Affinage

FEN1

Flap endonuclease 1 · UniProt P39748

Length
380 aa
Mass
42.6 kDa
Annotated
2026-06-09
100 papers in source corpus 32 papers cited in narrative 32 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

FEN1 is a structure-specific, sequence-independent nuclease that recognizes, threads, and cleaves 5' flap DNA intermediates, serving as a central enzyme in DNA replication and repair (PMID:7926735, PMID:21496641). It carries flap endonuclease, 5'-3' double-stranded exonuclease, and gap-dependent endonuclease (GEN) activities within a single ~42 kDa enzyme (PMID:7876218, PMID:16582103). Substrate engagement requires the duplex template adjacent to the flap, and the enzyme tracks along the free single-stranded 5' tail to the cleavage point (PMID:7876218, PMID:8939893). Crystallographic and biophysical studies define a mechanism in which FEN1 binds and bends nicked dsDNA ~100°, captures the unpaired 3' flap, and threads the 5' ssDNA through a helical gateway/cap so that double-base unpairing at the scissile phosphate positions it over a two-metal-ion active site for precise incision (PMID:14718165, PMID:21496641, PMID:24234453). Through these activities FEN1 performs Okazaki fragment maturation and long-patch base excision repair, including LP-BER of oxidized abasic lesions in mitochondrial DNA, and contributes to stalled replication fork rescue, telomere maintenance, NHEJ, microhomology-mediated end joining, homologous recombination, and apoptotic DNA fragmentation (PMID:9990019, PMID:12840007, PMID:18541666, PMID:20551483, PMID:30686591). FEN1 is coordinated by partner proteins: PCNA stimulates its activity and promotes the open-flap conformation through two distinct binding modes, while WRN, RecQ helicases, and the 9-1-1 (Rad9-Hus1-Rad1) checkpoint clamp form alternative complexes that direct repair versus replication functions, and PARP1 is required for FEN1 recruitment to BER sites (PMID:8668533, PMID:10899134, PMID:20551483, PMID:22586102, PMID:22810208, PMID:24234453). FEN1 activity is timed by sequential post-translational modifications: arginine methylation (Arg192) suppresses Ser187 phosphorylation to favor PCNA binding, whereas an ordered phosphorylation→SUMOylation→ubiquitination cascade drives its proteasomal degradation (PMID:20729856, PMID:22749529). Loss or mutation of FEN1 causes genomic instability, aneuploidy, and cancer: disruption of the FEN1-PCNA interaction or of the FEN1-WRN interaction (E359K, ablating GEN activity) produces fragile telomeres, chromosomal anomalies, and tumors in knock-in mice, and inhibition of FEN1 selectively kills BRCA-deficient cells (PMID:21383776, PMID:24608430, PMID:30686591).

Mechanistic history

Synthesis pass · year-by-year structured walk · 26 steps
  1. 1994 High

    Established the foundational identity of FEN1 as a structure-specific endonuclease conserved across species, answering what kind of DNA structures it acts on.

    Evidence Gene cloning and in vitro nuclease assays on branched substrates, with conservation to yeast RAD27/RAD2

    PMID:7926735

    Open questions at the time
    • Catalytic mechanism and metal dependence not yet defined
    • In vivo pathway roles not yet assigned
  2. 1995 High

    Defined the substrate determinants of flap recognition and showed both endo- and exonuclease activities reside in one enzyme, clarifying how FEN1 selects its targets.

    Evidence Mobility shift and nuclease assays with defined flap substrate variants including the adjacent strand

    PMID:7876218

    Open questions at the time
    • Structural basis of dual activity unresolved
    • Loading mechanism onto substrate undefined
  3. 1996 High

    Identified PCNA as a stimulatory partner and revealed FEN1 loads by tracking along the 5' ssDNA branch, connecting FEN1 to the replication machinery and explaining its directional engagement.

    Evidence Physical association assays plus nuclease stimulation assays and footprinting on adducted substrates

    PMID:8668533 PMID:8939893

    Open questions at the time
    • Molecular structure of the PCNA-FEN1 interface not yet solved
    • Two-mode PCNA binding not yet distinguished
  4. 1999 High

    Connected FEN1 cleavage failure on repeat-derived secondary structures to repeat expansion, and assigned FEN1 a role in NHEJ via 5' flap processing, expanding its pathway repertoire beyond replication.

