FEN1 (flap endonuclease 1, also called DNase IV and maturation factor 1) is a structure-specific, magnesium-dependent nuclease of the XPG/RAD2 family. Its principal activity is 5'-flap endonuclease cleavage: it threads onto the free 5' end of a displaced single-stranded flap, tracks to the flap base, and incises one nucleotide into the annealed duplex of a double-flap substrate, leaving a nick that DNA ligase I can seal. The same two-metal-ion active site supports a 5'-to-3' exonuclease activity on nicked and gapped double-stranded DNA and an RNase H activity on RNA:DNA hybrids, which lets FEN1 remove ribonucleotide-containing flaps and incise the RNA strand of R-loops. During lagging-strand replication FEN1 carries out Okazaki fragment maturation, cleaving the RNA/DNA primer flap displaced by DNA polymerase delta; in long-patch base excision repair it removes the abasic-site-terminated flap generated by strand-displacement synthesis. It is targeted to these sites by PCNA, which binds a C-terminal PIP box and stimulates cleavage 10- to 50-fold, and is further modulated by the RecQ helicases WRN and BLM, by MUS81 complexes, DDX11 and WDR4, and by acetylation, phosphorylation and arginine methylation of its C-terminal region. FEN1 acts principally in the nucleus, concentrating in nucleoli at steady state and redistributing to the nucleoplasm after DNA damage; a pool also functions in mitochondria alongside DNA2, and an alternatively initiated isoform, FENMIT, is mitochondrial and catalytically inactive but binds RNA flaps and R-loops. By preventing flaps from equilibrating into structures that seed duplications and deletions, FEN1 is a major determinant of repeat tract and overall genome stability.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006260 DNA replication | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic (PANTHER PTN000118792) inference that FEN1 acts in DNA replication. True but under-specified: the replication role of FEN1 is confined to lagging-strand Okazaki fragment maturation, where it removes the RNA/DNA primer flap displaced by DNA polymerase delta. Reason: FEN1 is not a general replication factor; its documented replication activity is the cleavage of 5' flaps generated during Okazaki fragment processing, leaving a ligatable nick. GO:0033567 (DNA replication, Okazaki fragment processing) captures this precisely and is supported for the human protein by structural and biochemical work. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000118792 · FEN1 ancestral node SUPPORTS TRANSFER Node-level 'DNA replication' is correct for the family but every characterized member acts specifically in Okazaki fragment maturation. SGD:S000001596 · RAD27 SUPPORTS TRANSFER Yeast orthologue's replication role is likewise restricted to Okazaki fragment processing. MGI:MGI:102779 · Fen1 SUPPORTS TRANSFER Proposed replacements: DNA replication, Okazaki fragment processing Supporting Evidence: PMID:9778254 Flap endonuclease (FEN-1) removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. PMID:36672839 Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). |
| GO:0006281 DNA repair | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that FEN1 acts in DNA repair. FEN1 participates in more than one repair route - long-patch base excision repair, flap trimming during microhomology-mediated end joining, and processing of damaged replication intermediates - so the grouping term is appropriate here. Reason: Unlike the replication annotation, which maps to a single pathway, FEN1's repair contributions genuinely span several sub-pathways; the specific children (GO:0006284 base-excision repair, GO:0006287 base-excision repair gap-filling) are separately annotated, so retaining the parent as an IBA statement is reasonable rather than over-general. Supporting Evidence: PMID:36672839 Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). PMID:8131753 The repair of some types of DNA double-strand breaks is thought to proceed through DNA flap structure intermediates. |
| GO:0006310 DNA recombination | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference that FEN1 acts in DNA recombination. FEN1 does trim 5' flaps at recombination and end-joining intermediates, but this is a peripheral consequence of its structure-specific nuclease activity rather than a dedicated recombination function. Reason: No experimental evidence assigns FEN1 a strand-exchange, resection or Holliday-junction resolution role; it explicitly fails to cleave Holliday junctions. Its involvement in recombination-associated repair is limited to removing displaced flaps, which is already captured by the flap endonuclease MF and the end-joining BP annotations. Supporting Evidence: PMID:8131753 Other branch structures, including Holliday junctions, are also not cleaved by FEN-1. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that FEN1 is active in the nucleus. This is the principal compartment in which FEN1 acts on nuclear replication and repair intermediates, and it is confirmed by direct immunostaining of the human protein. Reason: Human FEN1 is a nuclear enzyme (nucleolar at steady state, redistributing to nucleoplasm after damage); the is_active_in qualifier is correct because its substrates are nuclear replication and repair intermediates. Supporting Evidence: PMID:12427278 Flap endonuclease 1 (FEN-1) is a nuclear enzyme involved in DNA metabolism, such as replication, repair, and recombination. PMID:7961795 A nuclear 42-kDa 5'-->3'-exonuclease, DNase IV, was found previously in animal tissues. |
| GO:0017108 5'-flap endonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of 5'-flap endonuclease activity. This is the defining catalytic activity of FEN1 and is demonstrated directly for the human enzyme. Reason: Core molecular function. The purified human enzyme cleaves 5' single-stranded flap strands specifically, and the reaction is abolished by active-site mutations, establishing that FEN1 itself enables the activity. Supporting Evidence: PMID:8131753 The enzyme described here, flap endonuclease-1 (FEN-1), cleaves DNA flap strands that terminate with a 5' single-stranded end. PMID:8621570 Mutants D34A, D86A, and D181A lost their cleavage activity completely but retained substrate binding ability |
| GO:0008409 5'-3' exonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of 5'-3' exonuclease activity. FEN1 has a genuine 5'-3' exonuclease activity, acting on nicked and gapped double-stranded DNA using the same active site as the flap endonuclease reaction. Reason: Directly demonstrated for the purified human enzyme, and mutations that alter substrate engagement (R70A) selectively eliminate the exonuclease mode, showing it is an intrinsic property of FEN1. GO:0008409 is retained rather than narrowed because an IBA annotation records the family-level consensus; the human-specific narrowing to a dsDNA 5'-3' term is carried by the GO:0008309 MODIFY on PMID:8131753, which is the entry whose cited evidence establishes the duplex specificity. Supporting Evidence: PMID:8131753 In addition to endonuclease activity, FEN-1 has a 5'-3' exonuclease activity which is specific for double-stranded DNA. PMID:11986308 Mutation of the Arg-70 significantly reduced flap endonuclease activity and eliminated exonuclease activity. |
