FAN1 is a nuclear structure-selective DNA nuclease that contributes to interstrand-crosslink repair, replication-stress control and maintenance of trinucleotide repeats. It recognizes branched DNA and catalyzes both 5β²-to-3β² exonucleolytic processing and internal incision of flaps or extrahelical DNA extrusions. Recruitment through ubiquitinated FANCD2 supports nuclease-dependent restraint of stressed replication forks, but this recruitment can be dispensable for crosslink resistance. DNA-loaded PCNA stimulates strand-directed cleavage near CAG or CTG extrusions, enabling a short-patch removal pathway that can compete with MutSΞ²-dependent mismatch repair. FAN1 deficiency causes karyomegalic interstitial nephritis, and human variation in FAN1 modifies Huntington disease onset. The 1017-residue protein and natural 533-residue product differ in their C-terminal sequences; the shorter product lacks the nuclease region, and its biological activity and localization remain unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | TAS PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | KEEP AS NON CORE | Summary: Metal binding supports nuclease chemistry but is not the defining molecular function. Reason: The cited Kratz paper is accessible here only as a verified PubMed abstract; its individual metal assay has not been inspected. Independent human FAN1 experiments in PMID:20603073 use MgCl2 in the cleavage assay, and PMID:20671156 Figure 3 explicitly reports Mg2+-dependent assay conditions. Retain the curated cofactor annotation as non-core, with catalytic endonuclease/exonuclease activity carrying the functional summary. Do not infer metal transport or metal homeostasis, and do not confuse the MnCl2 conditions in PMID:20603015 with direct measurement of Mg2+ binding. |
| GO:0000724 double-strand break repair via homologous recombination | IMP PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | KEEP AS NON CORE | Summary: FAN1 depletion reduces a human homologous-recombination reporter, without establishing a specific recombination reaction. Reason: PMID:20603015 Results and Figure 7A show reduced I-SceI-induced GFP recombination after two FAN1 siRNAs in U2OS cells. RPA recruitment and initial RAD51 loading remain intact; subsequent RAD51-foci resolution is delayed. Preserve this experimentally supported repair phenotype as non-core to the defining structure-selective nuclease activity. The proposed late HR or synthesis-dependent strand-annealing role is a model, not a demonstrated FAN1-catalyzed resection, strand-invasion or Holliday-junction-resolution step. Supporting Evidence: |
| GO:0000724 double-strand break repair via homologous recombination | IMP PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | UNDECIDED | Summary: The reference-specific homologous-recombination claim requires the unavailable full paper. Reason: The verified PMID:20603016 abstract describes ICL sensitivity, nuclease activity and FANCD2-dependent recruitment, but mentions HR as pathway context rather than presenting the annotated FAN1 HR experiment. Publisher access failed and the authentic ZORA original is access restricted. PMID:20603015 provides a separate positive HR reporter result; it cannot establish what the Kratz experiment measured. Preserve the original IMP assertion and defer judgment without alleging a curation error. |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: Refine the broad nucleic-acid-binding prediction to experimentally established flap-structured DNA binding. Reason: IPR011856 is the tRNA-endonuclease-like superfamily and currently maps to the broad binding term; its name does not establish human FAN1 RNA binding or Holliday-junction specificity. PMID:25430771 directly measures human FAN1 binding to defined phosphorylated short-flap DNA, with quantitative affinities and a DNA-bound structure of residues 364β1017. This supplies the target-specific basis for GO:0070336, a current descendant of nucleic acid binding. The engineered nuclease construct is not the natural 533-residue product, and the family mapping is retained as the original source rather than relabeled as an experimental assay. Proposed replacements: flap-structured DNA binding |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: Replace general DNA binding with the supported flap-structured DNA recognition activity. Reason: The literal mapping is IPR006642, the Rad18-type UBZ4 domain, not the SAP DNA-binding region. In PMID:20603015, UBZ mutations disrupt FANCD2/FANCI association and damage-site recruitment; this does not itself demonstrate that the UBZ domain binds DNA. Independent human FAN1 DNA-binding measurements and the 364β1017 DNA-bound structure in PMID:25430771 establish flap-structured DNA recognition by a construct lacking that N-terminal UBZ domain. Refine the whole-product annotation to GO:0070336 on this independent evidence, preserving the original InterPro assertion and avoiding a mistaken assignment of DNA-binding chemistry to UBZ. Proposed replacements: flap-structured DNA binding |
| GO:0004518 nuclease activity | IEA GO_REF:0000002 | MODIFY | Summary: Represent the family-level nuclease prediction with the two measured FAN1 nuclease activities. Reason: IPR033315 identifies the FAN1-like family and maps to nuclease activity. Purified human FAN1 and catalytic-site controls in PMID:20603015 establish 5β²-flap incision and 5β²-to-3β² exonucleolytic shortening; PMID:24981866 independently assays human and mouse FAN1 on asymmetric DNA substrates. GO:0017108 and GO:0008409 specify these distinct, non-ancestral catalytic activities. The DNA-specific exonuclease child GO:0035312 is inappropriate because its definition requires sequential mononucleotide release, whereas PMID:25430771 resolves predominantly three-nucleotide cleavage products. The flap activity does not establish physiological Okazaki-fragment processing or confer every substrate specificity found in the larger nuclease superfamily. Proposed replacements: 5'-3' exonuclease activity 5'-flap endonuclease activity |
