FAN-1 (Fanconi-associated nuclease 1 homolog) is a structure-specific nuclease required for DNA interstrand cross-link (ICL) repair in C. elegans. The protein contains an N-terminal UBZ4-type zinc finger that binds monoubiquitinated FANCD2, a winged-helix DNA-binding domain, a TPR scaffold domain, and a C-terminal VRR-NUC catalytic domain that provides both 5'-3' exonuclease and 5'-flap endonuclease activities. fan-1 mutant worms show no visible phenotype under normal conditions but exhibit strong embryonic lethality upon treatment with ICL-inducing agents (cisplatin, nitrogen mustard, mitomycin C). Recent work in C. elegans demonstrates that FAN-1 also mediates error-prone translesion synthesis during ICL repair, generating SNVs via POLH and REV1/3-mediated bypass, while suppressing deletion-prone POLQ/HELQ-mediated end joining (TMEJ) - i.e. FAN-1 acts as a determinant of ICL repair pathway choice in a pathway parallel to canonical Fanconi anemia factors. FAN-1 localizes to the nucleus and is dynamically recruited to the nucleoplasm after crosslinks in an UNC-84 (SUN-domain/LINC)-dependent manner; in the germline its recruitment is coordinated with the FNCM-1/FCD-2 replication-stress relocalization program. FAN-1 interacts with SMO-1 (SUMO).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IDA PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | ACCEPT | Summary: GFP-tagged FAN-1 localizes to the nucleus in C. elegans, directly demonstrated by Kratz et al. 2010. Well supported by the protein's function as a nuclear DNA repair nuclease. Falcon deep research adds that FAN-1 is dynamically recruited to the nucleoplasm after crosslinks in an UNC-84 (SUN-domain/LINC)-dependent manner (Lawrence 2016). Supporting Evidence: PMID:20603016 KIAA1018 is a 5'-->3' exonuclease and a structure-specific endonuclease...recruitment to DNA damage through interaction of its UBZ domain with monoubiquitylated FANCD2 PMID:27956467 nuclease FAN-1 to the nucleoplasm, suggesting that UNC-84 both alters the extent file:worm/fan-1/fan-1-deep-research-falcon.md FAN-1 is reported to be **not efficiently recruited to the nucleoplasm in the absence of UNC-84** |
| GO:0006281 DNA repair | IMP PMID:20603015 Identification of KIAA1018/FAN1, a DNA repair nuclease recru... | ACCEPT | Summary: fan-1 mutant worms show strong increase in embryonic lethality following treatment with ICL-inducing agents, demonstrating involvement in DNA repair. Accept but note this is less specific than ICL repair. Falcon deep research adds C. elegans-specific phenotypic evidence: after TMP/UVA crosslinking, fan-1 mutants have WT-like mitotic features but a disorganized, non-functional germline resulting in sterility, and an increased incidence of protruding vulva (Wilson 2017). Reason: Experimentally supported by mutant phenotype. The more specific term ICL repair (GO:0036297) better captures the core function, but DNA repair is not incorrect. Supporting Evidence: PMID:20603015 Depletion of FAN1 from human cells causes hypersensitivity to ICLs, defects in ICL repair, and genome instability PMID:28934497 fan-1 and slx-1 mutant animals had WT-like mitotic features, yet possessed no or a disorganized, non-functional germline (resulting in sterility) file:worm/fan-1/fan-1-deep-research-falcon.md **fan-1 mutants** were among strains showing high/modest sensitivity. Post-treatment imaging (3 days) found that fan-1 animals had WT-like mitotic features but **severely disrupted germlines** (no or disorganized, non-functional germline leading to **sterility**) |
| GO:0006281 DNA repair | IMP PMID:20603016 Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensi... | ACCEPT | Summary: Same biological conclusion as above, independently confirmed by Kratz et al. C. elegans fan-1 mutants are sensitized to ICL agents. Reason: Independent experimental confirmation of DNA repair role Supporting Evidence: PMID:20603016 human cells depleted of KIAA1018 are sensitized to ICL-inducing agents and display chromosomal instability |