| GO:0000287 magnesium ion binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of magnesium ion binding. Mg2+ is the catalytic cofactor of the two-metal-ion FEN1 active site. Reason: UniProt records that FEN1 binds two magnesium ions per subunit which participate in catalysis, and the conserved active-site carboxylates that coordinate them (Asp-34, Asp-86, Asp-181) are essential for cleavage but not for substrate binding. Supporting Evidence: PMID:8621570 Mutants D34A, D86A, and D181A lost their cleavage activity completely but retained substrate binding ability, as measured by their ability to inhibit the wild type enzyme in a competition assay. |
| GO:0004523 RNA-DNA hybrid ribonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of RNA-DNA hybrid ribonuclease (RNase H) activity. Human FEN1 was shown to possess RNase H activity when first purified as DNase IV, and cleaves the RNA strand of RNA:DNA hybrid flap intermediates. Reason: Directly demonstrated for the human enzyme and mechanistically important: it is what allows FEN1 to remove ribonucleotide-containing Okazaki primers and to incise the RNA strand of R-loops. Supporting Evidence: PMID:7961795 DNase IV removes single-stranded 5' regions from splayed-arm DNA structures by endonucleolytic incision at the bifurcation point and possesses RNase H activity PMID:36672839 We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. |
| GO:0030145 manganese ion binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic inference of manganese ion binding. Mn2+ can substitute for Mg2+ in FEN1-family two-metal-ion active sites in vitro, but the physiological cofactor is magnesium. Reason: UniProt lists only Mg2+ as the cofactor for human FEN1 (two ions per subunit, with a possible third after substrate binding); manganese binding reflects in vitro metal substitution common to this nuclease fold rather than a distinct biological requirement. Retaining it implies a physiological manganese dependence that has not been shown. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN000871763 · XPG/RAD2 nuclease node SUPPORTS SOURCE BUT NOT TARGET Manganese binding in this family is in vitro metal substitution at the two-metal-ion site; UniProt lists only Mg2+ as the FEN1 cofactor. MGI:MGI:102779 · Fen1 UNRESOLVED Seed annotation not traceable to a demonstration of a physiological manganese requirement. |
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: Sequence-feature-based electronic transfer of magnesium ion binding. Consistent with the experimentally supported two-metal-ion active site. Reason: Duplicates the IBA magnesium annotation and is correct; the catalytic carboxylate cluster that coordinates Mg2+ is a conserved feature of the XPG/RAD2 nuclease domain present in human FEN1. Supporting Evidence: PMID:8621570 Mutants D34A, D86A, and D181A lost their cleavage activity completely but retained substrate binding ability |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of DNA binding. FEN1 must engage both the single-stranded flap and the flanking duplex to cleave, and DNA binding is measurable and separable from catalysis. Reason: General but correct and non-trivially informative for a structure-specific nuclease: catalytically dead active-site mutants still bind substrate, showing DNA binding is a distinct property of the protein. Supporting Evidence: PMID:8621570 Loss of both binding and cleavage competency for the flap substrate by mutants E156A, G231A, and D233A suggests that these amino acids are involved in substrate binding. |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to the ontology root-level term 'catalytic activity'. FEN1 is an enzyme, so the statement is true, but the term conveys no information about what it does. Reason: GO:0003824 is a top-level grouping term. The same InterPro signatures (flap endonuclease, XPG-I domain, 5'-3' exonuclease C-terminal domain) support the specific activity term GO:0017108, which is also independently supported experimentally. Proposed replacements: 5'-flap endonuclease activity Supporting Evidence: PMID:8131753 The enzyme described here, flap endonuclease-1 (FEN-1), cleaves DNA flap strands that terminate with a 5' single-stranded end. |
| GO:0004518 nuclease activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping to nuclease activity. An appropriate domain-level statement for a protein carrying the flap endonuclease and XPG-I domains. Reason: Unlike the 'catalytic activity' root mapping, 'nuclease activity' is a meaningful domain-derived assertion and is a direct parent of the experimentally supported flap endonuclease and 5'-3' exonuclease activities. |
| GO:0004520 DNA endonuclease activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning annotation of DNA endonuclease activity. Correct and consistent with the experimentally demonstrated structure-specific endonuclease activity. Reason: A reasonable parent of GO:0017108; the human enzyme was purified as a DNA structure-specific endonuclease, so the electronic assertion is not an over-reach. Supporting Evidence: PMID:8131753 This assay has allowed the first purification of a mammalian DNA structure-specific nuclease. |
| GO:0005634 nucleus | IEA GO_REF:0000104 | ACCEPT | Summary: Electronic transfer of nuclear localization. Correct for the major isoform. Reason: Nuclear localization of human FEN1 is directly established by immunostaining and by its purification as a nuclear enzyme. Supporting Evidence: PMID:7961795 A nuclear 42-kDa 5'-->3'-exonuclease, DNase IV, was found previously in animal tissues. |
| GO:0005654 nucleoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProt subcellular location vocabulary: nucleoplasm. FEN1 relocalizes from nucleoli to the nucleoplasm on DNA damage and acts on nucleoplasmic replication forks. Reason: Matches the curated UniProt subcellular location for isoform 1 and is where the enzyme engages replication and repair intermediates; corroborated by independent immunofluorescence (GO_REF:0000052) annotations in this same set. |
| GO:0005730 nucleolus | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic annotation from the UniProt subcellular location vocabulary: nucleolus. This is the steady-state localization of human FEN1. Reason: UniProt records that isoform 1 'resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage'; independent immunofluorescence annotation of nucleolar FEN1 is present in this same annotation set. |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of mitochondrial localization. Supported for human FEN1: a pool of the protein and the alternatively initiated FENMIT isoform are mitochondrial. Reason: Independent direct evidence places FEN1 in mitochondria, where it cooperates with DNA2 on 5' flap intermediates arising in mtDNA replication and long-patch BER. UniProt additionally assigns the FENMIT isoform (P39748-2) to the mitochondrion. Supporting Evidence: PMID:18995831 We further demonstrate that hDNA2 and flap endonuclease 1 synergistically process intermediate 5' flap structures occurring in DNA replication and long-patch base excision repair (LP-BER) in mitochondria. |