    Evidence In vitro cleavage with repeat-containing flaps plus yeast genetics; rad27 deletion NHEJ epistasis with flap substrates

    PMID:10635332 PMID:9990019

    Open questions at the time
    • Direct in vivo evidence for expansion mechanism in mammals lacking
    • NHEJ partner proteins not yet identified
  5. 2002 Medium

    Showed WRN stimulates FEN1 catalytic efficiency independent of substrate binding and even on end-blocked substrates, distinguishing WRN-mediated from PCNA-mediated activation.

    Evidence Biochemical kinetics with multiple Okazaki intermediates and streptavidin-blocked substrates

    PMID:12356323

    Open questions at the time
    • Structural basis of WRN stimulation unknown
    • Cellular context of WRN-FEN1 cooperation not yet established
  6. 2003 High

    Revealed a gap-dependent endonuclease (GEN) activity and cooperation with EndoG in apoptotic DNA fragmentation, broadening FEN1's functional scope to programmed cell death.

    Evidence RNAi and genetic epistasis in C. elegans with biochemical GEN characterization

    PMID:12840007

    Open questions at the time
    • Relevance of GEN activity to mammalian apoptosis not yet shown
    • Substrate basis of GEN versus FEN activity unresolved
  7. 2004 High

    Provided the first structural mechanism—3' flap binding, DNA kinking, and helical clamp closure plus an intermolecular beta-sheet linking PCNA and DNA-binding regions—explaining how FEN1 achieves specificity and is coordinated by PCNA.

    Evidence X-ray crystallography of FEN1:DNA and PCNA:FEN1-peptide complexes, FRET, mutagenesis

    PMID:14718165

    Open questions at the time
    • Conformation of the threaded 5' flap not captured
    • Two distinct PCNA binding modes not structurally reconciled
  8. 2004 Medium

    Reconstituted FEN1 within an ordered series of NHEJ pairwise interactions with Pol4 and Dnl4/Lif1, defining its biochemical place in end joining of incompatible ends.

    Evidence Physical interaction assays and in vitro end-joining reconstitution in S. cerevisiae

    PMID:15342630

    Open questions at the time
    • Conservation of these interactions in mammals not demonstrated
    • Single-lab interaction data without structural detail
  9. 2006 Medium

    Mapped the GEN activity to the same clamp/ssDNA-interaction region used by FEN activity and implicated the C-terminal extension in downstream duplex contact, unifying the multiple activities mechanistically.

    Evidence Comparative kinetics of FEN/EXO/GEN with DNA-binding-deficient mutants and WRN

    PMID:16582103

    Open questions at the time
    • Structural snapshot of GEN engagement absent
    • In vivo importance of GEN activity not yet tested with separation-of-function alleles
  10. 2005 Medium

    Placed FEN1 downstream of p53 in the stalled-fork recovery response, establishing transcriptional regulation of FEN1 by a tumor suppressor.

    Evidence Promoter reporter assays, ChIP of p53 binding, and replication-recovery rescue in p53-null cells

    PMID:16103874

    Open questions at the time
    • Direct contribution of FEN1 enzymatic activity to fork recovery not dissected
    • Single-lab transcriptional data
  11. 2008 High

    Localized FEN1 to mitochondria and showed it is required for long-patch BER of oxidized abasic sites in mtDNA, extending its repair role to the mitochondrial genome.

    Evidence Subcellular fractionation, immunofluorescence, protease protection, immunodepletion, and RNAi damage-recovery assays

    PMID:18541666

    Open questions at the time
    • Mitochondrial import mechanism not defined
    • Mitochondrial partner proteins not identified
  12. 2009 Medium

    Demonstrated that uncoupling of pol beta–FEN1 coordination during LP-BER allows FEN1 to ligate slipped hairpins, providing a repair-pathway mechanism for CAG repeat expansion.

