FANCI ubiquitination maintains FANCD2 ubiquitination by preventing its deubiquitination and enabling re-ubiquitination.","method":"Cryo-EM structure determination (4.1 Å), in vitro deubiquitination assay with USP1-UAF1, reconstituted ubiquitination assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure plus biochemical reconstitution establishing interdependent ubiquitination mechanism; single lab with multiple orthogonal methods","pmids":["36385258"],"is_preprint":false},{"year":2024,"finding":"FANCD2-FANCI is a sliding clamp that diffuses on dsDNA and stalls at ss-dsDNA junctions (structures formed at stalled replication forks); cryo-EM structures show that stalled D2-I makes specific contacts with the ss-dsDNA junction distinct from those of sliding D2-I, providing a unified mechanism for surveillance and recognition of stalled replication forks.","method":"Single-molecule imaging (total internal reflection fluorescence microscopy), cryo-EM structure determination of D2-I on DNA substrates","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — single-molecule imaging plus cryo-EM structures, two orthogonal structural/biophysical methods revealing dynamic mechanism","pmids":["39085614"],"is_preprint":false},{"year":2024,"finding":"PP2A phosphatase complex dephosphorylates an inhibitory cluster in FANCD2, licensing FANCD2/FANCI complex loading onto chromosomes and enabling monoubiquitination; this was reconstituted in vitro as a coupled dephosphorylation-ubiquitination reaction.","method":"In vitro reconstitution of coupled dephosphorylation-ubiquitination reaction with purified PP2A, super-resolution live-cell single-molecule tracking, genetic epistasis with PP2A depletion","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of coupled reaction plus live-cell single-molecule tracking; multiple orthogonal methods","pmids":["39535917"],"is_preprint":false},{"year":2024,"finding":"SRSF1 physically interacts with FANCD2 and acts together to suppress R-loop formation via mRNA export regulation; SRSF1 stimulates FANCD2 monoubiquitination in an RNA-dependent fashion; FANCD2 monoubiquitination is required for assembly of the SRSF1-NXF1 nuclear export complex and mRNA export.","method":"Co-immunoprecipitation, mRNA export assay, R-loop immunofluorescence, FANCD2 monoubiquitination assay, cancer-associated SRSF1 mutants","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, functional mRNA export assay, R-loop quantification; single lab but multiple orthogonal methods","pmids":["38165804"],"is_preprint":false},{"year":2024,"finding":"The FANCD2-FANCI heterodimer dynamically interacts with open chromatin regions including DSB-induced open chromatin; loaded FANCD2-FANCI stabilizes open chromatin and promotes DNA resection and RPA loading through increased BRCA1 and BLM association; chromatin-loaded FANCD2-FANCI promotes G2 cell cycle arrest via the ATR-CHK1-WEE1 axis.","method":"ATAC-seq, ChIP-seq, immunofluorescence, genetic epistasis with ATM/ATR/FA core complex perturbations, flow cytometry cell cycle assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — chromatin accessibility assays with genetic perturbations and defined phenotypic readouts; single lab","pmids":["41505257"],"is_preprint":false},{"year":2010,"finding":"In C. elegans, FANCI homolog is required for FANCD2 focus formation and ubiquitination after DNA crosslinking; FANCM, FANCI, and checkpoint proteins RPA, ATR, and CHK1 are all required for FANCD2 activation, demonstrating conservation of the FANCD2 activation pathway involving FANCI.","method":"RNAi knockdown, immunofluorescence foci assay, ubiquitination assay in C. elegans","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistatic analysis in C. elegans with defined foci/ubiquitination readouts; single lab, ortholog study","pmids":["20075016"],"is_preprint":false},{"year":2011,"finding":"RAD18 E3 ubiquitin ligase binds FANCD2 and is required for efficient monoubiquitination and chromatin localization of both FANCD2 and FANCI; mutation of the RAD18 RING domain ablates interaction with and chromatin loading of FANCD2; FANCD2 ubiquitination is normal in cells with ubiquitination-resistant PCNA.","method":"Co-immunoprecipitation, RAD18 knockout cells, RING domain mutants, chromatin fractionation, MMC sensitivity assay","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mutants and KO cells; single lab with multiple orthogonal methods","pmids":["21355096"],"is_preprint":false},{"year":2013,"finding":"FANCI is dispensable for FANCD2-dependent BLM complex regulation: FANCD2 (but not FANCI) maintains BLM stability, is required for complete BLMcx assembly, recruits BLMcx to replicating chromatin, and mediates BLMcx phosphorylation in response to DNA damage, demonstrating functional separation of the two ID complex partners.","method":"Co-immunoprecipitation, siRNA knockdown, chromatin fractionation, DNA fiber assay, BLM stability assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus multiple functional assays separating FANCI from FANCD2; single lab","pmids":["23658231"],"is_preprint":false},{"year":2010,"finding":"The C-terminus of FANCI (last 30 residues) contains two separable functional elements: a nuclear localization signal required for nuclear import of FANCI and robust FANCD2 monoubiquitination, and an EDGE motif important for DNA crosslink repair; the patient-derived R1299X mutation deletes both elements causing protein mislocalization.","method":"Patient-derived mutant complementation, nuclear fractionation, monoubiquitination assay, ICL sensitivity assay, site-directed mutagenesis","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutant complementation with defined localization and ubiquitination readouts; single lab","pmids":["20971953"],"is_preprint":false},{"year":2019,"finding":"FANCI directly binds IMPDH2 and prevents its degradation; this interaction activates MEK/ERK/MMP signaling in lung adenocarcinoma cells; FANCI knockdown inhibits proliferation, migration, and invasion which can be reversed by IMPDH2 overexpression.","method":"Co-immunoprecipitation, immunofluorescence co-localization, siRNA knockdown, rescue by IMPDH2 overexpression, xenograft","journal":"OncoTargets and therapy","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and rescue assay, single lab, functional readout is cancer cell behavior without defined molecular mechanism for FANCI's role in the complex","pmids":["32021289"],"is_preprint":false},{"year":2019,"finding":"CTDP1 interacts with FANCI (via CTDP1's BRCT domain) and regulates FANCI chromatin localization, γ-H2AX interaction, and S/TQ motif phosphorylations; CTDP1 expression promotes FANCA and FANCD2 foci formation and enhances homologous recombination repair efficiency.","method":"Co-immunoprecipitation, chromatin fractionation, phospho-FANCI western blot, HR repair assay, siRNA knockdown","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — Co-IP with functional phosphorylation and localization readouts; single lab","pmids":["31240132"],"is_preprint":false},{"year":2018,"finding":"BRMS1 directly interacts with FANCI (via its linker region between two coiled-coil motifs) and is required for efficient monoubiquitination of both FANCI and FANCD2 in response to ICL damage; BRMS1-deficient cells show suppressed FANCD2 foci formation and ICL hypersensitivity.","method":"Co-immunoprecipitation with domain mapping, BRMS1 knockout/knockdown, monoubiquitination assay, FANCD2 foci assay, ICL sensitivity assay","journal":"Oncology reports","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — Co-IP with domain mapping and functional KO/KD readouts; single lab","pmids":["30365131"],"is_preprint":false},{"year":2024,"finding":"FANCI interacts with PARP1 and suppresses its nuclear localization and functionality; FANCI inhibition sensitizes breast cancer cells to PARP inhibitor talazoparib in the absence of BRCA mutations.","method":"Co-immunoprecipitation, immunofluorescence (PARP1 nuclear localization), FANCI siRNA knockdown, PARP inhibitor sensitivity assay","journal":"Cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and localization assay; single lab, limited mechanistic detail in abstract","pmids":["39037758"],"is_preprint":false}],"current_model":"FANCI functions as a central component of the Fanconi anemia DNA interstrand crosslink repair pathway by forming a heterodimeric clamp with FANCD2 that slides on dsDNA, stalls specifically at ss-dsDNA junctions characteristic of stalled replication forks, and becomes locked onto DNA through sequential post-translational modifications: ATR-mediated phosphorylation at multiple S/TQ sites primes the complex by destabilizing its open conformation, PP2A dephosphorylates an inhibitory cluster in FANCD2 to license chromatin loading, and then the FA core complex (UBE2T-FANCL within a dimeric FANCB-FANCL-FAAP100 scaffold) monoubiquitinates FANCD2 (K561) and FANCI (K523)—with FANCI's ubiquitin acting to protect FANCD2's ubiquitin from USP1-UAF1 deubiquitination and enable re-ubiquitination; the resulting di-monoubiquitinated clamp recruits downstream repair nucleases (including FAN1) and stabilizes RAD51 filaments at stalled forks; independently of FANCD2, FANCI also regulates dormant origin firing, functions in ribosome biogenesis in the nucleolus, modulates splicing factor dynamics, can switch from a pro-repair mode (partnering with FANCD2) to a pro-apoptosis mode (partnering with PIDD1 to activate caspase-2) when repair fails, and negatively regulates Akt activation by facilitating PHLPP1-Akt interaction."