| GO:0006284 base-excision repair | IEA GO_REF:0000104 | ACCEPT | Summary: Electronic transfer of base-excision repair involvement. This is one of the two core biological processes of FEN1: it removes the abasic-site-terminated flap generated by strand-displacement synthesis during long-patch BER. Reason: Core function, independently supported experimentally and by Reactome curation of the long-patch BER reactions in which FEN1 cleaves the displaced flap. Supporting Evidence: PMID:36672839 Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). |
| GO:0006310 DNA recombination | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA electronic annotation of DNA recombination. As for the IBA equivalent, FEN1's recombination involvement is limited to flap trimming at end-joining and recombination intermediates. Reason: Not wrong, but peripheral: FEN1 has no strand-exchange or junction-resolution activity and does not cleave Holliday junctions. Retained as a non-core process annotation. Supporting Evidence: PMID:8131753 Other branch structures, including Holliday junctions, are also not cleaved by FEN-1. |
| GO:0008409 5'-3' exonuclease activity | IEA GO_REF:0000104 | ACCEPT | Summary: Electronic transfer of 5'-3' exonuclease activity, duplicating the experimentally supported activity. Reason: Correct; the human enzyme's dsDNA-specific 5'-3' exonuclease activity is directly demonstrated. Supporting Evidence: PMID:8131753 In addition to endonuclease activity, FEN-1 has a 5'-3' exonuclease activity which is specific for double-stranded DNA. |
| GO:0016788 hydrolase activity, acting on ester bonds | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to 'hydrolase activity, acting on ester bonds'. True of any nuclease and therefore uninformative about FEN1. Reason: Too general to be useful. The same domain content supports at minimum 'nuclease activity' and, given the flap endonuclease domain signature, the specific 5'-flap endonuclease activity term. Proposed replacements: 5'-flap endonuclease activity |
| GO:0017108 5'-flap endonuclease activity | IEA GO_REF:0000104 | ACCEPT | Summary: Electronic transfer of 5'-flap endonuclease activity, duplicating the core experimentally supported molecular function. Reason: Correct and at the right level of specificity. Supporting Evidence: PMID:8131753 The enzyme described here, flap endonuclease-1 (FEN-1), cleaves DNA flap strands that terminate with a 5' single-stranded end. |
| GO:0043137 DNA replication, removal of RNA primer | IEA GO_REF:0000104 | ACCEPT | Summary: Electronic transfer of 'DNA replication, removal of RNA primer'. This is the precise replication role of FEN1 and is directly demonstrated for the human enzyme. Reason: Core function; FEN1 removes the RNA/DNA primer flap during Okazaki fragment maturation, and depletion experiments in mitochondrial extracts show reduced primer removal. Supporting Evidence: PMID:18995831 Depletion of hDNA2 from a mitochondrial extract reduces its efficiency in RNA primer removal and LP-BER. PMID:36672839 Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). |
| GO:0005515 protein binding | IPI PMID:11598021 Werner syndrome protein interacts with human flap endonuclea... | MARK AS OVER ANNOTATED | Summary: IPI interaction with WRN (Q14191). WRN binds FEN1 and dramatically stimulates its cleavage of 5' flap substrates, independently of WRN helicase catalysis. Reason: The interaction is real and functionally meaningful, but 'protein binding' conveys no molecular function for FEN1. The informative content - that FEN1's flap endonuclease activity is stimulated in this complex - is already captured by GO:0017108. No more specific binding term (e.g. a RecQ-helicase-binding term) exists in GO. Supporting Evidence: PMID:11598021 WS protein (WRN) dramatically stimulates the rate of FEN-1 cleavage of a 5' flap DNA substrate. PMID:11598021 A physical interaction between WRN and FEN-1 is demonstrated by their co-immunoprecipitation from HeLa cell lysate |
| GO:0005515 protein binding | IPI PMID:14657243 WRN helicase and FEN-1 form a complex upon replication arres... | MARK AS OVER ANNOTATED | Summary: IPI interactions with PCNA (P12004) and WRN (Q14191). WRN and FEN-1 form a complex at arrested replication forks and WRN stimulates FEN-1 cleavage of branch-migrating double-flap substrates. Reason: Functionally informative interaction, but recorded under the uninformative 'protein binding' term. The relevant biology - stimulation of FEN1 double-flap cleavage at stalled forks - is covered by GO:0017108. Supporting Evidence: PMID:14657243 WRN effectively stimulates FEN-1 cleavage of branch-migrating double-flap structures that are the physiological substrates of FEN-1 |
| GO:0005515 protein binding | IPI PMID:14688284 Stimulation of flap endonuclease-1 by the Bloom's syndrome p... | MARK AS OVER ANNOTATED | Summary: IPI interactions with BLM (P54132) and WRN (Q14191). BLM binds FEN1 and stimulates its flap endonuclease activity. Reason: Real interaction with a functional consequence, but 'protein binding' adds no molecular-function information for FEN1 beyond the flap endonuclease activity already annotated. Supporting Evidence: PMID:14688284 We report here a novel interaction of the BLM protein with the human 5'-flap endonuclease/5'-3' exonuclease (FEN-1), a genome stability factor involved in Okazaki fragment processing and DNA repair. |
| GO:0005515 protein binding | IPI PMID:15576034 Structural and thermodynamic analysis of human PCNA with pep... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004), from a crystal structure of PCNA bound to the FEN1 PIP-box peptide (residues 331-350). Reason: High-quality structural evidence for a functionally central interaction, but the term used is uninformative. The consequence of PCNA binding - recruitment to and stimulation at the replication fork - is captured by the replication and flap endonuclease annotations; GO has no 'PCNA binding' molecular function term. Supporting Evidence: PMID:15576034 Both structures demonstrate that the pol-delta p66 and FEN1 peptides interact with hPCNA at the same site shown to bind the cdk-inhibitor p21(CIP1). |