    Evidence In vitro repeat-expansion reconstitution in mouse cell extracts dissecting individual enzymes including HMGB1 stimulation

    PMID:19674974

    Open questions at the time
    • In vivo confirmation in mammalian tissue lacking
    • Determinants of pol beta–FEN1 uncoupling unclear
  13. 2010 High

    Showed arginine methylation at Arg192 suppresses Ser187 phosphorylation to favor PCNA binding and proper foci localization, establishing PTM-controlled timing of FEN1 activity.

    Evidence Mass spectrometry, mutagenesis, PCNA co-IP, immunofluorescence, and cell-cycle/mutation-rate readouts

    PMID:20729856

    Open questions at the time
    • Identity of the responsible methyltransferase not established in this study
    • Phosphatase counteracting Ser187 unknown
  14. 2010 Medium

    Distinguished FEN1's telomere maintenance role as dependent on GEN activity and RecQ helicase interaction rather than Okazaki processing, refining which activities matter at telomeres.

    Evidence siRNA depletion with fragile/sister telomere assays and activity-specific FEN1 mutants

    PMID:20551483

    Open questions at the time
    • Which RecQ helicase predominates not resolved
    • Direct telomeric substrate not defined
  15. 2011 High

    Delivered the definitive human FEN1:DNA structural mechanism—~100° bending, dual-flap capture, helical gateway threading, double-base unpairing, and two-metal-ion catalysis—explaining structure-specific, sequence-independent incision.

    Evidence X-ray crystallography of FEN1:DNA substrate and product complexes with mutagenesis and functional assays

    PMID:21496641

    Open questions at the time
    • Dynamics of gateway opening not captured statically
    • Allosteric coupling to PCNA not fully resolved
  16. 2011 High

    Linked the FEN1-PCNA interaction directly to genome stability and cancer in vivo through a separation-of-function knock-in, demonstrating causal consequence of losing this interaction.

    Evidence FFAA knock-in mouse with BER/Okazaki biochemistry, cytogenetics, checkpoint, and tumor readouts

    PMID:21383776

    Open questions at the time
    • Tissue-specific tumor spectrum not fully explained
    • Contribution of residual activities not isolated
  17. 2011 Medium

    Uncovered a crosstalk between FEN1-mediated DNA damage response and cytoskeletal signaling (p38, RhoA, actin) in response to genotoxin, broadening FEN1's cellular consequences.

    Evidence Yeast mutant screen validated by human FEN1 siRNA with signaling and cytoskeleton readouts

    PMID:21807938

    Open questions at the time
    • Direct molecular link between FEN1 and signaling not defined
    • Generality beyond CDT genotoxin untested
  18. 2012 High

    Defined a sequential phosphorylation→SUMOylation→ubiquitination cascade controlling FEN1 proteasomal degradation, providing the off-switch that times FEN1 turnover with the cell cycle.

    Evidence PTM biochemistry, mutant FEN1 expression, proteasome inhibitor and cell-cycle analyses

    PMID:22749529

    Open questions at the time
    • Specific E3 ligase and SUMO ligase not identified here
    • Spatial coordination with chromatin not defined
  19. 2012 Medium

    Showed FEN1 forms a more stable complex with the 9-1-1 checkpoint clamp than with PCNA, suggesting clamp-specific partitioning between repair and replication.

    Evidence Single-particle EM reconstruction (18 Å) plus molecular dynamics simulations

    PMID:22586102

    Open questions at the time
    • High-resolution structure of the 9-1-1/FEN1 complex lacking
    • Functional consequence of differential stability not tested in vivo
  20. 2012 High

    Established that PARP1 is required for FEN1 recruitment to BER sites in living cells, defining the recruitment step for FEN1 at damage.

    Evidence Endogenous FEN1-YFP knock-in, live-cell laser microirradiation, and PARP1 inhibition

    PMID:22810208

    Open questions at the time
    • Direct PARP1-FEN1 physical contact not demonstrated
    • Role of PAR chains versus protein interaction unresolved
  21. 2013 Medium

    Revealed at single-molecule level that FEN1 bends and locks DNA into an open-flap state and that PCNA promotes 5' ssDNA threading through the gateway, mechanistically explaining PCNA stimulation.