},"narrative":{"mechanistic_narrative":"FANCI is a central effector of the Fanconi anemia DNA interstrand crosslink (ICL) repair pathway, functioning as the obligate partner of FANCD2 in a heterodimeric (ID2) clamp that recognizes and processes damaged replication forks [PMID:17412408, PMID:17460694]. The complex acts as a sliding clamp that diffuses on dsDNA and stalls specifically at single-strand/double-strand junctions characteristic of stalled forks, then encircles the DNA through a closed conformation [PMID:39085614, PMID:32066963]. Activation proceeds through ordered post-translational regulation: ATR phosphorylates conserved S/TQ motifs (notably S556, S559, S565), priming the complex by destabilizing its open state, stabilizing DNA and FANCD2 association, and protecting the eventual ubiquitin marks from USP1:UAF1 [PMID:18931676, PMID:32117957, PMID:36050501], and PP2A dephosphorylates an inhibitory FANCD2 cluster to license chromatin loading [PMID:39535917]. The UBE2T-FANCL E2-E3 pair then monoubiquitinates FANCD2 (K561) and FANCI (K523), a reaction strongly stimulated by FANCI's DNA binding and required for clamping the heterodimer on dsDNA [PMID:19111657, PMID:19589784, PMID:22287633, PMID:32167469]; FANCI's own ubiquitin reciprocally protects FANCD2's ubiquitin from USP1-UAF1 deubiquitination and enables re-ubiquitination, establishing an interdependent ubiquitin lock [PMID:32510829, PMID:36385258]. The activated clamp recruits the downstream nuclease FAN1 and directly stabilizes RAD51-DNA filaments to protect fork ends [PMID:20671156, PMID:27694619]. Beyond canonical repair, FANCI carries out FANCD2-independent functions: it restrains dormant origin firing under replication stress [PMID:25843623], localizes to the nucleolus to support pre-rRNA transcription and large-subunit processing in its deubiquitinated state [PMID:30692263], stimulates homologous recombination D-loop formation and is essential for meiosis and spermatogenesis [PMID:31219578, PMID:34373449], and can switch from FANCD2 partnering to PIDD1 binding to drive caspase-2/PIDDosome-dependent apoptosis when ICL repair fails [PMID:34256011]. Patient-derived mutations affecting the C-terminal NLS/EDGE region and the Tower domain disrupt these activities, linking FANCI to the Fanconi anemia phenotype [PMID:20971953, PMID:27405460].","teleology":[{"year":2007,"claim":"Establishing that FANCI is a damage-induced, monoubiquitinated partner of FANCD2 defined the ID complex as the activated effector module of the FA pathway.","evidence":"Reciprocal Co-IP, chromatin fractionation, and patient cell complementation, with MS phosphoproteomics identifying FANCI as an ATM/ATR substrate","pmids":["17412408","17460694"],"confidence":"High","gaps":["Mechanism by which the two ubiquitin marks maintain each other was not structurally defined","DNA substrate specificity not yet established"]},{"year":2008,"claim":"Showing that S/TQ phosphorylation acts as a molecular switch and that FANCI directs FANCL-mediated FANCD2 ubiquitination to the correct lysine established the activation logic of the pathway.","evidence":"Alanine/phosphomimetic mutagenesis with DT40 complementation and in vitro reconstituted ubiquitination with purified UBE2T-FANCL-FANCI","pmids":["18931676","19111657"],"confidence":"High","gaps":["Which kinase acts at which site and the temporal order were not resolved","Structural basis of phospho-activation unknown"]},{"year":2009,"claim":"Defining direct, branched-DNA-preferring binding by FANCI and the precise K523 acceptor lysine connected FANCI's DNA recognition to its biochemical activation.","evidence":"EMSA and Co-IP with purified recombinant proteins, truncation/point-mutant mapping, and in vitro ubiquitination identifying K523","pmids":["19561358","19589784"],"confidence":"High","gaps":["How DNA binding feeds into ubiquitination stimulation not yet mechanistically linked","In vivo relevance of branched-DNA preference untested"]},{"year":2010,"claim":"Identifying FAN1 recruitment as strictly dependent on ID complex monoubiquitination connected the activated clamp to a downstream repair nuclease, and ortholog studies confirmed pathway conservation.","evidence":"Co-IP, epistatic knockdown, and foci assays in human cells; RNAi epistasis in C. elegans; C-terminal NLS/EDGE mutant complementation","pmids":["20671156","20075016","20971953"],"confidence":"High","gaps":["How ubiquitin recruits FAN1 mechanistically not defined","Functional separability of NLS versus EDGE elements partially resolved"]},{"year":2011,"claim":"The first crystal structure of the ID complex mapped ubiquitination and phosphorylation sites to the I-D interface and revealed DNA-binding surfaces, providing the structural framework for regulated DNA engagement.","evidence":"X-ray crystallography (3.4 Å ID complex; FANCI-DNA electron density) with in vitro DNA binding; RAD18 Co-IP/KO defining an upstream ligase requirement","pmids":["21764741","21355096"],"confidence":"High","gaps":["Conformational changes upon ubiquitination not captured","Mechanism of RAD18 contribution to ID loading incompletely defined"]},{"year":2012,"claim":"DNA-dependent stimulation of FANCD2 ubiquitination, FANCI's role in nucleosome assembly, and phosphorylation-triggered ID dissociation refined the model of how DNA and modifications gate complex activity.","evidence":"In vitro reconstituted ubiquitination with defined DNA substrates and DNA-binding mutants, nucleosome assembly assays, and Co-IP with phosphomutants","pmids":["22287633","22828868","22753026"],"confidence":"Medium","gaps":["Whether ID dissociation versus clamping is the activating step was unresolved at this stage","Histone chaperone role of FANCI is stimulatory, not direct"]},{"year":2014,"claim":"Demonstrating that FANCI DNA binding is required for DNA-stimulated FANCD2 ubiquitination within ID2, while DNA stimulates FANCI ubiquitination FANCL-independently in FANCD2's absence, dissected the differential roles of the two subunits.","evidence":"In vitro reconstitution with purified human FANCD2/FANCI/UBE2T/FANCL, multiple DNA substrates, and DNA-binding mutants","pmids":["24623813"],"confidence":"High","gaps":["Physiological significance of FANCL-independent FANCI ubiquitination unclear","Single-lab biochemistry"]},{"year":2015,"claim":"Defining FANCD2-independent roles—restraint of dormant origin firing and a requirement for FA core complex recruitment—established FANCI as more than a passive FANCD2 partner.","evidence":"STORM super-resolution imaging, DNA fiber assays, phosphomutants, and foci assays with ATR inhibition and USP1 depletion","pmids":["25843623","26430909"],"confidence":"High","gaps":["Molecular mechanism by which FANCI restrains origin firing not defined","How deubiquitinated FANCI promotes core complex recruitment unknown"]},{"year":2016,"claim":"Cryo-EM of the unmodified complex, demonstration of RAD51 filament stabilization, mapping of the dimeric FANCL catalytic module, and discovery of Akt regulation expanded both the structural and signaling reach of FANCI.","evidence":"Cryo-EM with recruitment assays and patient mutations, purified-protein RAD51/nuclease assays, EM/crosslink-MS of the core complex, and Co-IP/phospho-Akt assays","pmids":["27405460","27694619","27986592","27097374"],"confidence":"High","gaps":["Akt/PHLPP1 regulation rests on single-method Co-IP/knockdown evidence","Core complex catalytic module model lacked mutagenesis validation"]},{"year":2017,"claim":"Resolving two temporally distinct phosphorylation phases (ubiquitination-independent S556 versus ubiquitination-linked S559/S565) and identifying spliceosome (SF3B1) association revealed layered regulation and RNA-related roles.","evidence":"Phospho-specific antibodies, USP1 depletion, phosphomutant complementation, ICL repair assays; Co-IP, PLA, and chromatin fractionation for SF3B1","pmids":["28636932","29030393"],"confidence":"Medium","gaps":["Kinase responsible for each phosphorylation phase not fully assigned","Direct versus indirect role in splicing factor dynamics unclear"]},{"year":2019,"claim":"Defining nucleolar/rRNA functions, ssRNA/R-loop binding, and direct HR D-loop stimulation broadened FANCI's repertoire into RNA metabolism and FANCD2-independent recombination.","evidence":"Nucleolar IF with rRNA labeling and USP1/USP36 perturbation, EMSA/ubiquitination with RNA and R-loop substrates, and D-loop assays with KO mouse phenotypes; plus CTDP1 Co-IP","pmids":["30692263","30650351","31219578","31240132"],"confidence":"Medium","gaps":["Mechanistic role of FANCI in pre-rRNA processing not defined","How RNA/R-loop binding integrates with ICL repair unknown"]},{"year":2020,"claim":"A series of cryo-EM and reconstitution studies established the ubiquitin-clamping mechanism: monoubiquitination converts the open ID complex into a closed clamp encircling dsDNA, with FANCI's ubiquitin protecting FANCD2's mark from USP1-UAF1, and ATR phosphorylation reinforcing this lock.","evidence":"Cryo-EM of modified complexes, in vitro clamping/EMSA and EM filament assays, deubiquitination assays with ubiquitin-surface mutants, and ATR reconstitution","pmids":["32066963","32167469","32510829","32117957"],"confidence":"High","gaps":["How the clamp transitions to recruiting downstream factors not structurally captured","Mechanism converting clamping into productive repair incomplete"]},{"year":2021,"claim":"Discovery of a FANCD2-versus-PIDD1 partner switch and an essential meiotic role established FANCI as a decision point between repair and apoptosis and a germline-critical factor.","evidence":"Reciprocal Co-IP, caspase-2 activation, genetic epistasis with nuclease deletions and ubiquitination-resistant mutants; Fanci KO mouse with meiotic/epigenetic readouts","pmids":["34256011","34373449"],"confidence":"High","gaps":["Signal that triggers the partner switch upon repair failure not defined","Mechanism linking FANCI to meiotic histone methylation unclear"]},{"year":2022,"claim":"Phosphomimetic and IUbD2 cryo-EM structures revealed how phosphorylation primes closure independent of the core complex and how the two subunits' ubiquitinations are mechanistically interdependent.","evidence":"Cryo-EM of phosphomimetic and FANCI-ubiquitinated complexes with reconstituted ubiquitination/deubiquitination assays","pmids":["36050501","36385258"],"confidence":"High","gaps":["Coupling of phospho-priming to the in vivo kinase cascade not addressed","Single-lab structural studies"]},{"year":2024,"claim":"Single-molecule and cryo-EM evidence unified the model as a sliding clamp that stalls at ss-dsDNA junctions, while PP2A licensing, R-loop/SRSF1 functions, open-chromatin engagement, and PARP1 regulation extended FANCI into broader genome maintenance and therapeutic contexts.","evidence":"TIRF single-molecule imaging and cryo-EM of D2-I on DNA; reconstituted PP2A dephosphorylation-ubiquitination; Co-IP/mRNA export/R-loop assays; ATAC/ChIP-seq; PARP1 Co-IP and PARP-inhibitor sensitivity","pmids":["39085614","39535917","38165804","41505257","39037758"],"confidence":"High","gaps":["PARP1 regulation by FANCI rests on limited mechanistic evidence","How fork-junction surveillance integrates with downstream nuclease choice not fully resolved"]},{"year":null,"claim":"How FANCI's diverse FANCD2-independent activities (origin firing, nucleolar rRNA processing, RNA/R-loop metabolism, apoptotic switching) are coordinately regulated and prioritized within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating canonical ICL repair with non-canonical functions","Determinants of partner choice (FANCD2 vs PIDD1 vs others) across stress contexts unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,7,9,11,22,23,31]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[21]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3,9,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[6,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[16,24,30]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,38]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[0,10,34]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[20]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,6,14,31]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[12,34]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,5,24,30]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[26]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[20,21]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[27,28]}],"complexes":["FANCI-FANCD2 (ID2) complex","FA core complex","PIDDosome (PIDD1-RAIDD-caspase-2)"],"partners":["FANCD2","FANCL","UBE2T","FAN1","RAD51","USP1","PIDD1","PHLPP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NVI1","full_name":"Fanconi anemia group I protein","aliases":[],"length_aa":1328,"mass_kda":149.3,"function":"Plays an essential role in the repair