| GO:0005515 protein binding | IPI PMID:14704431 A map of the interactome network of the metazoan C. elegans. | KEEP AS NON CORE | Summary: High-throughput Y2H interactome screen detected interaction between FAN-1 and SMO-1 (SUMO). The term protein binding is uninformative per curation guidelines. The interaction with SUMO suggests FAN-1 may be SUMOylated or interact with SUMOylated partners, but the biological significance is unclear from a HT screen alone. Reason: Protein binding is too generic to be informative. The interaction with SMO-1 was detected in a HT interactome screen without validation of biological relevance. Supporting Evidence: PMID:14704431 more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens |
| GO:0005515 protein binding | IPI PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans... | KEEP AS NON CORE | Summary: Independent Y2H screen also detected FAN-1/SMO-1 interaction, providing additional support. Still, protein binding is uninformative per curation guidelines. Reason: Same rationale - protein binding is too generic. Duplicate detection of SMO-1 interaction is encouraging but does not make the GO term more informative. Supporting Evidence: PMID:19123269 We present an expanded C. elegans protein-protein interaction network |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred nuclear localization, consistent with IDA evidence from PMID:20603016 and the protein's function as a nuclear DNA repair enzyme. Reason: Concordant with direct experimental IDA evidence |
| GO:0036297 interstrand cross-link repair | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred ICL repair role. This is the core biological function of FAN-1, well supported by experimental data from three independent 2010 papers and subsequent C. elegans-specific studies. Reason: Core function, strongly supported by experimental evidence across species. BioReason deep research confirms domain architecture consistent with ICL repair role. Falcon deep research adds C. elegans-specific genetic and localization evidence (MacKay 2010, Wilson 2017, Lawrence 2016, Kim 2018, Tijsterman 2024) reinforcing this as the core biological function. Supporting Evidence: file:worm/fan-1/fan-1-deep-research-bioreason-sft.md A nuclear DNA cross-link repair nuclease...that is recruited to ubiquitin-marked damage sites, binds and positions duplex DNA, and uses a metal-dependent nuclease core to incise DNA near interstrand cross-links file:worm/fan-1/fan-1-deep-research-falcon.md The best-supported annotation is that **fan-1/P90740** encodes a **structure-specific DNA nuclease** acting mainly during **interstrand crosslink repair** and **replication-associated DNA damage processing**, likely via incision/unhooking of branched/5′-flap-like intermediates; it acts in FA-linked but partly parallel pathways, is recruited in the germline by **FNCM-1/FCD-2**, and is relocalized to the nucleoplasm by **UNC-84** after crosslinks. PMID:28934497 fan-1 or slx-1 resulted in germline-restricted sensitivity, revealing context-dependent contributions of these two nucleases |
| GO:0008409 5'-3' exonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred 5'-3' exonuclease activity. Human FAN1 has been directly shown to have this activity via the VRR-NUC domain. Crystal structures confirm the 3-nucleotide interval cleavage mechanism. Falcon deep research notes that this FAN1 nuclease activity extends beyond classical ICL unhooking: a PCNA- and RFC-dependent, strand-directed mode removes triplet-repeat extrahelical extrusions (Phadte 2023); the PCNA/RFC replisome machinery is conserved, suggesting analogous regulation of worm FAN-1. Reason: Well-characterized enzymatic activity of the FAN1 family via VRR-NUC domain Supporting Evidence: PMID:37549289 we describe a strand-directed, extrusion-provoked nuclease function of FAN1 that |
| GO:0017108 5'-flap endonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred 5'-flap endonuclease activity. All three discovery papers demonstrated this activity for human FAN1, and it is a hallmark of the FAN1 family. The VRR-NUC domain and associated structures are conserved in C. elegans. Falcon deep research adds biochemical detail: recombinant FAN1 has strong endonuclease activity on 5' flap substrates and weaker activity on replication-fork-like DNA, cleaving the flap-containing strand in the duplex region near the branchpoint (~4 nt), with WT cleavage rates >0.2 s-1 versus 0.0003 s-1 for a catalytic mutant (MacKay 2010). Reason: Core enzymatic activity of FAN1, conserved across the family Supporting Evidence: file:worm/fan-1/fan-1-deep-research-falcon.md cleavage occurs on the flap-containing strand, in the duplex region near the branchpoint (about **4 nt from the branchpoint**) |