| GO:0005515 protein binding | IPI PMID:18692475 A protein domain-based interactome network for C. elegans ea... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) recorded from a large-scale domain-based yeast two-hybrid interactome study whose stated subject is C. elegans early embryogenesis. Reason: Uninformative term supported only by a high-throughput binary interaction screen. The FEN1-PCNA interaction is well established from dedicated biochemistry and structural work, so this entry adds no evidence value. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:22551069 Human MUS81 complexes stimulate flap endonuclease 1. | MARK AS OVER ANNOTATED | Summary: IPI interaction with MUS81 (Q96NY9). MUS81-EME1 and MUS81-EME2 bind FEN1 and increase its nuclease activity by improving substrate turnover. Reason: Genuine functional interaction, but recorded under 'protein binding'. The relevant molecular function (stimulated flap endonuclease activity) is separately annotated. Supporting Evidence: PMID:22551069 We found that both MUS81-EME1 and MUS81-EME2 increased the activity of FEN1, but FEN1 did not stimulate the activity of MUS81-EME1/EME2. |
| GO:0005515 protein binding | IPI PMID:26030842 A fluorescent bimolecular complementation screen reveals MAF... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from a bimolecular fluorescence complementation screen for PCNA-interacting proteins. Reason: Screen-derived support for an already well-established interaction, annotated to an uninformative term. Supporting Evidence: PMID:26030842 To fully characterize the set of proteins that interact with PCNA we developed a bimolecular fluorescence complementation (BiFC) screen for PCNA-interactors in human cells. |
| GO:0005515 protein binding | IPI PMID:26496610 A human interactome in three quantitative dimensions organiz... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from a quantitative affinity-purification mass spectrometry interactome map. Reason: High-throughput proteomic support for a known interaction, annotated to the uninformative 'protein binding' term. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:26751069 Wuho Is a New Member in Maintaining Genome Stability through... | MARK AS OVER ANNOTATED | Summary: IPI interactions with PCNA (P12004) and WDR4/Wuho (P57081). WDR4 was identified as a FEN1 interactor that modulates FEN1 activity and replication-fork genome stability. Reason: Functionally relevant interaction (UniProt records that WDR4 regulates FEN1 endonuclease activity), but 'protein binding' is uninformative as a molecular function for FEN1. Supporting Evidence: PMID:26751069 We identify that the flap endonuclease 1 (FEN1) is one of the interacting proteins. |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from the BioPlex affinity-purification mass spectrometry interactome. Reason: Large-scale proteomic redetection of a known interaction; the term carries no functional information. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:29997244 LuTHy: a double-readout bioluminescence-based two-hybrid tec... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) detected by the LuTHy bioluminescence two-hybrid assay. Reason: Methodology-development screen redetecting a known interaction; annotated to an uninformative term. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:31467278 Maximizing binary interactome mapping with a minimal number ... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from a benchmarking study of binary interactome assays. Reason: Assay-benchmarking redetection of a known interaction; no functional information is conveyed by 'protein binding'. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from a systematic survey of how coding variants disrupt protein interactions. Reason: Variant-effect screen redetecting a known interaction; the term itself is uninformative for FEN1's function. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from the BioPlex 3.0 cell-line-resolved interactome. Reason: High-throughput redetection of a known interaction, annotated to an uninformative term. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0005515 protein binding | IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004) from the OpenCell endogenous-tagging interactome and localization resource. Reason: High-throughput redetection of a known interaction; 'protein binding' conveys no molecular function. No supporting quote is attached: the paper reports this interaction only as a row in a large-scale dataset, and its abstract contains no FEN1-specific statement. |
| GO:0007613 memory | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Electronic ortholog projection (Ensembl Compara, GO_REF:0000107) of 'memory' from rat Fen1 (UniProtKB:Q5XIP6). No human evidence links FEN1 to memory, and the term describes an organism-level behavioural phenotype rather than anything FEN1 does. Reason: FEN1 is a ubiquitously expressed housekeeping nuclease acting in Okazaki fragment maturation and base excision repair. Any effect on memory would be a distal, pleiotropic consequence of impaired genome maintenance in neurons, not a function of the gene product, and projecting a behavioural annotation across orthologs compounds that over-reach. |
| GO:0000724 double-strand break repair via homologous recombination | TAS Reactome:R-HSA-5693538 | MODIFY | Summary: Reactome TAS placing FEN1 in 'Homology Directed Repair'. Within Reactome, FEN1's actual reaction in that hierarchy is flap cleavage during microhomology-mediated end joining, not homologous recombination proper. Reason: FEN1 has no demonstrated role in strand invasion, resection or D-loop metabolism. The specific Reactome reaction that involves FEN1 (R-HSA-5687664, 'FEN1 cleaves displaced ssDNA flaps during MMEJ') belongs to the microhomology-mediated (alternative) end-joining branch, which GO:0097681 represents accurately. Proposed replacements: double-strand break repair via alternative nonhomologous end joining |
| GO:0032201 telomere maintenance via semi-conservative replication | TAS Reactome:R-HSA-174446 | ACCEPT | Summary: Reactome TAS for telomere maintenance via semi-conservative replication, from the reaction 'Removal of remaining Flap from the C-strand'. Telomeric lagging-strand (C-strand) synthesis requires the same Okazaki flap processing that FEN1 performs genome-wide. Reason: Consistent with FEN1's core Okazaki fragment processing role applied at telomeres, and independently corroborated by proteomic detection of FEN1 at telomeric chromatin. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence-based (GO_REF:0000052) localization to the nucleoplasm. Reason: Agrees with the curated UniProt subcellular location for isoform 1 and with the damage-induced redistribution of FEN1 from nucleoli to nucleoplasm. |
| GO:0005730 nucleolus | IDA GO_REF:0000052 | ACCEPT | Summary: Immunofluorescence-based (GO_REF:0000052) localization to the nucleolus, the steady-state compartment of human FEN1. Reason: Matches the curated UniProt statement that FEN1 resides mostly in nucleoli, consistent with a role in rDNA replication and repair. |