of DNA double-strand breaks by homologous recombination and in the repair of interstrand DNA cross-links (ICLs) by promoting FANCD2 monoubiquitination by FANCL and participating in recruitment to DNA repair sites (PubMed:17412408, PubMed:17460694, PubMed:17452773, PubMed:19111657, PubMed:36385258). The FANCI-FANCD2 complex binds and scans double-stranded DNA (dsDNA) for DNA damage; this complex stalls at DNA junctions between double-stranded DNA and single-stranded DNA (PubMed:19589784). Participates in S phase and G2 phase checkpoint activation upon DNA damage (PubMed:25862789)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9NVI1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FANCI","classification":"Not Classified","n_dependent_lines":223,"n_total_lines":1208,"dependency_fraction":0.18460264900662252},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FKBP5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/FANCI","total_profiled":1310},"omim":[{"mim_id":"615514","title":"CYCLIN-DEPENDENT KINASE 12; CDK12","url":"https://www.omim.org/entry/615514"},{"mim_id":"614817","title":"INTERSTITIAL NEPHRITIS, KARYOMEGALIC; KMIN","url":"https://www.omim.org/entry/614817"},{"mim_id":"613984","title":"FANCD2 GENE; FANCD2","url":"https://www.omim.org/entry/613984"},{"mim_id":"613899","title":"FANCC GENE; FANCC","url":"https://www.omim.org/entry/613899"},{"mim_id":"613534","title":"FANCD2/FANCI-ASSOCIATED NUCLEASE 1; FAN1","url":"https://www.omim.org/entry/613534"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":28.0},{"tissue":"lymphoid tissue","ntpm":41.4},{"tissue":"testis","ntpm":29.9}],"url":"https://www.proteinatlas.org/search/FANCI"},"hgnc":{"alias_symbol":["FLJ10719"],"prev_symbol":["KIAA1794"]},"alphafold":{"accession":"Q9NVI1","domains":[{"cath_id":"-","chopping":"806-927","consensus_level":"medium","plddt":90.2904,"start":806,"end":927},{"cath_id":"1.10.357","chopping":"621-683_697-792","consensus_level":"medium","plddt":91.6313,"start":621,"end":792},{"cath_id":"1.20.930","chopping":"950-1041","consensus_level":"medium","plddt":92.9893,"start":950,"end":1041},{"cath_id":"1.20.190","chopping":"1054-1065_1080-1113_1128-1226_1233-1284","consensus_level":"medium","plddt":84.9709,"start":1054,"end":1284}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVI1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVI1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVI1-F1-predicted_aligned_error_v6.png","plddt_mean":83.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FANCI","jax_strain_url":"https://www.jax.org/strain/search?query=FANCI"},"sequence":{"accession":"Q9NVI1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NVI1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NVI1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVI1"}},"corpus_meta":[{"pmid":"17412408","id":"PMC_17412408","title":"Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair.","date":"2007","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/17412408","citation_count":586,"is_preprint":false},{"pmid":"17460694","id":"PMC_17460694","title":"FANCI is a second monoubiquitinated member of the Fanconi anemia pathway.","date":"2007","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17460694","citation_count":233,"is_preprint":false},{"pmid":"20671156","id":"PMC_20671156","title":"FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross-link repair.","date":"2010","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/20671156","citation_count":209,"is_preprint":false},{"pmid":"18931676","id":"PMC_18931676","title":"FANCI phosphorylation functions as a molecular switch to turn on the Fanconi anemia pathway.","date":"2008","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18931676","citation_count":186,"is_preprint":false},{"pmid":"19111657","id":"PMC_19111657","title":"Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI.","date":"2008","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/19111657","citation_count":158,"is_preprint":false},{"pmid":"25843623","id":"PMC_25843623","title":"ATR-mediated phosphorylation of FANCI regulates dormant origin firing in response to replication stress.","date":"2015","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/25843623","citation_count":130,"is_preprint":false},{"pmid":"21764741","id":"PMC_21764741","title":"Structure of the FANCI-FANCD2 complex: insights into the Fanconi anemia DNA repair pathway.","date":"2011","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/21764741","citation_count":125,"is_preprint":false},{"pmid":"26119737","id":"PMC_26119737","title":"Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia.","date":"2015","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/26119737","citation_count":114,"is_preprint":false},{"pmid":"17452773","id":"PMC_17452773","title":"Identification of the Fanconi anemia complementation group I gene, FANCI.","date":"2007","source":"Cellular oncology : the official journal of the International Society for Cellular Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/17452773","citation_count":110,"is_preprint":false},{"pmid":"32066963","id":"PMC_32066963","title":"FANCD2-FANCI is a clamp stabilized on DNA by monoubiquitination of FANCD2 during DNA repair.","date":"2020","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/32066963","citation_count":99,"is_preprint":false},{"pmid":"23658231","id":"PMC_23658231","title":"FANCD2 regulates BLM complex functions independently of FANCI to promote replication fork recovery.","date":"2013","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/23658231","citation_count":90,"is_preprint":false},{"pmid":"19589784","id":"PMC_19589784","title":"FANCI binds branched DNA and is monoubiquitinated by UBE2T-FANCL.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19589784","citation_count":72,"is_preprint":false},{"pmid":"22952632","id":"PMC_22952632","title":"A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22952632","citation_count":72,"is_preprint":false},{"pmid":"30650351","id":"PMC_30650351","title":"Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/30650351","citation_count":71,"is_preprint":false},{"pmid":"21355096","id":"PMC_21355096","title":"The E3 ubiquitin ligase RAD18 regulates ubiquitylation and chromatin loading of FANCD2 and FANCI.","date":"2011","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/21355096","citation_count":70,"is_preprint":false},{"pmid":"22287633","id":"PMC_22287633","title":"DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22287633","citation_count":68,"is_preprint":false},{"pmid":"24623813","id":"PMC_24623813","title":"Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA.","date":"2014","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/24623813","citation_count":66,"is_preprint":false},{"pmid":"32167469","id":"PMC_32167469","title":"Monoubiquitination by the human Fanconi anemia core complex clamps FANCI:FANCD2 on DNA in filamentous arrays.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32167469","citation_count":65,"is_preprint":false},{"pmid":"27405460","id":"PMC_27405460","title":"The FANCD2-FANCI complex is recruited to DNA interstrand crosslinks before monoubiquitination of FANCD2.","date":"2016","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/27405460","citation_count":65,"is_preprint":false},{"pmid":"26430909","id":"PMC_26430909","title":"FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2.","date":"2015","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26430909","citation_count":63,"is_preprint":false},{"pmid":"30692263","id":"PMC_30692263","title":"Fanconi anemia protein FANCI functions in ribosome biogenesis.","date":"2019","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30692263","citation_count":55,"is_preprint":false},{"pmid":"22828868","id":"PMC_22828868","title":"Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair.","date":"2012","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/22828868","citation_count":54,"is_preprint":false},{"pmid":"19561358","id":"PMC_19561358","title":"FANCI protein binds to DNA and interacts with FANCD2 to recognize branched structures.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19561358","citation_count":53,"is_preprint":false},{"pmid":"27986592","id":"PMC_27986592","title":"The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2.","date":"2016","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27986592","citation_count":51,"is_preprint":false},{"pmid":"22753026","id":"PMC_22753026","title":"Fanconi anemia proteins FANCD2 and FANCI exhibit different DNA damage responses during S-phase.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22753026","citation_count":49,"is_preprint":false},{"pmid":"33436409","id":"PMC_33436409","title":"Oncogenic HPV promotes the expression of the long noncoding RNA lnc-FANCI-2 through E7 and YY1.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/33436409","citation_count":48,"is_preprint":false},{"pmid":"27694619","id":"PMC_27694619","title":"FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5'-DNA end.","date":"2016","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/27694619","citation_count":41,"is_preprint":false},{"pmid":"31219578","id":"PMC_31219578","title":"A Fanci knockout mouse model reveals common and distinct functions for FANCI and FANCD2.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31219578","citation_count":38,"is_preprint":false},{"pmid":"32510829","id":"PMC_32510829","title":"Differential functions of FANCI and FANCD2 ubiquitination stabilize ID2 complex on DNA.","date":"2020","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/32510829","citation_count":37,"is_preprint":false},{"pmid":"29059323","id":"PMC_29059323","title":"FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response.","date":"2017","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29059323","citation_count":34,"is_preprint":false},{"pmid":"31167143","id":"PMC_31167143","title":"Phosphorylation of FANCD2 Inhibits the FANCD2/FANCI Complex and Suppresses the Fanconi Anemia Pathway in the Absence of DNA Damage.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31167143","citation_count":31,"is_preprint":false},{"pmid":"32117957","id":"PMC_32117957","title":"ATR-Mediated FANCI Phosphorylation Regulates Both Ubiquitination and Deubiquitination of FANCD2.","date":"2020","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/32117957","citation_count":30,"is_preprint":false},{"pmid":"28636932","id":"PMC_28636932","title":"Ubiquitination-Linked Phosphorylation of the FANCI S/TQ Cluster Contributes to Activation of the Fanconi Anemia I/D2 Complex.","date":"2017","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/28636932","citation_count":30,"is_preprint":false},{"pmid":"38165804","id":"PMC_38165804","title":"The FANCI/FANCD2 complex links DNA damage response to R-loop regulation through SRSF1-mediated mRNA export.