    Evidence Single-molecule FRET, protein-induced fluorescence enhancement, and ensemble FRET

    PMID:24234453

    Open questions at the time
    • Kinetics relative to in vivo replication rates not established
    • Threading intermediate not structurally captured
  22. 2014 High

    Demonstrated via the E359K germline mutation that the FEN1-WRN interaction and GEN activity are jointly required for stalled-fork resolution and tumor suppression, separating these from flap endonuclease activity.

    Evidence Knock-in mouse, co-IP, activity assays, cytogenetics, and tumor incidence

    PMID:24608430

    Open questions at the time
    • Molecular basis for E359K disrupting both interaction and GEN activity unresolved
    • Human germline relevance not established
  23. 2016 Medium

    Showed the cancer-associated L209P mutation abolishes all nuclease activities while retaining DNA binding, acting dominant-negatively to impair wild-type FEN1 and drive transformation.

    Evidence Biochemical activity/binding assays, dominant-negative cellular expression, in vitro BER, and xenograft

    PMID:27270424

    Open questions at the time
    • Structural basis of catalytic-dead-but-binding phenotype not defined
    • Human tumor frequency of L209P unestablished
  24. 2019 High

    Identified FEN1 flap endonuclease activity as a synthetic-lethal vulnerability in BRCA-deficient cells via MMEJ, nominating FEN1 inhibition as a targeted therapeutic strategy.

    Evidence CRISPR screens in isogenic BRCA2-deficient lines, MMEJ reporter, activity-specific mutants, and a small-molecule inhibitor

    PMID:30686591

    Open questions at the time
    • FEN1 partners in MMEJ not identified
    • Inhibitor specificity and in vivo efficacy not fully defined here
  25. 2019 Low

    Proposed a non-canonical oncogenic role in which a FEN1/PCNA/DNMT3a complex epigenetically suppresses miR-200a-5p to derepress MET/EGFR, linking FEN1 to breast cancer proliferation.

    Evidence Co-IP, luciferase reporters, methylation-specific PCR, and siRNA knockdown

    PMID:31266372

    Open questions at the time
    • Single Co-IP without reciprocal or structural validation of the complex
    • Direct DNA methylation role of FEN1 not mechanistically established
  26. 2020 Medium

    Identified post-transcriptional and transcriptional-cofactor roles supporting FEN1's oncogenic expression—m6A-IGF2BP2 stabilization of FEN1 mRNA, PRMT1 methylation maintaining FEN1 levels, and FEN1 facilitating ERα coactivator recruitment.

    Evidence RIP and mRNA stability (IGF2BP2), co-IP and knockdown (PRMT1), and ERα co-IP/coactivator and inhibitor assays

    PMID:32193286 PMID:32861926 PMID:33224879

    Open questions at the time
    • IGF2BP2 and PRMT1 findings rest on single-method, single-lab data
    • Mechanism of FEN1-ERα coactivator facilitation not structurally defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How FEN1's many activities and partner complexes are spatially and temporally partitioned among replication, BER, telomere maintenance, end joining, and its proposed transcriptional/epigenetic roles in vivo remains unresolved.
  • No unified model assigning specific complexes to specific pathways in cells
  • Non-canonical transcriptional/epigenetic roles lack high-confidence mechanistic validation
  • The methyltransferase, E3, and SUMO ligase enzymes of the PTM cascade not all identified

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140097 catalytic activity, acting on DNA 4 GO:0003677 DNA binding 3 GO:0016787 hydrolase activity 2
Localization
GO:0005634 nucleus 2 GO:0005739 mitochondrion 1
Pathway
R-HSA-69306 DNA Replication 3 R-HSA-73894 DNA Repair 3 R-HSA-5357801 Programmed Cell Death 1
Partners
DNL4/LIF1IGF2BP2PARP1PCNAPOL4PRMT1RAD9-HUS1-RAD1WRN
Complex memberships
9-1-1 (Rad9-Hus1-Rad1) checkpoint clampFEN1/PCNA/DNMT3a complex