| GO:0005515 protein binding | IPI PMID:26760506 R152C DNA Pol β mutation impairs base excision repair and in... | MARK AS OVER ANNOTATED | Summary: IPI interaction with DNA polymerase beta (P06746), the gap-filling polymerase that hands the displaced flap to FEN1 in long-patch base excision repair. Reason: Pathway-relevant interaction, but 'protein binding' is uninformative; the functional content is captured by the base-excision repair and flap endonuclease annotations. Reactome models this handoff explicitly (R-HSA-5651782, 'FEN1 bound to POLB cleaves displaced DNA strand (flap)'). |
| GO:0006287 base-excision repair, gap-filling | TAS Reactome:R-HSA-110373 | ACCEPT | Summary: Reactome TAS for base-excision repair gap-filling, from 'Resolution of AP sites via the multiple-nucleotide patch replacement pathway' (long-patch BER). FEN1 excises the AP-site-containing flap created by strand-displacement synthesis. Reason: This is the standard GO term for participants in the long-patch BER sub-pathway and matches FEN1's directly demonstrated role there. Supporting Evidence: PMID:36672839 Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). |
| GO:0005634 nucleus | IDA PMID:12427278 Two overlapping divergent transcription units in the human g... | ACCEPT | Summary: IDA of nuclear localization, from immunostaining that contrasted FEN-1 with the cytoplasmic C11orf10 product encoded at the same divergent locus. Reason: Direct cell-biological evidence for nuclear FEN1 in human cells. Supporting Evidence: PMID:12427278 Immunostaining revealed that the C11orf10 protein, unlike FEN-1, is located in the cytoplasm |
| GO:0017108 5'-flap endonuclease activity | TAS Reactome:R-HSA-110363 | ACCEPT | Summary: Reactome TAS for 5'-flap endonuclease activity in the reaction 'FEN1 bound to PCNA and APEX1 cleaves flap ssDNA' (long-patch BER). Reason: Correct molecular function assigned in the correct pathway context. |
| GO:0017108 5'-flap endonuclease activity | TAS Reactome:R-HSA-174446 | ACCEPT | Summary: Reactome TAS for 5'-flap endonuclease activity in 'Removal of remaining Flap from the C-strand' during telomere lagging-strand replication. Reason: Correct molecular function; the telomeric context is captured by the accompanying GO:0032201 annotation. |
| GO:0017108 5'-flap endonuclease activity | TAS Reactome:R-HSA-5651782 | ACCEPT | Summary: Reactome TAS for 5'-flap endonuclease activity in 'FEN1 bound to POLB cleaves displaced DNA strand (flap)' during long-patch BER. Reason: Correct molecular function in the POLB-driven long-patch BER route. |
| GO:0017108 5'-flap endonuclease activity | TAS Reactome:R-HSA-5687664 | ACCEPT | Summary: Reactome TAS for 5'-flap endonuclease activity in 'FEN1 cleaves displaced ssDNA flaps during MMEJ'. Reason: Correct molecular function; the same reaction is the basis for the proposed alternative end-joining process term replacing the over-broad homology-directed repair annotation. |
| GO:0017108 5'-flap endonuclease activity | TAS Reactome:R-HSA-69152 | ACCEPT | Summary: Reactome TAS for 5'-flap endonuclease activity in 'Removal of remaining Flap' during Okazaki fragment processing. Reason: Core molecular function in its canonical pathway context. |
| GO:0032991 protein-containing complex | IDA PMID:25378300 Opposing roles of mitochondrial and nuclear PARP1 in the reg... | MARK AS OVER ANNOTATED | Summary: IDA of 'protein-containing complex' membership from a study of mitochondrial versus nuclear PARP1 and its interactions with mitochondrial BER enzymes. Reason: GO:0032991 is a root-level cellular component term that asserts only that the protein is in some complex, which is true of almost any protein and conveys nothing about FEN1. The paper's focus is PARP1, EXOG and DNA polymerase gamma; it does not define a named FEN1-containing complex that could be annotated more specifically. Supporting Evidence: PMID:25378300 Here we investigated the role of PARP1 in the repair of the mitochondrial DNA in the baseline and oxidative stress conditions. |
| GO:0045876 positive regulation of sister chromatid cohesion | IMP PMID:18499658 Studies with the human cohesin establishment factor, ChlR1. ... | KEEP AS NON CORE | Summary: IMP of positive regulation of sister chromatid cohesion: siRNA depletion of FEN1 (or of its interactor ChlR1/DDX11) causes precocious sister chromatid separation. Reason: The phenotype is real but is a downstream consequence of defective lagging-strand processing, which the authors themselves frame as the mechanism ('its action may contribute to lagging strand processing events important in cohesion'). FEN1 is not a cohesion regulator in its own right, so this is retained as a non-core process annotation. Supporting Evidence: PMID:18499658 Selective depletion of either hChlR1 or Fen1 by targeted small interfering RNA treatment results in the precocious separation of sister chromatids. |
| GO:0048256 flap endonuclease activity | IDA PMID:18499658 Studies with the human cohesin establishment factor, ChlR1. ... | MODIFY | Summary: IDA of flap endonuclease activity, from assays showing that DDX11/ChlR1 stimulates FEN1 flap cleavage. The term used is the parent of the 5'-specific term. Reason: FEN1 cleaves flaps that terminate in a 5' single-stranded end and does not act on 3' flaps, so the 5'-specific child term GO:0017108 is the accurate description of the assayed activity. Proposed replacements: 5'-flap endonuclease activity Supporting Evidence: PMID:18499658 The interactions between Fen1 and hChlR1 stimulate the flap endonuclease activity of Fen1. |
| GO:0000781 chromosome, telomeric region | IDA PMID:24270157 A quantitative telomeric chromatin isolation protocol identi... | KEEP AS NON CORE | Summary: IDA (colocalizes_with) of telomeric chromatin, from quantitative telomeric chromatin isolation (QTIP) proteomics. Reason: FEN1 is expected at telomeres because telomeric C-strand synthesis generates the same Okazaki flap intermediates it processes genome-wide, and the hedged colocalizes_with qualifier is appropriate for a crosslinking-proteomics detection. It is a location where FEN1 acts, not a distinct core function. Supporting Evidence: PMID:24270157 With QTIP, we specifically enrich telomeric DNA and all shelterin components. |