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/38165804","citation_count":29,"is_preprint":false},{"pmid":"34137174","id":"PMC_34137174","title":"Mechanism, specificity, and function of FANCD2-FANCI ubiquitination and deubiquitination.","date":"2021","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/34137174","citation_count":29,"is_preprint":false},{"pmid":"19737859","id":"PMC_19737859","title":"Mutational analysis of FANCL, FANCM and the recently identified FANCI suggests that among the 13 known Fanconi Anemia genes, only FANCD1/BRCA2 plays a major role in high-risk breast cancer predisposition.","date":"2009","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/19737859","citation_count":28,"is_preprint":false},{"pmid":"27097374","id":"PMC_27097374","title":"FANCI is a negative regulator of Akt activation.","date":"2016","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/27097374","citation_count":27,"is_preprint":false},{"pmid":"26590883","id":"PMC_26590883","title":"Novel FANCI mutations in Fanconi anemia with VACTERL association.","date":"2015","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/26590883","citation_count":26,"is_preprint":false},{"pmid":"36050501","id":"PMC_36050501","title":"The DNA-damage kinase ATR activates the FANCD2-FANCI clamp by priming it for ubiquitination.","date":"2022","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/36050501","citation_count":25,"is_preprint":false},{"pmid":"27026368","id":"PMC_27026368","title":"A FANCD2/FANCI-Associated Nuclease 1-Knockout Model Develops Karyomegalic Interstitial Nephritis.","date":"2016","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/27026368","citation_count":25,"is_preprint":false},{"pmid":"20075016","id":"PMC_20075016","title":"The involvement of FANCM, FANCI, and checkpoint proteins in the interstrand DNA crosslink repair pathway is conserved in C. elegans.","date":"2010","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/20075016","citation_count":24,"is_preprint":false},{"pmid":"39085614","id":"PMC_39085614","title":"FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.","date":"2024","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/39085614","citation_count":23,"is_preprint":false},{"pmid":"29030393","id":"PMC_29030393","title":"Fanconi anemia FANCD2 and FANCI proteins regulate the nuclear dynamics of splicing factors.","date":"2017","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29030393","citation_count":22,"is_preprint":false},{"pmid":"31240132","id":"PMC_31240132","title":"CTDP1 regulates breast cancer survival and DNA repair through BRCT-specific interactions with FANCI.","date":"2019","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/31240132","citation_count":22,"is_preprint":false},{"pmid":"34373449","id":"PMC_34373449","title":"FANCI plays an essential role in spermatogenesis and regulates meiotic histone methylation.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/34373449","citation_count":21,"is_preprint":false},{"pmid":"32021289","id":"PMC_32021289","title":"FANCI Cooperates with IMPDH2 to Promote Lung Adenocarcinoma Tumor Growth via a MEK/ERK/MMPs Pathway.","date":"2020","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/32021289","citation_count":19,"is_preprint":false},{"pmid":"34256011","id":"PMC_34256011","title":"FANCI functions as a repair/apoptosis switch in response to DNA crosslinks.","date":"2021","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/34256011","citation_count":17,"is_preprint":false},{"pmid":"20971953","id":"PMC_20971953","title":"Patient-derived C-terminal mutation of FANCI causes protein mislocalization and reveals putative EDGE motif function in DNA repair.","date":"2010","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/20971953","citation_count":17,"is_preprint":false},{"pmid":"26336824","id":"PMC_26336824","title":"FANCJ protein is important for the stability of FANCD2/FANCI proteins and protects them from proteasome and caspase-3 dependent degradation.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26336824","citation_count":16,"is_preprint":false},{"pmid":"32725171","id":"PMC_32725171","title":"Structural insight into FANCI-FANCD2 monoubiquitination.","date":"2020","source":"Essays in biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32725171","citation_count":15,"is_preprint":false},{"pmid":"35703356","id":"PMC_35703356","title":"UBE2T regulates FANCI monoubiquitination to promote NSCLC progression by activating EMT.","date":"2022","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/35703356","citation_count":14,"is_preprint":false},{"pmid":"30850063","id":"PMC_30850063","title":"Enzymatic preparation of monoubiquitinated FANCD2 and FANCI proteins.","date":"2019","source":"Methods in enzymology","url":"https://pubmed.ncbi.nlm.nih.gov/30850063","citation_count":14,"is_preprint":false},{"pmid":"34861889","id":"PMC_34861889","title":"A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene.","date":"2021","source":"Genome medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34861889","citation_count":14,"is_preprint":false},{"pmid":"36385258","id":"PMC_36385258","title":"Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination.","date":"2022","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/36385258","citation_count":13,"is_preprint":false},{"pmid":"33051438","id":"PMC_33051438","title":"Inactivation of ribosomal protein S27-like impairs DNA interstrand cross-link repair by destabilization of FANCD2 and FANCI.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/33051438","citation_count":12,"is_preprint":false},{"pmid":"24278431","id":"PMC_24278431","title":"Coordinate nuclear targeting of the FANCD2 and FANCI proteins via a FANCD2 nuclear localization signal.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24278431","citation_count":12,"is_preprint":false},{"pmid":"39037758","id":"PMC_39037758","title":"FANCI Inhibition Induces PARP1 Redistribution to Enhance the Efficacy of PARP Inhibitors in Breast Cancer.","date":"2024","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/39037758","citation_count":10,"is_preprint":false},{"pmid":"35362384","id":"PMC_35362384","title":"Silencing of FANCI Promotes DNA Damage and Sensitizes Ovarian Cancer Cells to Carboplatin.","date":"2022","source":"Current cancer drug targets","url":"https://pubmed.ncbi.nlm.nih.gov/35362384","citation_count":9,"is_preprint":false},{"pmid":"36833203","id":"PMC_36833203","title":"Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/36833203","citation_count":6,"is_preprint":false},{"pmid":"37168687","id":"PMC_37168687","title":"TXNL4B regulates radioresistance by controlling the PRP3-mediated alternative splicing of FANCI.","date":"2023","source":"MedComm","url":"https://pubmed.ncbi.nlm.nih.gov/37168687","citation_count":6,"is_preprint":false},{"pmid":"38483614","id":"PMC_38483614","title":"Novel compound heterozygous variants in FANCI cause premature ovarian insufficiency.","date":"2024","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38483614","citation_count":6,"is_preprint":false},{"pmid":"25489943","id":"PMC_25489943","title":"Defective FANCI binding by a fanconi anemia-related FANCD2 mutant.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25489943","citation_count":6,"is_preprint":false},{"pmid":"38023254","id":"PMC_38023254","title":"Fanconi anemia pathway regulation by FANCI in prostate cancer.","date":"2023","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38023254","citation_count":5,"is_preprint":false},{"pmid":"25168188","id":"PMC_25168188","title":"Expression and purification of human FANCI and FANCD2 using Escherichia coli cells.","date":"2014","source":"Protein expression and purification","url":"https://pubmed.ncbi.nlm.nih.gov/25168188","citation_count":4,"is_preprint":false},{"pmid":"30365131","id":"PMC_30365131","title":"BRMS1 participates in regulating cell sensitivity to DNA interstrand crosslink damage by interacting with FANCI.","date":"2018","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/30365131","citation_count":4,"is_preprint":false},{"pmid":"39535917","id":"PMC_39535917","title":"PP2A licenses the FANCD2/FANCI complex for chromosome loading.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39535917","citation_count":3,"is_preprint":false},{"pmid":"40878909","id":"PMC_40878909","title":"The long noncoding RNA lnc-FANCI-2 intrinsically restricts RAS signaling in human papillomavirus type 16-infected cervical cancer cells.","date":"2025","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/40878909","citation_count":3,"is_preprint":false},{"pmid":"27686023","id":"PMC_27686023","title":"Structural and biophysical properties of h-FANCI ARM repeat protein.","date":"2016","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/27686023","citation_count":3,"is_preprint":false},{"pmid":"32563974","id":"PMC_32563974","title":"Generation of a human induced pluripotent stem cell line (CMCi001-A) from a patient with karyomegalic interstitial nephritis with homozygous frameshift deletion mutation c.1985_1994del10 of the FANCD2/FANCI-Associated Nuclease 1 gene.","date":"2020","source":"Stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/32563974","citation_count":3,"is_preprint":false},{"pmid":"40417238","id":"PMC_40417238","title":"Expression and clinical significance of FANCI gene in pan-cancer: a comprehensive analysis based on multi-omics data.","date":"2025","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40417238","citation_count":2,"is_preprint":false},{"pmid":"39795882","id":"PMC_39795882","title":"Novel FANCI and RAD54B Variants and the Observed Clinical Outcomes in a Hungarian Melanoma Cohort.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39795882","citation_count":1,"is_preprint":false},{"pmid":"41486508","id":"PMC_41486508","title":"Betulinic Acid Suppresses UBE2T Expression via MAPK/ERK Inhibition to Block FANCI and FANCD2 Monoubiquitination in Glioblastoma.","date":"2026","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41486508","citation_count":1,"is_preprint":false},{"pmid":"40040987","id":"PMC_40040987","title":"Knockdown of FANCI suppresses hepatocellular carcinoma development via the PI3K/Akt/GSK-3β pathway.","date":"2025","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/40040987","citation_count":1,"is_preprint":false},{"pmid":"41505257","id":"PMC_41505257","title":"The FANCD2-FANCI heterodimer coordinates chromatin openness and cell cycle progression throughout DNA double-strand break repair.","date":"2026","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/41505257","citation_count":0,"is_preprint":false},{"pmid":"39533770","id":"PMC_39533770","title":"SSX2IP promotes cell proliferation and migration in breast cancer by regulating FANCI.","date":"2024","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/39533770","citation_count":0,"is_preprint":false},{"pmid":"40358883","id":"PMC_40358883","title":"FANCI is involved in the malignant progression of glioma cells by regulating the Akt/Bcl-2 signaling pathway.