| GO:0004528 phosphodiesterase I activity | EXP PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | MODIFY | Summary: Replace a directionally mismatched phosphodiesterase term with the demonstrated 5-prime exonuclease activity. Reason: PMID:20603015 Figures 2 and 3 compare purified human wild-type FAN1 with the Asp981Ala/Arg982Ala mutant on DNA substrates labeled at either end. The Results explicitly establish progressive cleavage from the 5-prime end. Current GO:0004528 instead defines removal from a 3-prime-hydroxy terminus. GO:0008409 captures the observed direction. Do not select GO:0035312 solely for its DNA-specific name: its current definition requires mononucleotide release, whereas PMID:25430771 demonstrates predominantly three-nucleotide excision. This is an activity-mapping correction, not removal of the positive experimental evidence. Proposed replacements: 5'-3' exonuclease activity |
| GO:0004528 phosphodiesterase I activity | EXP PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | MODIFY | Summary: The source reports 5-prime-to-3-prime exonuclease activity, rather than the reverse-polarity phosphodiesterase-I definition. Reason: The verified PMID:20603016 abstract explicitly identifies FAN1 as a 5-prime-to-3-prime exonuclease. Its full experimental text was not accessible, so no unseen assay or figure is described. That stated direction, independently demonstrated with purified human FAN1 in PMID:20603015, differs from current GO:0004528, which removes nucleotides from a 3-prime-hydroxy terminus. Replace the mapping with GO:0008409; retain the original reference and evidence code. Proposed replacements: 5'-3' exonuclease activity |
| GO:0004528 phosphodiesterase I activity | IEA GO_REF:0000120 | MODIFY | Summary: Correct the terminus-specific phosphodiesterase-I label to the measured 5β²-to-3β² exonuclease activity. Reason: Current GO:0004528 and EC:3.1.4.1 specify release of 5β²-nucleotides from a 3β²-hydroxy terminus. The controlled human FAN1 assays in PMID:20603015 instead establish cleavage proceeding from the 5β² end; PMID:25430771 resolves successive, distributive three-nucleotide products. GO:0008409 captures that direction without a mononucleotide restriction. The current ARBA00088592 condition set does not match the current human FunFam assignments, so a historical rule match is not claimed. That provenance limit is separate from the positive target chemistry and the definition mismatch. Preserve the imported ARBA and EC identifiers; do not equate a shared alternative enzyme name with the reaction actually defined. Proposed replacements: 5'-3' exonuclease activity |
| GO:0005515 protein binding | IPI PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | KEEP AS NON CORE | Summary: Retain the positive FAN1βFANCD2 association without treating generic binding as a core function. Reason: PMID:20603015 Figure 4 and the associated Results identify FANCD2 in tagged and endogenous human FAN1 immunoprecipitates. Recovery required the reversible protein crosslinker DSP, and the authors tested nuclease/ethidium-bromide conditions against DNA-mediated co-recovery. Figure 5 links the association to an intact UBZ domain. This supports cellular co-association, not purified binary affinity, obligatory complex stoichiometry, or an independently demonstrated adaptor mechanism. The supported-binding campaign exception retains the literal IPI row as non-core. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | KEEP AS NON CORE | Summary: Retain the positive FAN1βFANCI association without treating generic binding as a core function. Reason: PMID:20603015 Figure 4 and the associated Results identify FANCI in tagged and endogenous human FAN1 immunoprecipitates. Recovery required the reversible protein crosslinker DSP, and the authors tested nuclease/ethidium-bromide conditions against DNA-mediated co-recovery. Figure 5 links the association to an intact UBZ domain. This supports cellular co-association, not purified binary affinity, obligatory complex stoichiometry, or an independently demonstrated adaptor mechanism. The supported-binding campaign exception retains the literal IPI row as non-core. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | KEEP AS NON CORE | Summary: Retain the reported FANCD2 association as non-core. Reason: The verified PMID:20603016 abstract explicitly reports recruitment through interaction of the FAN1 UBZ domain with monoubiquitinated FANCD2. Full methods and figures remain inaccessible; no particular pull-down construct or control is attributed to this paper. Independent human co-immunoprecipitation evidence in PMID:20603015 supports the association. Retain the curated positive IPI context under the supported-binding exception, without inferring a purified binary interaction or stable complex. |
| GO:0005515 protein binding | IPI PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | KEEP AS NON CORE | Summary: Human FAN1 co-associates with MLH1; this does not itself establish mismatch-repair activity. Reason: PMID:20603073 Figure 3 and its Results identify MLH1 in HA-FAN1 complexes and targeted immunoprecipitation experiments. The paper separately validates endogenous FAN1βMLH1 association. These are cellular complex-association assays; they do not establish direct binary binding for every pair. FAN1 depletion still sensitizes MLH1-defective HCT116 cells to crosslinking agents, and the authors report no demonstrated mismatch-repair defect in FAN1-depleted extracts. Retain this supported generic-binding IPI row as non-core without transferring the partnerβs mismatch-repair mechanism to FAN1. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | KEEP AS NON CORE | Summary: Human FAN1 co-associates with PMS2; this does not itself establish mismatch-repair activity. Reason: PMID:20603073 Figure 3 and its Results identify PMS2 in HA-FAN1 complexes and targeted immunoprecipitation experiments. The paper separately validates endogenous FAN1βMLH1 association. These are cellular complex-association assays; they do not establish direct binary binding for every pair. FAN1 depletion still sensitizes MLH1-defective HCT116 cells to crosslinking agents, and the authors report no demonstrated mismatch-repair defect in FAN1-depleted extracts. Retain this supported generic-binding IPI row as non-core without transferring the partnerβs mismatch-repair mechanism to FAN1. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | KEEP AS NON CORE | Summary: Retain FANCD2 co-association as a non-core interaction. Reason: PMID:20603073 Figure 6D and the Results describe GFP-FAN1 co-immunoprecipitation with FANCD2 in human cells. FANCD2/FANCI depletion and the FANCD2 K561R mutant also impair FAN1 damage-focus recruitment. The original Figure 6 caption and Results were read; its pixels were not separately inspected. These data support association and recruitment, not an established native stoichiometric complex or a third-protein bridging mechanism. Retain the literal IPI context under the supported-binding exception. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | KEEP AS NON CORE | Summary: Human FAN1 co-associates with MLH3; this does not itself establish mismatch-repair activity. Reason: PMID:20603073 Figure 3 and its Results identify MLH3 in HA-FAN1 complexes and targeted immunoprecipitation experiments. The paper separately validates endogenous FAN1βMLH1 association. These are cellular complex-association assays; they do not establish direct binary binding for every pair. FAN1 depletion still sensitizes MLH1-defective HCT116 cells to crosslinking agents, and the authors report no demonstrated mismatch-repair defect in FAN1-depleted extracts. Retain this supported generic-binding IPI row as non-core without transferring the partnerβs mismatch-repair mechanism to FAN1. Supporting Evidence: |
| GO:0005634 nucleus | EXP PMID:20671156 FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross... | ACCEPT | Summary: Retain the experimentally supported nuclear localization, including damage-associated chromatin. Reason: PMID:20671156 reports FAN1 nuclear damage foci and chromatin recruitment in MMC-treated human HeLa cells, dependent on FANCD2/FANCI (Figure 1D/E). Nucleus correctly preserves this nuclear compartment. A replacement with site of DNA damage alone would lose the nuclear qualification because that term is not a typed descendant of nucleus; nucleoplasm alone would exclude the chromosomal pool. This does not imply constitutive occupancy or localization of the natural short product. Supporting Evidence: |
| GO:0005634 nucleus | EXP PMID:20935496 Human KIAA1018/FAN1 localizes to stalled replication forks v... | ACCEPT | Summary: Retain the nuclear compartment explicitly reported in the primary abstract. Reason: The PMID:20935496 abstract identifies FAN1 as a nuclear protein with damage-induced foci, RPA colocalization and UBZ-dependent recruitment. This supports nucleus without requiring an unseen microscopy panel or a claim of constitutive replisome membership. Full publisher text remains inaccessible. The separately supported nucleoplasmic and chromosomal damage-associated pools are not interchangeable, so retaining the encompassing nuclear compartment preserves the warranted breadth. Supporting Evidence: |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Retain the valid inherited nuclear compartment across distinct nuclear pools. Reason: The saved PANTHER v19 tree places the exact human target below PTN000405526, whose matching IBD asserts nucleus; the target self-source and other experimental descendants are valid support. Independent human imaging establishes nuclear damage-associated chromatin, while HPA detects a broader nucleoplasmic pool. Nucleus encompasses these distinct locations. Nucleoplasm explicitly excludes chromosomes, and site of DNA damage is not a typed nucleus descendant, so either alone would discard part of the supported compartment claim. Retaining nucleus preserves the sound ancestral assertion without inventing a more specific IBD or extending the tested localization to the natural short product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000405526 SUPPORTS TRANSFER The saved PANTHER v19 tree places the exact 1017-residue human target PTN002496574 below PTN000405526; the matching experimental-descendant IBD and absence of a relevant target-path NOT were checked. Human FAN1 among the descendant sources is valid experimental grounding. The original nucleus assertion is retained. Independent target imaging resolves nuclear pools but does not alter the ancestral term. |
| GO:0005634 nucleus | IDA PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | ACCEPT | Summary: Retain nuclear localization across the damage-responsive FAN1 pool. Reason: PMID:20603015 Figure 5B/F and the corresponding Results demonstrate GFP-FAN1 nuclear foci colocalizing with FANCD2 after MMC; UBZ mutations and FANCD2 K561R impair recruitment. Nucleus remains a correct functional compartment. The independent damage-site location describes where FAN1 accumulates on chromosomes, but does not by itself entail nuclear location in the current ontology. Restricting this assertion to nucleoplasm would instead exclude chromosomes. Supporting Evidence: |
| GO:0005634 nucleus | IDA PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | ACCEPT | Summary: Retain the curated nuclear localization with the original source-access limit explicit. Reason: The accessible PMID:20603016 abstract reports recruitment to DNA damage through monoubiquitinated FANCD2. Its full Methods and imaging remain unavailable, so this assessment does not independently verify that paper's nuclear images. The experimental nuclear assertion is consistent with independent human imaging in PMID:20603015 and PMID:20603073 and is retained on that combined evidence. Nucleus encompasses the supported nucleoplasmic and chromosomal pools; replacing it with either nucleoplasm alone or a damage-site term lacking nuclear ancestry would discard part of the localization claim. |