Evidence

Reading pass · 32 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 FEN-1 is a structure-specific endonuclease that cleaves DNA flap structures (5' flap and pseudo Y-structures); the murine FEN-1 gene was cloned and shown to be homologous to S. cerevisiae YKL510 (RAD27) and RAD2. YKL510 and a truncated RAD2 protein were also demonstrated to be structure-specific endonucleases with similar substrate specificity. Gene cloning, in vitro nuclease assays with branched DNA substrates Genes & development High 7926735
1995 FEN-1 binding and cleavage of flap DNA structures requires the adjacent (Fadj) strand that provides a double-stranded template near the elbow of the flap; absence or recession of this strand dramatically reduces binding efficiency. FEN-1 possesses both 5'-flap endonuclease and double-stranded DNA 5'-exonuclease activity within the same 42 kDa enzyme. Mobility shift assay, in vitro nuclease assays with defined DNA substrates The Journal of biological chemistry High 7876218
1996 Human PCNA physically associates with human FEN-1 and stimulates its endonucleolytic activity at branched DNA (flap) structures and its exonucleolytic activity at nick and gap structures. PCNA loads onto substrates at double-stranded DNA ends, while FEN-1 loads by tracking along the single-stranded DNA branch from its free 5' terminus. Physical association (co-purification/interaction assays), in vitro nuclease stimulation assays with defined DNA substrates Nucleic acids research High 8668533
1996 FEN-1 (RAD2 homologue 1) tracks along the single-stranded 5' tail of a flap substrate from its 5' end to the cleavage point, protecting a ~25 nucleotide region adjacent to the cleavage site, and can cleave past adducts (CDDP) located within or beyond the protected region, but is inhibited by an adduct immediately adjacent to the cleavage point. Micrococcal nuclease footprinting, in vitro cleavage assays with site-specifically adducted DNA substrates The Journal of biological chemistry Medium 8939893
1999 DNA secondary structures formed at trinucleotide repeat sequences (CAG, CGG, CTG) inhibit FEN-1 cleavage in a length-dependent manner by concealing the 5' end of the flap required for FEN-1 binding and cleavage, providing a mechanism for repeat expansion. In vitro FEN-1 cleavage assays with repeat-containing flap substrates; genetic studies in yeast lacking FEN-1 Molecular cell High 10635332
1999 Deletion of RAD27 (yeast FEN-1) leads to a 4.4-fold reduction specifically in NHEJ events predicted to proceed via 5' flap intermediates, establishing a role for FEN-1 in non-homologous DNA end joining through processing of 5' flap structures that arise after end alignment. Genetic epistasis in S. cerevisiae; NHEJ assay with specific substrates in rad27 deletion strains Proceedings of the National Academy of Sciences of the United States of America Medium 9990019
2000 FEN1 interacts with PCNA through two distinct modes: in solution (without DNA), FEN1 binds primarily through the PCNA interdomain connector loop (IDCL); when PCNA encircles DNA, the C-terminal domain of PCNA (not the IDCL) is critical for FEN1 binding and stimulation of activity. An FF→GA mutation in FEN1's PCNA-interaction domain abolishes both modes and causes replication and repair defects in vivo. Yeast genetics with PCNA mutants (pcna-79, pcna-90), DNA-bead retention assay, FEN1 mutagenesis, in vivo complementation The EMBO journal High 10899134
2002 WRN protein physically interacts with FEN-1 and stimulates its cleavage activity by enhancing catalytic efficiency rather than DNA substrate binding. WRN stimulates FEN-1 on multiple Okazaki fragment processing intermediates including flaps with terminal monoribonucleotides, long 5' ssDNA tracts, and pseudo-Y structures, and does so even when a free upstream end is blocked (unlike PCNA-mediated stimulation). Biochemical kinetics of FEN-1 cleavage in the presence/absence of WRN, substrate binding assays, streptavidin-blocked substrate experiments Biochemistry Medium 12356323
2003 C. elegans CRN-1 (FEN-1 homolog) cooperates with CPS-6/EndoG to promote apoptotic DNA degradation. CRN-1 utilizes its 5'-3' exonuclease activity and a newly identified gap-dependent endonuclease (GEN) activity together with CPS-6 endonuclease activity for stepwise DNA fragmentation during apoptosis. RNAi knockdown in C. elegans, genetic interaction with cps-6 mutant, biochemical characterization of GEN activity The EMBO journal High 12840007
2004 Crystal structures of FEN-1:DNA and PCNA:FEN-1-peptide complexes reveal that FEN-1 binds the unpaired 3' DNA end (3' flap), opens and kinks DNA, and promotes conformational closing of a flexible helical clamp to facilitate 5' cleavage specificity. Ordering of unstructured C-terminal regions in FEN-1 and PCNA creates an intermolecular beta-sheet interface directly linking PCNA and DNA binding regions of FEN-1. FRET and mutagenesis support a kinked DNA pivot point for coordinated handoffs. X-ray crystallography, FRET, site-directed mutagenesis Cell High 14718165