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40358883","citation_count":0,"is_preprint":false},{"pmid":"41732159","id":"PMC_41732159","title":"Possible link between the apparently pathogenic FANCI variant and beneficial effects in sports performance.","date":"2026","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41732159","citation_count":0,"is_preprint":false},{"pmid":"34310468","id":"PMC_34310468","title":"Genetic Study of Fanconi Anemia in Infancy Revealed FANCI Mutations and Defective ALDH2 Variant: A Case Report.","date":"2022","source":"Journal of pediatric hematology/oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34310468","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.18.683233","title":"Human cytomegalovirus regulates host DNA repair machinery for viral genome integrity","date":"2025-10-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.18.683233","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.11.648246","title":"Genomic comparisons shed light on the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew","date":"2025-04-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.11.648246","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.02.610668","title":"Molecular insights into dynamic protein structures by high-contrast crosslinking mass spectrometry","date":"2024-09-02","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.02.610668","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.14.24311337","title":"Investigating chromosomal radiosensitivity in inborn errors of immunity: insights from DNA repair disorders and beyond","date":"2024-08-20","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.14.24311337","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":37443,"output_tokens":10225,"usd":0.132852,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":20726,"output_tokens":5804,"usd":0.124365,"stage2_stop_reason":"end_turn"},"total_usd":0.257217,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"FANCI is monoubiquitinated (on K523) and forms the FANCI-FANCD2 (ID) complex that localizes to chromatin in response to DNA damage; ubiquitination of each protein is required for maintenance of ubiquitin on the other, indicating a dual ubiquitin-locking mechanism.\",\n      \"method\": \"Co-immunoprecipitation, western blot, chromatin fractionation, siRNA knockdown, patient cell complementation\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, chromatin fractionation, functional complementation; independently replicated in two simultaneous papers (PMID:17412408, PMID:17460694)\",\n      \"pmids\": [\"17412408\", \"17460694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"FANCI is an ATM/ATR kinase substrate required for resistance to mitomycin C-induced DNA interstrand crosslinks; it is a paralog of FANCD2 likely evolving from a common ancestral gene.\",\n      \"method\": \"Mass spectrometry phosphoproteomics, siRNA knockdown, MMC sensitivity assay\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — MS-based substrate identification, functional knockdown, replicated across two independent labs\",\n      \"pmids\": [\"17412408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Multiple phosphorylation of conserved Ser/Thr-Gln (S/TQ) motifs in FANCI acts as a molecular switch to activate the FA pathway: alanine substitutions at six clustered S/TQ sites abrogate monoubiquitination and focus formation of both FANCI and FANCD2, while phosphomimetic mutations constitutively activate monoubiquitination and confer crosslink resistance.\",\n      \"method\": \"Site-directed mutagenesis (alanine and phosphomimetic substitutions), chicken DT40 cell complementation, MMC sensitivity assay, immunofluorescence\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with multiple orthogonal functional readouts (ubiquitination, foci, cell survival), conserved mechanism validated in human cells\",\n      \"pmids\": [\"18931676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"FANCI enhances FANCD2 monoubiquitination by Ube2t-FANCL in vitro and restricts ubiquitination to the correct in vivo lysine residue on FANCD2.\",\n      \"method\": \"In vitro reconstituted ubiquitination assay with purified Ube2t, FANCL, and FANCI proteins\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified components, site-specific ubiquitination confirmed; single lab but rigorous biochemical approach\",\n      \"pmids\": [\"19111657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FANCI directly binds DNA with a preference for branched structures; the DNA-binding domain spans approximately residues 200–1000; the FANCI-FANCD2 complex shows enhanced and preferential binding to branched DNA substrates compared to either protein alone; FANCI interacts with FANCD2 through its C-terminal region (residues 1001–1328).\",\n      \"method\": \"Purified recombinant protein DNA-binding assays (EMSA), co-immunoprecipitation with purified proteins, truncation and point mutant analysis, immunofluorescence\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro binding assays with purified proteins plus mutagenesis, confirmed by two independent papers (PMID:19561358, PMID:19589784)\",\n      \"pmids\": [\"19561358\", \"19589784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FANCI is monoubiquitinated specifically on Lys-523 by the UBE2T-FANCL E2-E3 pair in vitro.\",\n      \"method\": \"In vitro ubiquitination assay with purified recombinant proteins\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution identifying precise ubiquitin acceptor lysine; consistent with in vivo data from other studies\",\n      \"pmids\": [\"19589784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The monoubiquitinated FANCI-FANCD2 (ID) complex recruits the downstream nuclease FAN1 to sites of DNA damage to facilitate ICL repair; FAN1 accumulation is strictly dependent on ID complex monoubiquitination.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, immunofluorescence foci assay, ICL sensitivity assay\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, epistatic knockdown with defined phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"20671156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of the ~300 kDa FANCI-FANCD2 (ID) complex at 3.4 Å reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface; electron density maps of FANCI-DNA crystals show binding sites for both single- and double-stranded DNA, suggesting the ID complex recognizes DNA structures formed at replication fork-ICL encounters.\",\n      \"method\": \"X-ray crystallography (3.4 Å crystal structure of ID complex; 7.8 Å electron density of FANCI-DNA), in vitro DNA binding assays\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation; landmark structural study\",\n      \"pmids\": [\"21764741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FANCI stimulates FANCD2-mediated nucleosome assembly (histone chaperone activity) in vitro, although FANCI alone lacks nucleosome-assembly activity; this activity is required for DNA crosslink repair.\",\n      \"method\": \"In vitro nucleosome assembly assay, histone H3 mobility assay in FANCD2-knockdown cells, cisplatin survival assay with assembly-defective FANCD2 mutants\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution plus cell-based functional assay, but FANCI's role is stimulatory rather than direct\",\n      \"pmids\": [\"22828868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Various forms of DNA (ssDNA, dsDNA, branched DNA) robustly stimulate FANCD2 monoubiquitination in vitro in a manner strictly requiring FANCI; a FANCI mutant defective in DNA binding is also defective in stimulating FANCD2 monoubiquitination.\",\n      \"method\": \"In vitro reconstituted ubiquitination assay with purified components and defined DNA substrates; FANCI DNA-binding mutants\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified proteins, mutagenesis, multiple DNA substrates tested; consistent with PMID:24623813\",\n      \"pmids\": [\"22287633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FANCI phosphorylation (at S/TQ sites) is the molecular trigger for FANCD2-FANCI dissociation: phosphodead FANCI fails to dissociate from FANCD2, while phosphomimetic FANCI cannot interact with FANCD2; FANCD2-FANCI complex represents the inactive form and dissociates upon DNA damage-induced FA pathway activation.\",\n      \"method\": \"Co-immunoprecipitation, phosphomimetic and phosphodead FANCI mutant expression, chromatin fractionation, flow cytometry cell-cycle analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with phosphomutants and chromatin fractionation; single lab\",\n      \"pmids\": [\"22753026\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"FANCI DNA-binding activity is required for DNA-stimulated FANCD2 monoubiquitination within the ID2 complex; duplex or branched DNA strongly stimulates FANCD2 monoubiquitination in the ID2 complex via FANCL interaction, but in the absence of FANCD2, DNA stimulates FANCI monoubiquitination in a FANCL-independent manner.\",\n      \"method\": \"In vitro reconstituted ubiquitination assay with purified human FANCD2, FANCI, UBE2T, FANCL and defined DNA substrates; FANCI DNA-binding mutants\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with multiple DNA substrates and mutagenesis; single lab but rigorous biochemistry\",\n      \"pmids\": [\"24623813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ATR-mediated phosphorylation of FANCI inhibits dormant origin firing while promoting replication fork restart/DNA repair; FANCI co-localizes with MCM-bound chromatin under replication stress; cells lacking FANCI have reduced origins and increased inter-origin distances.\",\n      \"method\": \"Super-resolution microscopy (STORM), DNA fiber assay, phosphomimetic/phosphodead FANCI mutants, siRNA knockdown\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (fiber assay, super-resolution imaging, phosphomutants), novel function clearly defined\",\n      \"pmids\": [\"25843623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FANCI, but not its partner FANCD2, is required for efficient FA core complex recruitment to sites of DNA damage (nuclear foci formation); FANCI deubiquitination by USP1 is required for this function; monoubiquitination and ATR-dependent phosphorylation of FANCI are not required for core complex recruitment.\",\n      \"method\": \"Immunofluorescence foci assay, ATR inhibition, USP1 depletion, FANCI mutant complementation in isogenic cell lines\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — foci assay with multiple genetic perturbations; single lab but epistatic evidence places FANCI upstream of core complex\",\n      \"pmids\": [\"26430909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The FANCI-FANCD2 (I-D) complex directly binds RAD51 and stabilizes RAD51-DNA filaments; DNA binding activity of FANCI (but not FANCD2) is required for this stabilization; the stabilized RAD51 filament protects DNA ends from FAN1 nucleolytic degradation.\",\n      \"method\": \"Pulldown assay with purified proteins, RAD51-DNA filament stabilization assay, nuclease protection assay, FANCI DNA-binding mutants\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro biochemical reconstitution with purified proteins, mutagenesis, and nuclease assay; multiple orthogonal methods\",\n      \"pmids\": [\"27694619\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The FA core complex contains a homo-dimeric catalytic module (FANCB-FANCL-FAAP100 dimer of trimers) with two FANCL molecules positioned to ubiquitinate both FANCI and FANCD2; FANCC-FANCE-FANCF bridges the catalytic module to FANCI-FANCD2 and stabilizes the dimerization interface.