| GO:0005634 nucleus | IDA PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | ACCEPT | Summary: Retain the nuclear location established by damage-track and focus imaging. Reason: PMID:20603073 Figure 4C/D and the corresponding Results place GFP-FAN1 on gamma-H2AX-marked microirradiation tracks and MMC-induced nuclear foci colocalizing with FANCD2 in human U2OS cells. These observations support the encompassing nuclear compartment as well as the independent damage-site location. Nucleoplasm excludes chromosomes, while site of DNA damage lacks typed nucleus ancestry, so neither alone replaces the full nuclear assertion. No constitutive replisome residence or exclusive localization is inferred. Supporting Evidence: |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the correctly mapped nucleus term as the encompassing compartment. Reason: The SL-0191 mapping correctly denotes nucleus, consistent with independently observed human FAN1 nuclear localization. HPA supports a nucleoplasmic pool and the human damage-recruitment studies support chromosome-associated foci or microirradiated tracks. Nucleoplasm excludes chromosomes, whereas site of DNA damage does not entail nuclear location in the current typed ontology. Nucleus therefore retains warranted breadth across these pools; it is not an erroneous or merely underspecified location. Damage-site localization remains an independently supported core context, without an exclusive-location or natural-short-product claim. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: Retain the directly imaged nucleoplasmic pool with antibody and product scope explicit. Reason: Current Human Protein Atlas immunofluorescence using HPA048198 reports nucleoplasm in A-431 and HeLa cells, with additional HeLa cytosolic and cytokinetic-bridge annotations. The two selected multichannel images were inspected and show green signal within the blue nuclear interior, with additional cytoplasmic signal in HeLa. The assay is marked supported and the overall gene localization approved. Its 90-residue antigen maps to residues 921β1010 of the 1017-residue protein and is absent from the natural 533-residue product. These observations support nucleoplasm at the assay resolution; they neither identify DNA-damage foci nor establish localization of the short product. Supporting Evidence: GO_REF:0000052 |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6785732 | ACCEPT | Summary: Retain the explicit nucleoplasmic location of FAN1 in the modeled nuclease-recruitment event. Reason: R-HSA-6785732 explicitly includes human FAN1 entity R-HSA-6785736, Q9Y2M0 residues 1β1017, as an input and as part of the output nuclease-loaded ID2 complex. The target entity itself has nucleoplasm as its compartment; this is not inferred solely from the reaction title or another participant. The source models FAN1 through a dimer entity within the assembly. The location is consistent with independently observed human nuclear recruitment, but neither a universal oligomeric state nor activity of the 533-residue natural product follows from this graph. Preserve this source-specific nucleoplasmic assertion alongside the more spatially resolved damage-site recommendations. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6785986 | ACCEPT | Summary: Retain nucleoplasmic FAN1 in the modeled interstrand-crosslink unhooking reaction. Reason: The exact target route is R-HSA-6785986 to catalyst activity 6785992, its physical entity R-HSA-6785734, the FAN1 subcomplex R-HSA-6785733 and human FAN1 R-HSA-6785736. The latter is Q9Y2M0 residues 1β1017 and explicitly carries the nucleoplasm compartment; FAN1 is also released among the outputs. Its role is a recruited nuclease component, not the damaged DNA substrate. PMID:25430771 independently demonstrates human FAN1 incision past a synthetic crosslink. Retain the modeled compartment without treating the entire multi-nuclease sequence or stoichiometry as directly reconstituted by that experiment, and without extending the model to the short natural product. |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | MODIFY | Summary: Refine broad DNA repair to the supported interstrand-crosslink repair role. Reason: The source is the IPR006642 UBZ4-domain mapping, whose generic DNA-repair association is broader than the established FAN1 role. Actual human FAN1 depletion, damage recruitment and catalytic assays in PMID:20603015 and PMID:20603073 support interstrand-crosslink repair. PMID:25430771 additionally shows that a human FAN1 nuclease construct directly processes a synthetic crosslinked DNA substrate, establishing performed cleavage rather than necessity alone. GO:0036297 is a current descendant of DNA repair. This target-level refinement does not assert that the UBZ domain itself cuts DNA, that every FAN1 repair role has been exhausted, or that the unrelated nucleotide-excision-repair process is synonymous with crosslink repair. Proposed replacements: interstrand cross-link repair |
| GO:0006281 DNA repair | IMP PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | MODIFY | Summary: Narrow DNA repair to the interstrand-crosslink repair function supported by the source. Reason: PMID:20603073 combines human-cell sensitivity to multiple crosslinking agents, damage-site recruitment and intrinsic FAN1 nuclease assays with catalytic mutants. The human experiments are distinguished from the C. elegans mutant analysis. This supports GO:0036297, with direct biochemical ICL unhooking independently demonstrated in PMID:25430771. Do not infer mismatch repair merely from MutL associations or assign all steps of the Fanconi pathway to FAN1. Proposed replacements: interstrand cross-link repair |
| GO:0006289 nucleotide-excision repair | IDA PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | MODIFY | Summary: Use interstrand-crosslink repair for the source-specific repair evidence. Reason: PMID:20603015 documents ICL-agent hypersensitivity, persistent damage markers, chromosome instability and nuclease activity; its Discussion treats several possible ICL-processing steps as models. It also reports no UV hypersensitivity in its tested FAN1-depletion experiment. Current GO:0006289 describes nucleotide-excision repair of a damaged strand, whereas the demonstrated FAN1 context is ICL repair. Refine to GO:0036297 rather than treating all nucleolytic lesion removal as canonical NER. This does not claim that FAN1 can never contribute to NER in another setting. Proposed replacements: interstrand cross-link repair Supporting Evidence: |