2004 In S. cerevisiae NHEJ, FEN-1 (Rad27) physically and functionally interacts with Pol4 and Dnl4/Lif1, and together these proteins coordinately process and join DNA molecules with incompatible 5' ends, establishing a series of pairwise interactions that complete DSB repair by NHEJ. Physical interaction assays (co-immunoprecipitation/pulldown), in vitro end-joining reconstitution with defined substrates The Journal of biological chemistry Medium 15342630
2005 FEN-1-deficient chicken DT40 cells show decreased efficiency of immunoglobulin gene conversion (HR between divergent sequences) but are proficient in sister chromatid recombination, indicating FEN-1 eliminates heterologous sequences at DNA break sites to facilitate HR. This was confirmed by I-SceI-induced DSB experiments with divergent donor/recipient substrates. Gene knockout in chicken DT40 cells, I-SceI-induced recombination assays, gene conversion frequency measurement Molecular and cellular biology Medium 16055708
2006 FEN-1's gap endonuclease (GEN) activity uses the same clamp region that FEN activity uses to interact with single-stranded DNA substrates. The C-terminal extension of human FEN-1 likely interacts with the downstream duplex in all substrate types, and GEN activity in complex with WRN can cleave hairpin and internal loop substrates, suggesting a role in preventing repeat expansions. Kinetic analysis of FEN, EXO, and GEN activities; DNA-binding deficient FEN1 mutants; biochemical assays with WRN Nucleic acids research Medium 16582103
2008 FEN1 is present in human mitochondria (confirmed by protease protection of mitochondria, immunofluorescence, and subcellular fractionation) and participates in long-patch base excision repair (LP-BER) of oxidized abasic sites (2-deoxyribonolactone) in mitochondrial DNA. Immunodepletion of FEN1 from mitochondrial extracts strongly diminishes LP-BER activity. Subcellular fractionation, immunofluorescence, protease protection assay, immunodepletion of mitochondrial extracts, RNAi knockdown with damage recovery assay Molecular and cellular biology High 18541666
2009 FEN1 promotes CAG repeat expansion during long-patch BER by facilitating ligation of hairpins formed by strand slippage, resulting from uncoupling of normal pol beta–FEN1 coordination during multinucleotide gap-filling synthesis. HMGB1 promotes expansion by stimulating APE1 and FEN1. In vitro reconstitution of repeat expansion using mouse cell extracts; biochemical assays dissecting individual enzyme contributions The Journal of biological chemistry Medium 19674974
2010 FEN1 is methylated at arginine residues (primarily Arg192) by an arginine methyltransferase; this methylation suppresses phosphorylation at Ser187. The methylated form (but not the phosphorylated form) strongly interacts with PCNA, ensuring proper timing of FEN1 activity. Mutations disrupting arginine methylation cause unscheduled phosphorylation, failure to localize to DNA replication/repair foci, defects in Okazaki fragment maturation, cell cycle delay, impaired DNA repair, and elevated genome-wide mutation rates. Mass spectrometry identification of methylation sites, site-directed mutagenesis, co-immunoprecipitation with PCNA, immunofluorescence localization, cell cycle analysis Nature chemical biology High 20729856
2010 FEN1 is required for efficient replication fork re-initiation at telomeres. FEN1 gap endonuclease activity (not Okazaki fragment processing activity) and the FEN1 interaction with RecQ helicases are vital for telomere stability, as FEN1 depletion causes fragile telomere expression and sister telomere loss. FEN1 siRNA depletion, fragile telomere and sister telomere loss assays, functional dissection using FEN1 activity mutants The Journal of biological chemistry Medium 20551483
2011 Crystal structures and functional analyses of human FEN1:DNA complexes reveal structure-specific, sequence-independent recognition: FEN1 binds nicked dsDNA bent ~100° with unpaired 3' and 5' flaps. A helical cap over a gateway formed by two helices enforces ssDNA threading and specificity for free 5' ends. Double-base unpairing flanking the scissile phosphate and the two-metal-ion active site control precise flap incision. X-ray crystallography of FEN1:DNA product and substrate complexes, mutagenesis, functional assays Cell High 21496641
2011 A FEN1 point mutation (F343A/F344A, FFAA) that specifically abolishes the FEN1/PCNA interaction causes defects in RNA primer removal and long-patch BER, resulting in DNA breaks, G2/M checkpoint activation (via Chk1), near-tetraploid aneuploidy, elevated cellular transformation frequency, and cancer in knock-in mice. Knock-in mouse model, biochemical assays for BER and Okazaki fragment processing, cytogenetic analysis, transformation assays Cell research High 21383776
2012 FEN1 undergoes sequential post-translational modifications controlling its proteasomal degradation: phosphorylation stimulates SUMOylation, which in turn stimulates ubiquitination and proteasomal degradation. Blocking any step in this cascade suppresses FEN1 degradation and causes accumulation of Cyclin B, G1/G2M phase delays, and polyploidy. Biochemical characterization of PTMs, mutant FEN1 expression, cell cycle analysis, proteasome inhibitor experiments Molecular cell High 22749529