\",\n      \"method\": \"Structural electron microscopy combined with crosslink-coupled mass spectrometry\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structural EM with crosslink-MS; single study, no mutagenesis validation reported in abstract\",\n      \"pmids\": [\"27986592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"FANCI acts as a negative regulator of Akt activation: depletion of FANCI (but not FANCD2 or USP1) results in increased Akt phosphorylation/activation due to reduced PHLPP1-Akt interaction; FANCI forms a complex with Akt, PHLPP1, PHLPP2, FANCD2, USP1, and UAF1.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, phospho-Akt western blot, apoptosis assay\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — Co-IP and knockdown with defined signaling readout; single lab, single method type\",\n      \"pmids\": [\"27097374\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Cryo-EM structure of the human FANCD2-FANCI complex reveals an inner cavity large enough to accommodate dsDNA and a protruding Tower domain; the complex is recruited to a stalled replication fork before monoubiquitination, and this recruitment triggers the activating monoubiquitination event; disease-causing mutations in the Tower domain impair this function.\",\n      \"method\": \"Cryo-EM structure determination, recruitment assay at defined ICL substrates, patient mutation analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with functional epistasis establishing recruitment precedes ubiquitination; multiple orthogonal approaches\",\n      \"pmids\": [\"27405460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"FANCI phosphorylation at S/TQ sites occurs in two temporally distinct phases: serine 556 is phosphorylated upstream of monoubiquitination (ubiquitination-independent), while serines 559 and 565 are phosphorylated downstream (ubiquitination-linked); ubiquitination-linked phosphorylation inhibits FANCD2 deubiquitination by USP1 and is required for effective ICL repair.\",\n      \"method\": \"Phospho-specific antibodies against S556, S559, S565; USP1 depletion; phosphomimetic/phosphodead mutant complementation; ICL repair assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phospho-specific antibodies with multiple mutants and functional readout; single lab\",\n      \"pmids\": [\"28636932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"FANCI and FANCD2 associate with spliceosomal protein SF3B1 (U2 snRNP); replication stress induces ATR-dependent release of SF3B1 from nuclear speckles requiring FANCI; chromatin-bound FANCI and FANCD2 prevent accumulation of post-catalytic intron lariats and contribute to eviction of splicing factors.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, chromatin fractionation, proximity ligation assay, siRNA knockdown\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP and multiple localization/functional assays; single lab\",\n      \"pmids\": [\"29030393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FANCI localizes to the nucleolus and functions in pre-rRNA transcription and large ribosomal subunit pre-rRNA processing independently of FANCD2; in the nucleolus FANCI is predominantly in the deubiquitinated state, requiring both nucleoplasmic deubiquitinase USP1 and nucleolar deubiquitinase USP36.\",\n      \"method\": \"Immunofluorescence (nucleolar localization), RNA metabolic labeling (pre-rRNA processing), siRNA knockdown, USP1/USP36 inhibition/knockdown\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment tied to functional consequence (rRNA processing), multiple orthogonal methods; single lab\",\n      \"pmids\": [\"30692263\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Purified human FANCI-FANCD2 (ID2) complex binds single-stranded RNA (ssRNA) and R-loop substrates with high affinity, preferring guanine-rich sequences; R-loop binding is via the displaced ssDNA and ssRNA but not the RNA:DNA hybrid; RNA and R-loop substrates strongly stimulate ID2 monoubiquitination in vitro.\",\n      \"method\": \"Electrophoretic mobility shift assay (EMSA), in vitro ubiquitination assay with purified components, R-loop immunofluorescence (DART assay)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemistry with purified proteins, defined substrates, and functional ubiquitination readout; multiple orthogonal methods\",\n      \"pmids\": [\"30650351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structures show that monoubiquitinated FANCD2-FANCI adopts a closed conformation that encircles dsDNA; ubiquitin at the FANCD2-FANCI interface acts as a covalent molecular pin to trap the complex on DNA; unmodified isolated FANCD2 forms a homodimer unable to bind DNA, suggesting an autoinhibitory mechanism.\",\n      \"method\": \"Cryo-EM structure determination of recombinant chicken FANCD2-FANCI complexes, DNA binding assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structures with biochemical validation; replicated by multiple labs (PMID:32066963, PMID:32167469)\",\n      \"pmids\": [\"32066963\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Monoubiquitination of FANCI:FANCD2 clamps the heterodimer onto dsDNA, forming filament-like arrays on long dsDNA; clamping requires monoubiquitination of only the FANCD2 subunit; monoubiquitination does not promote specific exogenous protein-protein interactions.\",\n      \"method\": \"In vitro reconstitution of FA pathway with purified components, electron microscopy of FANCI:FANCD2-DNA complexes, EMSA\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with EM visualization, multiple orthogonal methods; replicates and extends PMID:32066963\",\n      \"pmids\": [\"32167469\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Ubiquitination of FANCD2 promotes a large-scale conformational change in the ID2 complex that increases affinity for dsDNA by forming a secondary 'Arm' interface that encircles DNA; ubiquitination of FANCI protects the ubiquitin on FANCD2 from USP1-UAF1 deubiquitination via key hydrophobic residues on FANCI's ubiquitin.\",\n      \"method\": \"Cryo-EM, biochemical ubiquitination/deubiquitination assays, mutagenesis of ubiquitin hydrophobic surface\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structural evidence plus biochemical reconstitution with mutagenesis; single lab\",\n      \"pmids\": [\"32510829\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATR directly phosphorylates FANCI on serines 556, 559, and 565 to stabilize its association with DNA and FANCD2; this phosphorylation stimulates ubiquitin conjugation to both FANCI and FANCD2 and inhibits deubiquitination by USP1:UAF1; S559 and S565 are particularly important for protecting the complex from USP1:UAF1.\",\n      \"method\": \"In vitro reconstitution with recombinant ATR, FANCI phosphomimetic/phosphodead mutants, deubiquitination assay with USP1:UAF1\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution with recombinant proteins and site-specific mutants; multiple orthogonal readouts\",\n      \"pmids\": [\"32117957\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FANCI switches between two mutually exclusive binding partners depending on ICL repair status: it binds FANCD2 for repair, or alternatively binds PIDD1 to enable PIDDosome (PIDD1-RAIDD-caspase-2) formation and apoptosis when ICL repair fails; monoubiquitination and deubiquitination at K523 regulate interactor selection.\",\n      \"method\": \"Co-immunoprecipitation, caspase-2 activation assay, genetic epistasis with endonuclease deletions, ubiquitination-resistant FANCI mutants\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, genetic epistasis, multiple loss-of-function combinations with defined apoptosis readout; single lab\",\n      \"pmids\": [\"34256011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FANCI is essential for spermatogenesis in mice: FANCI deletion causes massive germ cell apoptosis, loss of undifferentiated spermatogonia, and impairs FANCD2 foci formation; FANCI is required for H3K4 and H3K9 methylation on meiotic sex chromosomes.\",\n      \"method\": \"Fanci knockout mouse model, immunofluorescence, histone methylation analysis, germ cell apoptosis assay\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO mouse with defined meiotic phenotypes and epigenetic readout; single lab\",\n      \"pmids\": [\"34373449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FANCI interacts with RAD51 and stimulates D-loop formation (homologous recombination) independently of FANCD2; FANCI co-localizes with RPA along meiotic chromosomes; Fanci knockout mice display severe hypogonadism and meiotic phenotype.\",\n      \"method\": \"Fanci conditional knockout mouse, D-loop assay with purified proteins, immunofluorescence on meiotic chromosomes, co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro D-loop assay plus KO mouse phenotype; single lab\",\n      \"pmids\": [\"31219578\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structures of phosphomimetic FANCI-FANCD2 show that phosphorylation destabilizes the open state of the complex and promotes closure around DNA independent of the FA core complex; phosphomimetic mutations do not substantially alter DNA binding affinity but alter conformational dynamics to prime the complex for ubiquitination.\",\n      \"method\": \"Cryo-EM structure determination of phosphomimetic FANCI-FANCD2, biochemical ubiquitination assays, EMSA\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structures with biochemical reconstitution showing mechanistic basis of phosphorylation activation; single lab\",\n      \"pmids\": [\"36050501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structure of the FANCI-ubiquitinated/FANCD2-unmodified (IUbD2) complex shows the complex in the closed DNA-clamping conformation; FANCD2 target lysine K561 becomes fully exposed (primed for ubiquitination) in IUbD2-DNA, while FANCI's K523 is primed for ubiquitination in ID2Ub-DNA; FANCI ubiquitination maintains FANCD2 ubiquitination by preventing its deubiquitination and enabling re-ubiquitination.\",\n      \"method\": \"Cryo-EM structure determination (4.1 Å), in vitro deubiquitination assay with USP1-UAF1, reconstituted ubiquitination assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure plus biochemical reconstitution establishing interdependent ubiquitination mechanism; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"36385258\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FANCD2-FANCI is a sliding clamp that diffuses on dsDNA and stalls at ss-dsDNA junctions (structures formed at stalled replication forks); cryo-EM structures show that stalled D2-I makes specific contacts with the ss-dsDNA junction distinct from those of sliding D2-I, providing a unified mechanism for surveillance and recognition of stalled replication forks.