| GO:0006289 nucleotide-excision repair | IDA PMID:25430771 DNA repair. Mechanism of DNA interstrand cross-link processi... | MODIFY | Summary: The directly demonstrated reaction is ICL unhooking and supports interstrand-crosslink repair. Reason: PMID:25430771 Figure 4 and Results show purified human FAN1 incising on both sides of a defined synthetic triazole ICL, with product identity checked by LC-MS. This is direct enzymatic participation in ICL processing. Replace GO:0006289 with GO:0036297; the experiment does not reconstruct a canonical nucleotide-excision-repair pathway or show repair of every chemical ICL. The tested human 364β1017 construct is engineered, not the natural 533-residue product. Proposed replacements: interstrand cross-link repair Supporting Evidence: |
| GO:0006289 nucleotide-excision repair | IMP PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | UNDECIDED | Summary: The reference-specific nucleotide-excision-repair assignment cannot be resolved from the available abstract. Reason: PMID:20603016 is verified, but its full experimental text remained inaccessible. The abstract discusses excision repair within ICL repair and clearly reports ICL sensitivity, without distinguishing a FAN1 NER experiment. Other human FAN1 studies support ICL processing, but they do not exclude an additional experiment in this paper. Preserve the original IMP row as undecided rather than infer absence from the abstract or manufacture a specific UV-repair result. Supporting Evidence: |
| GO:0008409 5'-3' exonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Retain the inherited 5β²-to-3β² exonuclease activity at the correct product-size breadth. Reason: The PTN000405526 exonuclease IBD exactly matches the source human and mouse descendant identifiers, and the human target lies on the verified inheriting path. PMID:24981866 directly compares purified human and mouse FAN1 5β² exonucleolytic shortening of asymmetric DNA substrates; the mouse donor is not supported only by a phenotype or homology label. Human assays in PMID:20603015 and PMID:25430771 independently establish the same direction. GO:0008409 allows nucleotide-residue removal, whereas GO:0035312 requires mononucleotides and would misdescribe the predominantly three-nucleotide products resolved in the later assay. Retain the broader, chemically accurate inherited term. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000405526 SUPPORTS TRANSFER The saved PANTHER v19 tree places the exact 1017-residue human target PTN002496574 below PTN000405526; the matching experimental-descendant IBD and absence of a target-path NOT were checked. Human FAN1 among the descendant sources is valid experimental grounding. The actual mouse and human exonuclease assays independently support the inherited activity; no propagation failure is identified. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | ACCEPT | Summary: Retain the demonstrated 5-prime-to-3-prime exonuclease activity. Reason: PMID:20603015 Figure 3 uses purified human FAN1, opposite-end DNA labels, a catalytic DR mutant and time courses to establish 5-prime-to-3-prime processing. Current GO:0008409 allows removal of nucleotide residues from the 5-prime end and fits these data. The apparently narrower DNA-specific GO:0035312 currently requires sequential mononucleotide release; substituting it would overstate the product chemistry demonstrated in PMID:25430771. No RNA substrate activity or processive degradation is inferred. This explicit definition mismatch justifies retaining the broader term. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | ACCEPT | Summary: Retain the demonstrated 5-prime-to-3-prime exonuclease activity. Reason: The verified PMID:20603016 abstract directly reports 5-prime-to-3-prime exonuclease activity. Its full assays remain inaccessible; acceptance also relies on the independent purified-human experiments in PMID:20603015, without attributing their details to Kratz. Current GO:0008409 allows removal of nucleotide residues from the 5-prime end and fits these data. The apparently narrower DNA-specific GO:0035312 currently requires sequential mononucleotide release; substituting it would overstate the product chemistry demonstrated in PMID:25430771. No RNA substrate activity or processive degradation is inferred. This explicit definition mismatch justifies retaining the broader term. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | ACCEPT | Summary: Retain the demonstrated 5-prime-to-3-prime exonuclease activity. Reason: PMID:20603073 Figure 7 compares mammalian FAN1 complexes and bacterially expressed human 373β1017 FAN1 with catalytic mutants, using opposite-end-labeled DNA to establish the direction. The reported contaminating 3-prime activity in a bacterial preparation is explicitly distinguished from intrinsic FAN1 activity. Current GO:0008409 allows removal of nucleotide residues from the 5-prime end and fits these data. The apparently narrower DNA-specific GO:0035312 currently requires sequential mononucleotide release; substituting it would overstate the product chemistry demonstrated in PMID:25430771. No RNA substrate activity or processive degradation is inferred. This explicit definition mismatch justifies retaining the broader term. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:24981866 FAN1 activity on asymmetric repair intermediates is mediated... | ACCEPT | Summary: Retain the demonstrated 5-prime-to-3-prime exonuclease activity. Reason: PMID:24981866 Figure 1B/C includes a distinct human full-length FAN1 lane and shows 5-prime-to-3-prime processing after the initial flap cut. Pseudomonas-specific branch-processing kinetics and mouse-only AUC are not transferred to human FAN1. Current GO:0008409 allows removal of nucleotide residues from the 5-prime end and fits these data. The apparently narrower DNA-specific GO:0035312 currently requires sequential mononucleotide release; substituting it would overstate the product chemistry demonstrated in PMID:25430771. No RNA substrate activity or processive degradation is inferred. This explicit definition mismatch justifies retaining the broader term. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:25430771 DNA repair. Mechanism of DNA interstrand cross-link processi... | ACCEPT | Summary: Retain the demonstrated 5-prime-to-3-prime exonuclease activity. Reason: PMID:25430771 Figure 3 resolves successive major n+3 incisions and demonstrates a distributive mechanism on the tested phosphorylated nick/flap substrates. Minor n+2/n+4 products and salt/substrate dependence remain explicit. Current GO:0008409 allows removal of nucleotide residues from the 5-prime end and fits these data. The apparently narrower DNA-specific GO:0035312 currently requires sequential mononucleotide release; substituting it would overstate the product chemistry demonstrated in PMID:25430771. No RNA substrate activity or processive degradation is inferred. This explicit definition mismatch justifies retaining the broader term. Supporting Evidence: |
| GO:0008409 5'-3' exonuclease activity | IEA GO_REF:0000120 | ACCEPT | Summary: Retain the combined electronic exonuclease assertion with its current rule and mouse-donor trace. Reason: Current ARBA00028773 condition set 11 (zero-based index 10) matches the human FunFam 3.40.1350.10:FF:000004 and vertebrate lineage. The literal mouse donor Q69ZT1 is Fan1; its current UniProt Ensembl link is ENSMUSP00000130012.2, corresponding to the imported unversioned protein identifier. The mouse experimental GOA trace leads to PMID:24981866, which actually assays purified mouse and human FAN1 on defined DNA substrates. This corroborates the human 5β²-to-3β² exonuclease activity without treating multiple electronic paths as independent experiments. The trimer-product evidence in PMID:25430771 favors retaining GO:0008409 over the mononucleotide-specific DNA exonuclease child. |
| GO:0016788 hydrolase activity, acting on ester bonds | IEA GO_REF:0000002 | MODIFY | Summary: Replace generic ester hydrolysis with the two experimentally resolved FAN1 nuclease activities. Reason: IPR014883 is the virus-type replication-repair nuclease domain and maps broadly to ester-bond hydrolysis. Human FAN1 hydrolyzes DNA phosphodiester bonds: purified-enzyme and catalytic-mutant experiments in PMID:20603015 distinguish 5β²-flap incision from 5β²-to-3β² exonucleolytic shortening. The human and mouse comparison in PMID:24981866 supports the asymmetric-substrate specificity and does not transfer bacterial Holliday-junction cleavage to human FAN1. GO:0017108 and GO:0008409 are non-ancestral descendants of the broad hydrolase term. Retain both measured facets without assigning a myotubularin phosphatase function from the historical MTMR15 name or a mononucleotide-only exonuclease mechanism. Proposed replacements: 5'-3' exonuclease activity 5'-flap endonuclease activity |
| GO:0017108 5'-flap endonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Retain the inherited and directly measured 5β²-flap endonuclease activity. Reason: The actual flap-endonuclease IBD at PTN000405526 cites experimental human FAN1, and the sequence-matched human target inherits that node without a relevant NOT. PMID:20603015 demonstrates preferential incision of a 5β²-flap substrate, with the catalytic DR mutant strongly impaired; PMID:24981866 confirms corresponding human and mouse activity on asymmetric repair intermediates. This supports GO:0017108 as one activity of the multifunctional nuclease. It does not imply that FAN1 lacks its separately demonstrated exonuclease activity, nor does the term definition establish an untested physiological role in Okazaki-fragment processing. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000405526 SUPPORTS TRANSFER The saved PANTHER v19 tree places the exact 1017-residue human target PTN002496574 below PTN000405526; the matching experimental-descendant IBD and absence of a target-path NOT were checked. Human FAN1 among the descendant sources is valid experimental grounding. Target biochemical evidence supports transfer of the flap-endonuclease activity; no donor-count or self-source objection applies. |
| GO:0017108 5'-flap endonuclease activity | IDA PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | ACCEPT | Summary: Retain the directly supported 5-prime flap endonuclease activity. Reason: PMID:20603015 Figure 2 demonstrates preferential 5-prime flap incision by purified human FAN1, strongly reduced by Asp981Ala/Arg982Ala substitution. This annotation names the measured flap-cleavage activity; it does not assert that FAN1 has no other nuclease activities or that it performs Okazaki-fragment maturation. The current term definitionβs restrictive substrate/Okazaki wording merits clarification, but does not justify rejecting a directly demonstrated, curator-assigned activity. No Holliday-junction resolvase activity is inferred. Supporting Evidence: |
| GO:0017108 5'-flap endonuclease activity | IDA PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | ACCEPT | Summary: Retain the directly supported 5-prime flap endonuclease activity. Reason: The verified PMID:20603016 abstract directly identifies a structure-specific endonuclease that preferentially incises 5-prime flaps. Full original assays remain unavailable; independent human experiments in PMID:20603015 corroborate the activity. This annotation names the measured flap-cleavage activity; it does not assert that FAN1 has no other nuclease activities or that it performs Okazaki-fragment maturation. The current term definitionβs restrictive substrate/Okazaki wording merits clarification, but does not justify rejecting a directly demonstrated, curator-assigned activity. No Holliday-junction resolvase activity is inferred. |