| GO:0070336 flap-structured DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred flap-structured DNA binding. Consistent with the winged-helix DNA-binding domain and the demonstrated substrate specificity of FAN1 for 5' flap structures. Reason: Required for FAN1's nuclease activity on flap substrates |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based electronic annotation from tRNA endonuclease-like domain superfamily. Correct but very general - more specific DNA binding and flap-structured DNA binding terms are already annotated. Reason: Correct but subsumed by more specific terms (GO:0003677, GO:0070336) |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based annotation from UBZ4 zinc finger domain (IPR006642). FAN-1 does bind DNA, though via the winged-helix domain rather than the UBZ4 domain (which binds ubiquitin). The annotation is correct in substance even if the InterPro rationale is indirect. Reason: Correct that FAN-1 binds DNA, but subsumed by more specific GO:0070336 (flap-structured DNA binding) |
| GO:0004518 nuclease activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based annotation from FAN1-like family (IPR033315). Correct but very general - more specific terms (5'-3' exonuclease, 5'-flap endonuclease) are already annotated. Reason: Correct but subsumed by more specific terms GO:0008409 and GO:0017108 |
| GO:0004528 phosphodiesterase I activity | IEA GO_REF:0000003 | KEEP AS NON CORE | Summary: EC-based annotation from EC 3.1.4.1. This is a broad enzyme classification for phosphodiesterase activity. FAN1's nuclease activity is better described by the more specific exonuclease and endonuclease terms. Reason: Technically correct per EC classification but uninformative compared to more specific nuclease terms |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location-based annotation. Consistent with IDA evidence. Reason: Concordant with IDA experimental data from PMID:20603016 |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation from UBZ4 zinc finger domain (IPR006642). Correct and consistent with experimental IMP evidence. Reason: Concordant with IMP experimental data |
| GO:0016788 hydrolase activity, acting on ester bonds | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based annotation from VRR-NUC domain (IPR014883). Correct but extremely general - the nuclease and exonuclease terms are far more informative. Reason: Correct but too general, subsumed by specific nuclease activity terms |
| GO:0036297 interstrand cross-link repair | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based annotation from FAN1-like family (IPR033315). Consistent with experimental evidence and IBA annotation. Reason: Core function, consistent with multiple lines of evidence |
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Download this section (compressed HTML)Q: Does FAN-1 function independently of FCD-2/FANCD2 in all ICL repair contexts in C. elegans, or only in specific tissues or developmental stages?
Suggested experts: Tijsterman M, Schumacher B
Q: What is the biological significance of the FAN-1/SMO-1 (SUMO) interaction detected in Y2H screens? Is FAN-1 SUMOylated, and does this regulate its recruitment or activity?
Suggested experts: Gartner A, Hengartner MO
Q: Does FAN-1 homodimerize in C. elegans as human FAN1 does, and is dimerization required for efficient ICL repair in vivo?
Suggested experts: Xiong Y, Sung P
Experiment: Generate fcd-2 mutant worms carrying a GFP-tagged fan-1 transgene. Test whether FAN-1::GFP forms nuclear foci after ICL induction (e.g., MMC treatment) in fcd-2 mutant versus wild-type backgrounds.
Hypothesis: FAN-1 recruitment to ICL sites in C. elegans depends on FCD-2 monoubiquitination
Type: fluorescence microscopy
Experiment: Create catalytic-dead fan-1 alleles (e.g., mutations in the VRR-NUC active site metal-coordinating residues D810, E825, D826) by CRISPR and test ICL sensitivity compared to null alleles.
Hypothesis: FAN-1 nuclease activity, not just its presence, is required for ICL repair in C. elegans
Type: genetic complementation
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