| GO:0000781 chromosome, telomeric region | HDA PMID:19135898 Purification of proteins associated with specific genomic Lo... | KEEP AS NON CORE | Summary: HDA of telomeric chromatin localization from PICh (proteomics of isolated chromatin segments) purification of human telomeres. Reason: Consistent with the QTIP detection and with FEN1's role in telomeric lagging-strand replication, but derived from high-throughput locus proteomics and peripheral to the gene's core function. Supporting Evidence: PMID:19135898 Purification of human telomeric chromatin using PICh identified the majority of known telomeric factors and uncovered a large number of novel associations. |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | REMOVE | Summary: HDA of membrane localization from a mass-spectrometry survey of the NK-cell line membrane proteome. Reason: FEN1 is a soluble nuclear (and mitochondrial-matrix) nuclease with no transmembrane segment, signal peptide or lipid anchor in UniProt, and no mechanism by which it would be a membrane component. The source study itself reports that only about 40% of its identified proteins were plausible membrane proteins and that the remainder were nuclear and cytoplasmic proteins recovered with the membrane fraction, so this is background from a subcellular-fractionation proteomics screen. Supporting Evidence: PMID:19946888 On the basis of the presence of transmembrane regions or evidence of posttranslational modifications and prediction algorithms, approximately 40% of the identified proteins were predicted as plausible membrane proteins. PMID:19946888 The remaining species were largely involved in cellular processes and molecular functions that could be predicted to be transiently associated with membranes. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-110363 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'FEN1 bound to PCNA and APEX1 cleaves flap ssDNA'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-110364 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PCNA:POLD,POLE:RPA:RFC and FEN1 bind APEX1'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-110368 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'POLD,POLE-mediated DNA strand displacement synthesis'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-174446 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'Removal of remaining Flap from the C-strand'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649873 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PARP1,PARP2 dimers and FEN1 bind POLB and displace APEX1 from damaged AP site'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649883 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'POLB-mediated DNA strand displacement synthesis'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5651723 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PARP1,PARP2 dimers bound to FEN1 and POLB autoPARylate'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5651739 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PAR-PARP1,PAR-PARP2 dissociate from FEN1 and POLB'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5651782 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'FEN1 bound to POLB cleaves displaced DNA strand (flap)'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687484 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PARP1 or PARP2, FEN1 and POLQ are recruited to MMEJ site'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687640 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'POLQ extends annealed 3'-ssDNA overhangs in MMEJ'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687653 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'PARP1,PARP2 dimers bound to MMEJ sites autoPARylate'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687664 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'FEN1 cleaves displaced ssDNA flaps during MMEJ'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-69152 | ACCEPT | Summary: Reactome TAS assigning FEN1 to the nucleoplasm as a participant in 'Removal of remaining Flap'. Reason: Nucleoplasmic localization is correct for FEN1 acting on replication and repair intermediates and matches the curated UniProt subcellular location for isoform 1. These entries are redundant with each other (one per Reactome reaction) but individually accurate. |
| GO:0005515 protein binding | IPI PMID:18499658 Studies with the human cohesin establishment factor, ChlR1. ... | MARK AS OVER ANNOTATED | Summary: IPI interaction with DDX11/ChlR1 (Q96FC9), a helicase that binds FEN1 and stimulates its flap endonuclease activity. Reason: Functionally meaningful interaction recorded under the uninformative 'protein binding' term; the consequence (stimulated flap cleavage) is annotated via GO:0017108. Supporting Evidence: PMID:18499658 The interactions between Fen1 and hChlR1 stimulate the flap endonuclease activity of Fen1. |
| GO:0005634 nucleus | IDA PMID:18995831 Human DNA2 is a mitochondrial nuclease/helicase for efficien... | ACCEPT | Summary: IDA of nuclear localization in the study characterizing human DNA2 as a mitochondrial nuclease/helicase. Reason: Consistent with all other evidence for nuclear FEN1; the paper's contrast is that hDNA2, unlike FEN1, is not nuclear. Supporting Evidence: PMID:18995831 Our data demonstrate that, surprisingly, human DNA2 (hDNA2) does not localize to nuclei, as it lacks a nuclear localization signal equivalent to that present in yDna2. |
| GO:0005739 mitochondrion | IDA PMID:18995831 Human DNA2 is a mitochondrial nuclease/helicase for efficien... | ACCEPT | Summary: IDA of mitochondrial localization: FEN1 acts with DNA2 on 5' flap intermediates in mitochondrial extracts. Reason: Direct evidence for a functional mitochondrial pool of FEN1; UniProt additionally assigns the alternatively initiated FENMIT isoform to mitochondria. Supporting Evidence: PMID:18995831 We further demonstrate that hDNA2 and flap endonuclease 1 synergistically process intermediate 5' flap structures occurring in DNA replication and long-patch base excision repair (LP-BER) in mitochondria. |
| GO:0017108 5'-flap endonuclease activity | IDA PMID:18995831 Human DNA2 is a mitochondrial nuclease/helicase for efficien... | ACCEPT | Summary: IDA of 5'-flap endonuclease activity on mitochondrial replication and LP-BER intermediates. Reason: Core molecular function demonstrated directly on the physiologically relevant 5' flap substrates. Supporting Evidence: PMID:18995831 We further demonstrate that hDNA2 and flap endonuclease 1 synergistically process intermediate 5' flap structures occurring in DNA replication and long-patch base excision repair (LP-BER) in mitochondria. |
| GO:0043137 DNA replication, removal of RNA primer | IDA PMID:18995831 Human DNA2 is a mitochondrial nuclease/helicase for efficien... | ACCEPT | Summary: IDA of RNA primer removal during DNA replication, assayed in mitochondrial extracts. Reason: Core biological process; primer removal efficiency in the extract depends on the FEN1/DNA2 pair. Supporting Evidence: PMID:18995831 Depletion of hDNA2 from a mitochondrial extract reduces its efficiency in RNA primer removal and LP-BER. |
| GO:0003677 DNA binding | IMP PMID:11986308 Arginine residues 47 and 70 of human flap endonuclease-1 are... | ACCEPT | Summary: IMP of DNA binding, from mutation of Arg-47 and Arg-70, which are required for productive engagement of the flap substrate. Reason: Substrate binding is a distinct, mutationally separable property of FEN1 and is required for both its endonuclease and exonuclease modes. Supporting Evidence: PMID:11986308 We revealed that these alterations are due to the defects in DNA-protein interactions. |