\",\n      \"method\": \"Single-molecule imaging (total internal reflection fluorescence microscopy), cryo-EM structure determination of D2-I on DNA substrates\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — single-molecule imaging plus cryo-EM structures, two orthogonal structural/biophysical methods revealing dynamic mechanism\",\n      \"pmids\": [\"39085614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PP2A phosphatase complex dephosphorylates an inhibitory cluster in FANCD2, licensing FANCD2/FANCI complex loading onto chromosomes and enabling monoubiquitination; this was reconstituted in vitro as a coupled dephosphorylation-ubiquitination reaction.\",\n      \"method\": \"In vitro reconstitution of coupled dephosphorylation-ubiquitination reaction with purified PP2A, super-resolution live-cell single-molecule tracking, genetic epistasis with PP2A depletion\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of coupled reaction plus live-cell single-molecule tracking; multiple orthogonal methods\",\n      \"pmids\": [\"39535917\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SRSF1 physically interacts with FANCD2 and acts together to suppress R-loop formation via mRNA export regulation; SRSF1 stimulates FANCD2 monoubiquitination in an RNA-dependent fashion; FANCD2 monoubiquitination is required for assembly of the SRSF1-NXF1 nuclear export complex and mRNA export.\",\n      \"method\": \"Co-immunoprecipitation, mRNA export assay, R-loop immunofluorescence, FANCD2 monoubiquitination assay, cancer-associated SRSF1 mutants\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, functional mRNA export assay, R-loop quantification; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"38165804\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The FANCD2-FANCI heterodimer dynamically interacts with open chromatin regions including DSB-induced open chromatin; loaded FANCD2-FANCI stabilizes open chromatin and promotes DNA resection and RPA loading through increased BRCA1 and BLM association; chromatin-loaded FANCD2-FANCI promotes G2 cell cycle arrest via the ATR-CHK1-WEE1 axis.\",\n      \"method\": \"ATAC-seq, ChIP-seq, immunofluorescence, genetic epistasis with ATM/ATR/FA core complex perturbations, flow cytometry cell cycle assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — chromatin accessibility assays with genetic perturbations and defined phenotypic readouts; single lab\",\n      \"pmids\": [\"41505257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In C. elegans, FANCI homolog is required for FANCD2 focus formation and ubiquitination after DNA crosslinking; FANCM, FANCI, and checkpoint proteins RPA, ATR, and CHK1 are all required for FANCD2 activation, demonstrating conservation of the FANCD2 activation pathway involving FANCI.\",\n      \"method\": \"RNAi knockdown, immunofluorescence foci assay, ubiquitination assay in C. elegans\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistatic analysis in C. elegans with defined foci/ubiquitination readouts; single lab, ortholog study\",\n      \"pmids\": [\"20075016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RAD18 E3 ubiquitin ligase binds FANCD2 and is required for efficient monoubiquitination and chromatin localization of both FANCD2 and FANCI; mutation of the RAD18 RING domain ablates interaction with and chromatin loading of FANCD2; FANCD2 ubiquitination is normal in cells with ubiquitination-resistant PCNA.\",\n      \"method\": \"Co-immunoprecipitation, RAD18 knockout cells, RING domain mutants, chromatin fractionation, MMC sensitivity assay\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mutants and KO cells; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"21355096\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FANCI is dispensable for FANCD2-dependent BLM complex regulation: FANCD2 (but not FANCI) maintains BLM stability, is required for complete BLMcx assembly, recruits BLMcx to replicating chromatin, and mediates BLMcx phosphorylation in response to DNA damage, demonstrating functional separation of the two ID complex partners.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, chromatin fractionation, DNA fiber assay, BLM stability assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus multiple functional assays separating FANCI from FANCD2; single lab\",\n      \"pmids\": [\"23658231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The C-terminus of FANCI (last 30 residues) contains two separable functional elements: a nuclear localization signal required for nuclear import of FANCI and robust FANCD2 monoubiquitination, and an EDGE motif important for DNA crosslink repair; the patient-derived R1299X mutation deletes both elements causing protein mislocalization.\",\n      \"method\": \"Patient-derived mutant complementation, nuclear fractionation, monoubiquitination assay, ICL sensitivity assay, site-directed mutagenesis\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutant complementation with defined localization and ubiquitination readouts; single lab\",\n      \"pmids\": [\"20971953\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FANCI directly binds IMPDH2 and prevents its degradation; this interaction activates MEK/ERK/MMP signaling in lung adenocarcinoma cells; FANCI knockdown inhibits proliferation, migration, and invasion which can be reversed by IMPDH2 overexpression.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence co-localization, siRNA knockdown, rescue by IMPDH2 overexpression, xenograft\",\n      \"journal\": \"OncoTargets and therapy\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and rescue assay, single lab, functional readout is cancer cell behavior without defined molecular mechanism for FANCI's role in the complex\",\n      \"pmids\": [\"32021289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CTDP1 interacts with FANCI (via CTDP1's BRCT domain) and regulates FANCI chromatin localization, γ-H2AX interaction, and S/TQ motif phosphorylations; CTDP1 expression promotes FANCA and FANCD2 foci formation and enhances homologous recombination repair efficiency.\",\n      \"method\": \"Co-immunoprecipitation, chromatin fractionation, phospho-FANCI western blot, HR repair assay, siRNA knockdown\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — Co-IP with functional phosphorylation and localization readouts; single lab\",\n      \"pmids\": [\"31240132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"BRMS1 directly interacts with FANCI (via its linker region between two coiled-coil motifs) and is required for efficient monoubiquitination of both FANCI and FANCD2 in response to ICL damage; BRMS1-deficient cells show suppressed FANCD2 foci formation and ICL hypersensitivity.\",\n      \"method\": \"Co-immunoprecipitation with domain mapping, BRMS1 knockout/knockdown, monoubiquitination assay, FANCD2 foci assay, ICL sensitivity assay\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — Co-IP with domain mapping and functional KO/KD readouts; single lab\",\n      \"pmids\": [\"30365131\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FANCI interacts with PARP1 and suppresses its nuclear localization and functionality; FANCI inhibition sensitizes breast cancer cells to PARP inhibitor talazoparib in the absence of BRCA mutations.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence (PARP1 nuclear localization), FANCI siRNA knockdown, PARP inhibitor sensitivity assay\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and localization assay; single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"39037758\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FANCI functions as a central component of the Fanconi anemia DNA interstrand crosslink repair pathway by forming a heterodimeric clamp with FANCD2 that slides on dsDNA, stalls specifically at ss-dsDNA junctions characteristic of stalled replication forks, and becomes locked onto DNA through sequential post-translational modifications: ATR-mediated phosphorylation at multiple S/TQ sites primes the complex by destabilizing its open conformation, PP2A dephosphorylates an inhibitory cluster in FANCD2 to license chromatin loading, and then the FA core complex (UBE2T-FANCL within a dimeric FANCB-FANCL-FAAP100 scaffold) monoubiquitinates FANCD2 (K561) and FANCI (K523)—with FANCI's ubiquitin acting to protect FANCD2's ubiquitin from USP1-UAF1 deubiquitination and enable re-ubiquitination; the resulting di-monoubiquitinated clamp recruits downstream repair nucleases (including FAN1) and stabilizes RAD51 filaments at stalled forks; independently of FANCD2, FANCI also regulates dormant origin firing, functions in ribosome biogenesis in the nucleolus, modulates splicing factor dynamics, can switch from a pro-repair mode (partnering with FANCD2) to a pro-apoptosis mode (partnering with PIDD1 to activate caspase-2) when repair fails, and negatively regulates Akt activation by facilitating PHLPP1-Akt interaction.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FANCI is a central effector of the Fanconi anemia DNA interstrand crosslink (ICL) repair pathway, functioning as the obligate partner of FANCD2 in a heterodimeric (ID2) clamp that recognizes and processes damaged replication forks [#0, #1]. The complex acts as a sliding clamp that diffuses on dsDNA and stalls specifically at single-strand/double-strand junctions characteristic of stalled forks, then encircles the DNA through a closed conformation [#31, #22]. Activation proceeds through ordered post-translational regulation: ATR phosphorylates conserved S/TQ motifs (notably S556, S559, S565), priming the complex by destabilizing its open state, stabilizing DNA and FANCD2 association, and protecting the eventual ubiquitin marks from USP1:UAF1 [#2, #25, #29], and PP2A dephosphorylates an inhibitory FANCD2 cluster to license chromatin loading [#32]. The UBE2T-FANCL E2-E3 pair then monoubiquitinates FANCD2 (K561) and FANCI (K523), a reaction strongly stimulated by FANCI's DNA binding and required for clamping the heterodimer on dsDNA [#3, #5, #9, #23]; FANCI's own ubiquitin reciprocally protects FANCD2's ubiquitin from USP1-UAF1 deubiquitination and enables re-ubiquitination, establishing an interdependent ubiquitin lock [#24, #30]. The activated clamp recruits the downstream nuclease FAN1 and directly stabilizes RAD51-DNA filaments to protect fork ends [#6, #14]. Beyond canonical repair, FANCI carries out FANCD2-independent functions: it restrains dormant origin firing under replication stress [#12], localizes to the nucleolus to support pre-rRNA transcription and large-subunit processing in its deubiquitinated state [#20], stimulates homologous recombination D-loop formation and is essential for meiosis and spermatogenesis [#28, #27], and can switch from FANCD2 partnering to PIDD1 binding to drive caspase-2/PIDDosome-dependent apoptosis when ICL repair fails [#26]. Patient-derived mutations affecting the C-terminal NLS/EDGE region and the Tower domain disrupt these activities, linking FANCI to the Fanconi anemia phenotype [#38, #17].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing that FANCI is a damage-induced, monoubiquitinated partner of FANCD2 defined the ID complex as the activated effector module of the FA pathway.