2012 FEN1 forms a complex with the checkpoint clamp Rad9-Hus1-Rad1 (9-1-1) in addition to PCNA. The 9-1-1/FEN1/DNA assembly has greater stability than the PCNA/FEN1/DNA complex, as determined by 3D electron microscopy reconstruction at 18-Å resolution combined with molecular dynamics simulations, consistent with distinct roles in DNA repair versus replication. Single-particle electron microscopy, molecular dynamics simulations, computational modeling Proceedings of the National Academy of Sciences of the United States of America Medium 22586102
2012 Endogenous FEN1-YFP rapidly accumulates at local laser-induced DNA damage sites in living cells. PARP1 inhibition disrupts FEN1 accumulation at DNA repair intermediates, establishing that PARP1 is required for FEN1 recruitment to BER sites. Fluorescent knock-in mouse model (FEN1-YFP), live-cell multi-photon fluorescence microscopy, PARP1 inhibitor treatment Nucleic acids research High 22810208
2014 The FEN1 E359K germline mutation abolishes the FEN1-WRN interaction (critical for resolving stalled replication forks) and eliminates FEN1 gap-dependent endonuclease (GEN) activity while leaving flap endonuclease activity intact. E359K mouse embryonic fibroblasts are hypersensitive to DNA crosslinking agents, show fragile telomeres and increased chromosomal anomalies, and E359K homozygous mice develop cancer at high frequency. Knock-in mouse model, co-immunoprecipitation, in vitro biochemical activity assays, cytogenetic analysis, tumor incidence measurement Oncogene High 24608430
2013 Single-molecule FRET and protein-induced fluorescence enhancement studies reveal that upon FEN1 binding, a flap DNA substrate is bent and locked into an open flap conformation. PCNA enhances FEN1 recognition by further promoting the open flap conformation, likely by facilitating threading of the 5' ssDNA flap through the helical gateway. Single-molecule FRET, protein-induced fluorescence enhancement, ensemble FRET Nucleic acids research Medium 24234453
2016 The cancer-associated FEN1 L209P mutation abolishes FEN, EXO, and GEN nuclease activities but retains DNA-binding affinity, acting in a dominant-negative manner to impair wild-type FEN1 function and long-patch BER in vitro and in vivo, leading to genomic instability and cellular transformation. Biochemical activity assays, DNA binding assays, dominant-negative expression in cells, in vitro BER assays, mouse xenograft Oncogene Medium 27270424
2019 FEN1 participates in microhomology-mediated end-joining (MMEJ); BRCA2-deficient cells require specifically the 5' flap endonuclease activity (not the 5'-3' exonuclease activity) of FEN1, and chemical inhibition of FEN1 selectively targets BRCA-deficient cells. CRISPR-based genetic screens in isogenic BRCA2-deficient cell lines, MMEJ reporter assay, FEN1 activity-specific mutants, small-molecule FEN1 inhibitor Molecular cell High 30686591
2019 FEN1 promotes breast cancer cell proliferation via formation of a FEN1/PCNA/DNMT3a complex that suppresses miR-200a-5p expression through DNA methylation, thereby allowing expression of miR-200a target genes MET and EGFR. Co-immunoprecipitation (FEN1-PCNA-DNMT3a complex), luciferase reporter (miR-200a target sites), methylation-specific PCR, siRNA knockdown FASEB journal Low 31266372
2020 IGF2BP2 directly recognizes and binds the m6A site on FEN1 mRNA, enhancing FEN1 mRNA stability and thereby maintaining FEN1 protein expression in HCC cells. RNA immunoprecipitation (RIP), m6A site mapping, IGF2BP2 overexpression/knockdown with FEN1 mRNA stability measurement Frontiers in oncology Low 33224879
2020 FEN1 blockade induces proteasome-mediated degradation of activated ERα and loss of ERα-driven gene expression. FEN1 facilitates coactivator recruitment to the ERα transcriptional complex, thereby impacting ERα transcriptional activity and driving tumor cell proliferation in tamoxifen-resistant breast cancer. FEN1 siRNA depletion, ERα co-immunoprecipitation/coactivator recruitment assays, proteasome inhibitor rescue, small-molecule FEN1 inhibitor screen, proliferation assays Cancer research Medium 32193286
2020 PRMT1 methylates FEN1 as a post-translational modification, maintaining high FEN1 expression levels critical for DNA repair and chemotherapeutic drug resistance in lung cancer cells. PRMT1 knockdown with FEN1 protein level measurement, identification of FEN1 as PRMT1 substrate by co-immunoprecipitation DNA repair Low 32861926
2011 FEN1 regulates cell survival, MAPK p38 phosphorylation, RhoA activation, and actin cytoskeleton reorganization in response to DNA damage triggered by bacterial CDT genotoxin, revealing a crosstalk between DNA damage response and cytoskeleton dynamics mediated by FEN1. S. cerevisiae mutant screen, human cell FEN1 siRNA knockdown, RhoA activation assay, p38 phosphorylation measurement, actin cytoskeleton imaging Journal of cell science Medium 21807938
2005 p53 transcriptionally activates FEN1 expression via a p53 consensus binding site in the fen1 promoter. FEN1 induction by UV-C requires p53 and replication-competent cells. Transgenic FEN1 expression in p53-null cells attenuates UV-C-induced DNA replication inhibition, establishing FEN1 as involved in recovery from stalled replication forks downstream of p53. RT-PCR, Western blot, promoter cloning and reporter assays, ChIP (p53 binding to fen1 promoter), transgenic FEN1 expression in p53-null cells, DNA replication recovery assay Oncogene Medium 16103874