| GO:0004523 RNA-DNA hybrid ribonuclease activity | IDA PMID:7961795 Structural and functional homology between mammalian DNase I... | ACCEPT | Summary: IDA of RNA-DNA hybrid ribonuclease (RNase H) activity for purified human DNase IV/FEN1. Reason: Directly demonstrated for the purified human enzyme; this activity underlies removal of ribonucleotide-containing primer flaps and incision of the RNA strand in R-loops. Supporting Evidence: PMID:7961795 DNase IV removes single-stranded 5' regions from splayed-arm DNA structures by endonucleolytic incision at the bifurcation point and possesses RNase H activity |
| GO:0005515 protein binding | IPI PMID:11430825 Regulation of human flap endonuclease-1 activity by acetylat... | MARK AS OVER ANNOTATED | Summary: IPI interaction with EP300/p300 (Q09472), which acetylates the FEN1 C-terminus and thereby inhibits its DNA binding and nuclease activity. Reason: A regulatory interaction with a clear functional consequence, but recorded under the uninformative 'protein binding' term. The regulation is better represented as a PTM of FEN1 (UniProt records that acetylation by EP300 inhibits both endonuclease and exonuclease activity) than as a molecular function of FEN1. Supporting Evidence: PMID:11430825 p300 formed a complex with flap endonuclease-1 (Fen1) and acetylated Fen1 in vitro. PMID:11430825 Remarkably, acetylation of the Fen1 C terminus by p300 significantly reduced Fen1's DNA binding and nuclease activity. |
| GO:0005515 protein binding | IPI PMID:9305916 The DNA repair endonuclease XPG binds to proliferating cell ... | MARK AS OVER ANNOTATED | Summary: IPI interaction with PCNA (P12004), from the study showing that XPG shares the PCNA-binding sequence elements found in FEN-1 and p21. Reason: The FEN1 PIP-box/PCNA interaction is central to FEN1 targeting and stimulation, but 'protein binding' captures none of that; GO offers no specific PCNA-binding molecular function term. Supporting Evidence: PMID:9305916 The DNA repair endonuclease XPG binds to proliferating cell nuclear antigen (PCNA) and shares sequence elements with the PCNA-binding regions of FEN-1 and cyclin-dependent kinase inhibitor p21. |
| GO:0005634 nucleus | IDA PMID:7961795 Structural and functional homology between mammalian DNase I... | ACCEPT | Summary: IDA of nuclear localization for the purified human enzyme, originally characterized as the nuclear 42-kDa 5'-3' exonuclease DNase IV. Reason: Direct evidence for the nuclear compartment of the endogenous human protein. Supporting Evidence: PMID:7961795 A nuclear 42-kDa 5'-->3'-exonuclease, DNase IV, was found previously in animal tissues. |
| GO:0008409 5'-3' exonuclease activity | IDA PMID:7961795 Structural and functional homology between mammalian DNase I... | ACCEPT | Summary: IDA of 5'-3' exonuclease activity for the enzyme purified from HeLa cells. Reason: Core molecular function, directly demonstrated on the purified human protein. Supporting Evidence: PMID:7961795 The enzyme has been purified from HeLa cells and shown to possess two catalytic properties characteristic of the 5'-nuclease function of Escherichia coli DNA polymerase I |
| GO:0017108 5'-flap endonuclease activity | IMP PMID:11986308 Arginine residues 47 and 70 of human flap endonuclease-1 are... | ACCEPT | Summary: IMP of 5'-flap endonuclease activity from Arg-47/Arg-70 substitutions that reduce flap cleavage and shift the cleavage site. Reason: Mutational evidence that the assayed flap endonuclease activity is intrinsic to human FEN1 and depends on specific substrate-contacting residues. Supporting Evidence: PMID:11986308 Mutation of the Arg-70 significantly reduced flap endonuclease activity and eliminated exonuclease activity. |
| GO:0017108 5'-flap endonuclease activity | IMP PMID:8621570 Essential amino acids for substrate binding and catalysis of... | ACCEPT | Summary: IMP of 5'-flap endonuclease activity from alanine substitution of conserved active-site and substrate-binding residues. Reason: Establishes that the activity resides in FEN1's own active site: catalytic aspartate mutants lose cleavage while retaining substrate binding, and separate mutants lose binding. Supporting Evidence: PMID:8621570 Mutants D34A, D86A, and D181A lost their cleavage activity completely but retained substrate binding ability |
| GO:0003684 damaged DNA binding | TAS PMID:8007985 Structural and functional conservation of the human homolog ... | REMOVE | Summary: TAS of damaged DNA binding, traced to the 1994 paper that cloned the human homolog of S. pombe rad2. That study reported sequence conservation and complementation of UV sensitivity; it did not assay binding to damaged DNA. Reason: FEN1 is a structure-specific nuclease that recognizes the geometry of a double-flap junction, not chemically damaged bases; substrate discrimination is by branch structure, and it does not cleave substrates lacking the complete flap. No study establishes preferential binding of human FEN1 to damaged DNA, and the cited reference contains no such experiment. Supporting Evidence: PMID:8007985 Human cDNA has 55% amino acid sequence identity to the rad2 gene and is able to complement the UV sensitivity of the rad2 null mutant. PMID:8131753 Furthermore, efficient flap cleavage requires the presence of the entire flap structure. Substrates missing one strand are not cleaved by FEN-1. |
| GO:0003690 double-stranded DNA binding | TAS PMID:8131753 The characterization of a mammalian DNA structure-specific e... | ACCEPT | Summary: TAS of double-stranded DNA binding from the original mammalian FEN-1 characterization, whose exonuclease assays are duplex-specific. Reason: Supported by the requirement for the complete flap structure (including the annealed duplex) for cleavage and by the dsDNA specificity of the exonuclease mode. Supporting Evidence: PMID:8131753 In addition to endonuclease activity, FEN-1 has a 5'-3' exonuclease activity which is specific for double-stranded DNA. |
| GO:0004519 endonuclease activity | TAS PMID:8131753 The characterization of a mammalian DNA structure-specific e... | MODIFY | Summary: TAS of generic endonuclease activity from the paper that defined FEN-1 as a structure-specific flap endonuclease. Reason: The cited work established the far more specific activity - cleavage of flap strands terminating in a 5' single-stranded end, with no cleavage of Holliday junctions or incomplete flaps - so the generic parent term understates what the reference actually shows. Proposed replacements: 5'-flap endonuclease activity Supporting Evidence: PMID:8131753 The enzyme described here, flap endonuclease-1 (FEN-1), cleaves DNA flap strands that terminate with a 5' single-stranded end. |