| GO:0017108 5'-flap endonuclease activity | IDA PMID:20603073 A genetic screen identifies FAN1, a Fanconi anemia-associate... | ACCEPT | Summary: Retain the directly supported 5-prime flap endonuclease activity. Reason: PMID:20603073 Figure 7 demonstrates 5-prime flap incision using both human-cell complexes and purified engineered human 373β1017 FAN1, with multiple catalytic-mutant controls. This annotation names the measured flap-cleavage activity; it does not assert that FAN1 has no other nuclease activities or that it performs Okazaki-fragment maturation. The current term definitionβs restrictive substrate/Okazaki wording merits clarification, but does not justify rejecting a directly demonstrated, curator-assigned activity. No Holliday-junction resolvase activity is inferred. Supporting Evidence: |
| GO:0017108 5'-flap endonuclease activity | IDA PMID:24981866 FAN1 activity on asymmetric repair intermediates is mediated... | ACCEPT | Summary: Retain the directly supported 5-prime flap endonuclease activity. Reason: PMID:24981866 Figure 1B/C directly includes human FAN1 and resolves branch-associated flap incision; bacterial homologs and their separate Holliday-junction activities are not used as human evidence. This annotation names the measured flap-cleavage activity; it does not assert that FAN1 has no other nuclease activities or that it performs Okazaki-fragment maturation. The current term definitionβs restrictive substrate/Okazaki wording merits clarification, but does not justify rejecting a directly demonstrated, curator-assigned activity. No Holliday-junction resolvase activity is inferred. Supporting Evidence: |
| GO:0036297 interstrand cross-link repair | IBA GO_REF:0000033 | ACCEPT | Summary: Retain the conserved interstrand-crosslink repair role supported by target chemistry and cellular repair. Reason: The saved IBD at PTN000405526 contains the literal Arabidopsis, fission-yeast and human descendant sources, and the exact human target path is verified. This is a curator-placed ancestral assertion, not a pairwise transfer from a donor count. Independently read human experiments in PMID:20603015 and PMID:20603073 establish crosslink sensitivity and recruitment after FAN1 depletion or recruitment-defective mutation. PMID:25430771 demonstrates direct cleavage past a synthetic crosslink by a human FAN1 nuclease construct, identifying the work FAN1 performs. These data support the inherited process without requiring this lane to reinterpret the uninspected plant or yeast primary assays, or to infer full catalytic function for the 533-residue product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000405526 SUPPORTS TRANSFER The saved PANTHER v19 tree places the exact 1017-residue human target PTN002496574 below PTN000405526; the matching experimental-descendant IBD and absence of a target-path NOT were checked. Human FAN1 among the descendant sources is valid experimental grounding. The human cellular and direct crosslink-processing experiments corroborate the inherited process; other descendant primary assays were not independently reread here. |
| GO:0036297 interstrand cross-link repair | IDA PMID:25430771 DNA repair. Mechanism of DNA interstrand cross-link processi... | ACCEPT | Summary: FAN1 directly contributes nuclease chemistry to interstrand-crosslink processing. Reason: PMID:25430771 Figure 4 shows purified engineered human FAN1 unhooking synthetic triazole ICLs through flanking incisions, with LC-MS confirmation. The enzyme performs the cleavage step itself, so this is participation evidence, not merely a requirement inferred from loss of function. The evidence supports GO:0036297 while leaving the exact division of labor among nucleases and the range of physiological crosslinks open. Supporting Evidence: |
| GO:0036297 interstrand cross-link repair | IEA GO_REF:0000002 | ACCEPT | Summary: Retain the FAN1-family prediction of interstrand-crosslink repair. Reason: IPR033315 currently maps the FAN1-like family to GO:0036297 and spans the human protein containing the nuclease region. The assignment agrees with the actual human depletion and recruitment studies in PMID:20603015 and PMID:20603073 and with direct human nuclease processing of synthetic crosslinked DNA in PMID:25430771. FAN1 performs DNA incision in this repair context rather than merely being a molecule acted on by the pathway. The evidence does not establish every modeled ordering of the other repair nucleases, an obligate dimer under all conditions, or interchangeability of the two natural FAN1 products. |
| GO:0070336 flap-structured DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Retain inherited flap-structured DNA binding with direct human recognition evidence. Reason: The matching PTN000405526 binding IBD cites experimentally characterized human FAN1, and the target sequence and ancestral path are verified. PMID:25430771 measures binding to defined short phosphorylated DNA flaps, shows enhancement by a 3β² flap and resolves contacts in a human 364β1017 FAN1βDNA structure. Binding and structural recognition, rather than cleavage alone, support GO:0070336. Substrate length, terminal phosphorylation and salt conditions affect affinity and activity; this is not nonspecific binding to every nucleic acid. The assay construct lacks the N-terminal UBZ domain and is distinct from the 533-residue natural product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000405526 SUPPORTS TRANSFER The saved PANTHER v19 tree places the exact 1017-residue human target PTN002496574 below PTN000405526; the matching experimental-descendant IBD and absence of a target-path NOT were checked. Human FAN1 among the descendant sources is valid experimental grounding. Direct target binding and DNA-contact structures corroborate the inherited recognition activity without assigning it to the UBZ domain. |
| GO:0070336 flap-structured DNA binding | IDA PMID:25430771 DNA repair. Mechanism of DNA interstrand cross-link processi... | ACCEPT | Summary: Retain substrate binding to flap-containing DNA. Reason: PMID:25430771 measures affinity for defined nick/flap substrates and determines human FAN1βDNA structures. Binding strongly favors a phosphorylated short 5-prime flap or nick and is enhanced by a complementary 3-prime flap. The main Results and structures were read; supplemental binding plots were not independently inspected. This specific substrate-recognition function accompanies the nuclease activity and does not imply RNA binding, nonspecific chromatin binding or activity of the natural short isoform. Supporting Evidence: |