\",\n      \"evidence\": \"Reciprocal Co-IP, chromatin fractionation, and patient cell complementation, with MS phosphoproteomics identifying FANCI as an ATM/ATR substrate\",\n      \"pmids\": [\"17412408\", \"17460694\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which the two ubiquitin marks maintain each other was not structurally defined\", \"DNA substrate specificity not yet established\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showing that S/TQ phosphorylation acts as a molecular switch and that FANCI directs FANCL-mediated FANCD2 ubiquitination to the correct lysine established the activation logic of the pathway.\",\n      \"evidence\": \"Alanine/phosphomimetic mutagenesis with DT40 complementation and in vitro reconstituted ubiquitination with purified UBE2T-FANCL-FANCI\",\n      \"pmids\": [\"18931676\", \"19111657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which kinase acts at which site and the temporal order were not resolved\", \"Structural basis of phospho-activation unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defining direct, branched-DNA-preferring binding by FANCI and the precise K523 acceptor lysine connected FANCI's DNA recognition to its biochemical activation.\",\n      \"evidence\": \"EMSA and Co-IP with purified recombinant proteins, truncation/point-mutant mapping, and in vitro ubiquitination identifying K523\",\n      \"pmids\": [\"19561358\", \"19589784\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DNA binding feeds into ubiquitination stimulation not yet mechanistically linked\", \"In vivo relevance of branched-DNA preference untested\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identifying FAN1 recruitment as strictly dependent on ID complex monoubiquitination connected the activated clamp to a downstream repair nuclease, and ortholog studies confirmed pathway conservation.\",\n      \"evidence\": \"Co-IP, epistatic knockdown, and foci assays in human cells; RNAi epistasis in C. elegans; C-terminal NLS/EDGE mutant complementation\",\n      \"pmids\": [\"20671156\", \"20075016\", \"20971953\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How ubiquitin recruits FAN1 mechanistically not defined\", \"Functional separability of NLS versus EDGE elements partially resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The first crystal structure of the ID complex mapped ubiquitination and phosphorylation sites to the I-D interface and revealed DNA-binding surfaces, providing the structural framework for regulated DNA engagement.\",\n      \"evidence\": \"X-ray crystallography (3.4 Å ID complex; FANCI-DNA electron density) with in vitro DNA binding; RAD18 Co-IP/KO defining an upstream ligase requirement\",\n      \"pmids\": [\"21764741\", \"21355096\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational changes upon ubiquitination not captured\", \"Mechanism of RAD18 contribution to ID loading incompletely defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"DNA-dependent stimulation of FANCD2 ubiquitination, FANCI's role in nucleosome assembly, and phosphorylation-triggered ID dissociation refined the model of how DNA and modifications gate complex activity.\",\n      \"evidence\": \"In vitro reconstituted ubiquitination with defined DNA substrates and DNA-binding mutants, nucleosome assembly assays, and Co-IP with phosphomutants\",\n      \"pmids\": [\"22287633\", \"22828868\", \"22753026\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ID dissociation versus clamping is the activating step was unresolved at this stage\", \"Histone chaperone role of FANCI is stimulatory, not direct\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrating that FANCI DNA binding is required for DNA-stimulated FANCD2 ubiquitination within ID2, while DNA stimulates FANCI ubiquitination FANCL-independently in FANCD2's absence, dissected the differential roles of the two subunits.\",\n      \"evidence\": \"In vitro reconstitution with purified human FANCD2/FANCI/UBE2T/FANCL, multiple DNA substrates, and DNA-binding mutants\",\n      \"pmids\": [\"24623813\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological significance of FANCL-independent FANCI ubiquitination unclear\", \"Single-lab biochemistry\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defining FANCD2-independent roles—restraint of dormant origin firing and a requirement for FA core complex recruitment—established FANCI as more than a passive FANCD2 partner.\",\n      \"evidence\": \"STORM super-resolution imaging, DNA fiber assays, phosphomutants, and foci assays with ATR inhibition and USP1 depletion\",\n      \"pmids\": [\"25843623\", \"26430909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which FANCI restrains origin firing not defined\", \"How deubiquitinated FANCI promotes core complex recruitment unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Cryo-EM of the unmodified complex, demonstration of RAD51 filament stabilization, mapping of the dimeric FANCL catalytic module, and discovery of Akt regulation expanded both the structural and signaling reach of FANCI.\",\n      \"evidence\": \"Cryo-EM with recruitment assays and patient mutations, purified-protein RAD51/nuclease assays, EM/crosslink-MS of the core complex, and Co-IP/phospho-Akt assays\",\n      \"pmids\": [\"27405460\", \"27694619\", \"27986592\", \"27097374\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Akt/PHLPP1 regulation rests on single-method Co-IP/knockdown evidence\", \"Core complex catalytic module model lacked mutagenesis validation\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolving two temporally distinct phosphorylation phases (ubiquitination-independent S556 versus ubiquitination-linked S559/S565) and identifying spliceosome (SF3B1) association revealed layered regulation and RNA-related roles.\",\n      \"evidence\": \"Phospho-specific antibodies, USP1 depletion, phosphomutant complementation, ICL repair assays; Co-IP, PLA, and chromatin fractionation for SF3B1\",\n      \"pmids\": [\"28636932\", \"29030393\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase responsible for each phosphorylation phase not fully assigned\", \"Direct versus indirect role in splicing factor dynamics unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defining nucleolar/rRNA functions, ssRNA/R-loop binding, and direct HR D-loop stimulation broadened FANCI's repertoire into RNA metabolism and FANCD2-independent recombination.\",\n      \"evidence\": \"Nucleolar IF with rRNA labeling and USP1/USP36 perturbation, EMSA/ubiquitination with RNA and R-loop substrates, and D-loop assays with KO mouse phenotypes; plus CTDP1 Co-IP\",\n      \"pmids\": [\"30692263\", \"30650351\", \"31219578\", \"31240132\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic role of FANCI in pre-rRNA processing not defined\", \"How RNA/R-loop binding integrates with ICL repair unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A series of cryo-EM and reconstitution studies established the ubiquitin-clamping mechanism: monoubiquitination converts the open ID complex into a closed clamp encircling dsDNA, with FANCI's ubiquitin protecting FANCD2's mark from USP1-UAF1, and ATR phosphorylation reinforcing this lock.\",\n      \"evidence\": \"Cryo-EM of modified complexes, in vitro clamping/EMSA and EM filament assays, deubiquitination assays with ubiquitin-surface mutants, and ATR reconstitution\",\n      \"pmids\": [\"32066963\", \"32167469\", \"32510829\", \"32117957\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the clamp transitions to recruiting downstream factors not structurally captured\", \"Mechanism converting clamping into productive repair incomplete\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Discovery of a FANCD2-versus-PIDD1 partner switch and an essential meiotic role established FANCI as a decision point between repair and apoptosis and a germline-critical factor.\",\n      \"evidence\": \"Reciprocal Co-IP, caspase-2 activation, genetic epistasis with nuclease deletions and ubiquitination-resistant mutants; Fanci KO mouse with meiotic/epigenetic readouts\",\n      \"pmids\": [\"34256011\", \"34373449\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal that triggers the partner switch upon repair failure not defined\", \"Mechanism linking FANCI to meiotic histone methylation unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Phosphomimetic and IUbD2 cryo-EM structures revealed how phosphorylation primes closure independent of the core complex and how the two subunits' ubiquitinations are mechanistically interdependent.\",\n      \"evidence\": \"Cryo-EM of phosphomimetic and FANCI-ubiquitinated complexes with reconstituted ubiquitination/deubiquitination assays\",\n      \"pmids\": [\"36050501\", \"36385258\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Coupling of phospho-priming to the in vivo kinase cascade not addressed\", \"Single-lab structural studies\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Single-molecule and cryo-EM evidence unified the model as a sliding clamp that stalls at ss-dsDNA junctions, while PP2A licensing, R-loop/SRSF1 functions, open-chromatin engagement, and PARP1 regulation extended FANCI into broader genome maintenance and therapeutic contexts.\",\n      \"evidence\": \"TIRF single-molecule imaging and cryo-EM of D2-I on DNA; reconstituted PP2A dephosphorylation-ubiquitination; Co-IP/mRNA export/R-loop assays; ATAC/ChIP-seq; PARP1 Co-IP and PARP-inhibitor sensitivity\",\n      \"pmids\": [\"39085614\", \"39535917\", \"38165804\", \"41505257\", \"39037758\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"PARP1 regulation by FANCI rests on limited mechanistic evidence\", \"How fork-junction surveillance integrates with downstream nuclease choice not fully resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FANCI's diverse FANCD2-independent activities (origin firing, nucleolar rRNA processing, RNA/R-loop metabolism, apoptotic switching) are coordinately regulated and prioritized within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating canonical ICL repair with non-canonical functions\", \"Determinants of partner choice (FANCD2 vs PIDD1 vs others) across stress contexts unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 7, 9, 11, 22, 23, 31]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [21]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3, 9, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [6, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [16, 24, 30]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 38]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [0, 10, 34]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [20]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 6, 14, 31]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [12, 34]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 5, 24, 30]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [26]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [20, 21]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [27, 28]}\n    ],\n    \"complexes\": [\n      \"FANCI-FANCD2 (ID2) complex\",\n      \"FA core complex\",\n      \"PIDDosome (PIDD1-RAIDD-caspase-2)\"\n    ],\n    \"partners\": [\n      \"FANCD2\",\n      \"FANCL\",\n      \"UBE2T\",\n      \"FAN1\",\n      \"RAD51\",\n      \"USP1\",\n      \"PIDD1\",\n      \"PHLPP1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}