| GO:0004527 exonuclease activity | TAS PMID:9778254 Structure of the DNA repair and replication endonuclease and... | MODIFY | Summary: TAS of generic exonuclease activity from the FEN-1 structural study. FEN1's exonuclease mode is specifically 5'-to-3' and duplex-directed. Reason: The directionality is well established and is what makes the activity biologically meaningful (it is the eukaryotic functional equivalent of the E. coli Pol I 5'-nuclease domain), so the undirected parent term should be replaced by GO:0008409. Proposed replacements: 5'-3' exonuclease activity Supporting Evidence: PMID:9778254 The conserved FEN-1 C terminus binds proliferating cell nuclear antigen (PCNA) and positions FEN-1 to act primarily as an exonuclease in DNA replication, in contrast to its endonuclease activity in DNA repair. |
| GO:0006260 DNA replication | TAS PMID:9778254 Structure of the DNA repair and replication endonuclease and... | MODIFY | Summary: TAS of DNA replication from the FEN-1 structure paper, which describes the replication role specifically as processing the 5' ends of Okazaki fragments. Reason: As for the IBA annotation, the general replication term understates a well-defined role restricted to Okazaki fragment maturation. Proposed replacements: DNA replication, Okazaki fragment processing Supporting Evidence: PMID:9778254 Flap endonuclease (FEN-1) removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. |
| GO:0006281 DNA repair | TAS PMID:8007985 Structural and functional conservation of the human homolog ... | ACCEPT | Summary: TAS of DNA repair traced to the cloning of the human S. pombe rad2 homolog, which complemented the UV-repair defect of a rad2 null mutant. Reason: The grouping term is appropriate for the evidence actually presented (restoration of DNA-damage recovery by the human cDNA) and is consistent with FEN1's established repair roles; the more specific base-excision repair terms are separately annotated. Supporting Evidence: PMID:8007985 Human cDNA has 55% amino acid sequence identity to the rad2 gene and is able to complement the UV sensitivity of the rad2 null mutant. |
| GO:0006302 double-strand break repair | TAS PMID:8131753 The characterization of a mammalian DNA structure-specific e... | KEEP AS NON CORE | Summary: TAS of double-strand break repair, reflecting the framing of the original FEN-1 characterization that DSB repair proceeds through flap intermediates. Reason: FEN1's contribution to DSB repair is limited to trimming displaced 5' flaps at end-joining intermediates (modelled explicitly in Reactome for MMEJ); it has no role in break sensing, resection or ligation. Retained as a genuine but non-core process. Supporting Evidence: PMID:8131753 As expected for an enzyme which functions in double-strand break repair flap resolution, FEN-1 cleavage is flap strand-specific and independent of flap strand length. |
| GO:0008309 double-stranded DNA exodeoxyribonuclease activity | TAS PMID:8131753 The characterization of a mammalian DNA structure-specific e... | MODIFY | Summary: TAS of double-stranded DNA exodeoxyribonuclease activity. The cited work showed this activity is both duplex-specific and 5'-to-3' directed. Reason: GO:0008309 omits directionality, which is the biologically decisive feature of FEN1's exonuclease mode. GO:0051908 (double-stranded DNA 5'-3' DNA exonuclease activity) captures exactly what the reference demonstrates. Proposed replacements: double-stranded DNA 5'-3' DNA exonuclease activity Supporting Evidence: PMID:8131753 In addition to endonuclease activity, FEN-1 has a 5'-3' exonuclease activity which is specific for double-stranded DNA. |
| GO:0009650 UV protection | TAS PMID:8007985 Structural and functional conservation of the human homolog ... | MARK AS OVER ANNOTATED | Summary: TAS of UV protection, derived from the ability of the human cDNA to rescue the UV sensitivity of an S. pombe rad2 null mutant. Reason: The only evidence is heterologous complementation of a fission yeast phenotype; no experiment shows that human FEN1 protects human cells from UV. Human FEN1 is not a nucleotide excision repair enzyme (that role belongs to its paralog XPG/ERCC5), so annotating 'UV protection' to FEN1 risks conflating the two family members. Supporting Evidence: PMID:8007985 Human cDNA has 55% amino acid sequence identity to the rad2 gene and is able to complement the UV sensitivity of the rad2 null mutant. |
| GO:0062176 R-loop processing | IDA PMID:36672839 Flap Endonuclease 1 Endonucleolytically Processes RNA to Res... | NEW | Summary: FEN1 endonucleolytically cleaves the RNA strand of R-loops, and is recruited to R-loops in human fibroblasts, resolving them through the base excision repair pathway. No R-loop process term is currently annotated to FEN1. Reason: This is a distinct biological process supported by direct evidence in human cells and in reconstituted assays, and it is the process context for FEN1's otherwise orphaned RNA-DNA hybrid ribonuclease activity (GO:0004523). Recruitment increases after oxidative DNA damage, tying the activity to BER. Supporting Evidence: PMID:36672839 We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. PMID:36672839 We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. PMID:36672839 Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity. |
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Download this section (compressed HTML)Q: Does the catalytically inactive mitochondrial isoform FENMIT (P39748-2) have a distinct biological role, and should isoform-resolved GO annotations separate it from the nuclease-competent isoform 1?
Q: Is the rat-derived 'memory' annotation projected onto human FEN1 supported by any direct evidence, or does it reflect a distal consequence of impaired genome maintenance in post-mitotic neurons?
Q: GO lacks a PCNA-binding molecular function term, so the functionally decisive FEN1-PCNA PIP-box interaction can only be recorded as 'protein binding'. Would a 'sliding clamp binding' or 'PCNA binding' MF term be warranted?
Q: Which of FEN1's non-canonical roles (telomeric C-strand processing, microhomology-mediated end joining, sister chromatid cohesion) reflect direct enzymatic participation versus indirect consequences of defective Okazaki fragment maturation?
Experiment: Separation-of-function alleles that uncouple the endonuclease, exonuclease and RNase H modes of FEN1, assayed for Okazaki fragment maturation, long-patch BER and R-loop resolution in the same cell background, to establish which activity each process actually requires.
Experiment: Isoform-selective depletion and re-expression of FENMIT versus isoform 1 to test whether the mitochondrial phenotypes attributed to FEN1 depend on nuclease activity or on RNA-flap binding alone.
Experiment: DRIP-seq or R-ChIP in FEN1-depleted cells with and without oxidative damage, to determine the genomic scope of FEN1-dependent R-loop resolution and whether it is restricted to BER-associated loci.
Experiment: Quantitative measurement of metal preference (Mg2+ versus Mn2+) for human FEN1 under physiological intracellular metal concentrations, to test whether the manganese-binding annotation reflects anything beyond in vitro substitution.
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