| GO:0140036 ubiquitin-modified protein reader activity | IDA PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | UNDECIDED | Summary: Ubiquitin-dependent recruitment is supported; the current adaptor definition needs a separate mechanistic assessment. Reason: PMID:20603015: The original human UBZ-mutant and FANCD2 K561R co-immunoprecipitation/recruitment experiments were read in the main article and Figure 5. Current GO:0140036 defines an adaptor that recognizes a ubiquitinated target and brings it into contact with another protein. Recruitment of FAN1 itself to its DNA-processing site does not by itself demonstrate that third-protein bridging step. MutL associations and proposed repair complexes do not settle the mechanism. Preserve this curated annotation as undecided, without denying the positive recognition/recruitment evidence or asserting that no bridging function exists. Supporting Evidence: |
| GO:0140036 ubiquitin-modified protein reader activity | IDA PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | UNDECIDED | Summary: Ubiquitin-dependent recruitment is supported; the current adaptor definition needs a separate mechanistic assessment. Reason: PMID:20603016: The verified abstract reports UBZ-dependent recognition of monoubiquitinated FANCD2, but the full original experiments were inaccessible. Current GO:0140036 defines an adaptor that recognizes a ubiquitinated target and brings it into contact with another protein. Recruitment of FAN1 itself to its DNA-processing site does not by itself demonstrate that third-protein bridging step. MutL associations and proposed repair complexes do not settle the mechanism. Preserve this curated annotation as undecided, without denying the positive recognition/recruitment evidence or asserting that no bridging function exists. Supporting Evidence: |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Which DNA substrate and which catalytic mode account for FAN1-dependent restraint of HU-stressed replication forks? How does UBZ/FANCD2-dependent recruitment select this function separately from crosslink repair, without presupposing fork reversal or restart?
Q: Which additional nuclease, polymerase and ligase activities complete FAN1-dependent short-patch extrusion removal, and how do PCNA orientation and competition with MutSΞ² control pathway choice in repeat-bearing human chromatin?
Q: Can the ontology distinguish DNA-specific 5β² exonucleolysis yielding short oligonucleotides from the mononucleotide-only definition of GO:0035312, and represent 5β²-flap cleavage without the substrate-exclusivity and Okazaki-processing wording of GO:0017108?
Q: Does UBZ-dependent recognition of monoubiquitinated FANCD2 also organize a defined third-protein interaction, or does it primarily recruit FAN1 itself to DNA? How do the observed MutL associations relate to that recruitment and repair chemistry?
Q: Where is the natural 533-residue FAN1 product expressed, and does it have a regulatory or recognition role distinct from the 1017-residue nuclease?
Experiment: Compare sequence-verified human FAN1 catalytic and UBZ mutants in matched U2OS rescue experiments with and without HU, measuring nascent-track length, chromosome abnormalities and crosslink resistance separately. In parallel, map cleavage on defined stalled-fork structures and characterize separation-of-function mutants in both exonuclease and internal-incision assays. Link cellular rescue to verified catalytic selectivity and expression rather than treating a nuclease-dead mutant as evidence for one cleavage mode.
Hypothesis: FANCD2-dependent recruitment and particular DNA-cleavage reactions may account for stress-dependent restraint independently of the recruitment requirements of crosslink repair; the existing data do not identify that reaction or prove fork reversal.
Experiment: Extend purified human FAN1βPCNAβRFC extrusion-incision reactions to complete short-patch repair by adding candidate polymerases and ligases individually. Vary nick strand, extrusion size and sequence, ionic strength and PCNA loading; include D960A, no-ATP and PCNA-alone linear-DNA controls. Measure incision products, excision length, repair synthesis and restored duplex sequence separately, then test the resolved pathway in matched human repeat reporters with defined MutSΞ² and MutLΞ± status.
Hypothesis: Incision by FAN1 can initiate a short-patch route, while other enzymes complete removal, synthesis and sealing. Substrate occupancy and clamp orientation may determine competition with mismatch repair without making FAN1 a polymerase, ligase or obligatory MMR component.
Experiment: Reconstitute FAN1 recruitment using defined unmodified and monoubiquitinated FANCD2βFANCI, DNA, and candidate third partners. Measure recruitment and binary binding separately from formation of a ternary interaction and from nuclease output. Include UBZ, FANCD2 ubiquitination-site and catalytic controls, and test cellular co-association without assuming that every recovered partner contacts FAN1 directly.
Hypothesis: Recruitment alone can explain the current UBZ dependence. A distinct adaptor role would require evidence that FAN1 coordinates the modified target with another protein beyond its own localization to DNA.
Experiment: Establish product-specific endogenous expression with validated transcript and protein measurements, then compare matched amounts of sequence-verified 1017- and 533-residue products in localization, binding, nuclease and repair-rescue assays. Use reagents recognizing shared and product-specific regions; the existing C-terminal HPA antigen cannot detect the short product. Distinguish native products from engineered C-terminal fragments and control protein stability.
Hypothesis: Loss of the C-terminal nuclease region predicts a different catalytic capacity, but does not establish absence of all recognition, recruitment or regulatory function in the short product.
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)