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1997 The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. BioEssays : news and reviews in molecular, cellular and developmental biology 385 9080773
1998 The forkhead/winged helix gene Mf1 is disrupted in the pleiotropic mouse mutation congenital hydrocephalus. Cell 312 9635428
1994 Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes & development 278 7926735
2000 Murine forkhead/winged helix genes Foxc1 (Mf1) and Foxc2 (Mfh1) are required for the early organogenesis of the kidney and urinary tract. Development (Cambridge, England) 276 10704385
2011 Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 247 21496641
1995 Characterization of a mutant strain of Saccharomyces cerevisiae with a deletion of the RAD27 gene, a structural homolog of the RAD2 nucleotide excision repair gene. Journal of bacteriology 238 7814325
2004 Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 237 14718165
1996 Processing of branched DNA intermediates by a complex of human FEN-1 and PCNA. Nucleic acids research 187 8668533
2010 Functional regulation of FEN1 nuclease and its link to cancer. Nucleic acids research 186 20929870
2019 Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets. Molecular cell 170 30686591
2008 Removal of oxidative DNA damage via FEN1-dependent long-patch base excision repair in human cell mitochondria. Molecular and cellular biology 168 18541666
1996 Structure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins. Cell 168 8674116
1999 The RAD2 domain of human exonuclease 1 exhibits 5' to 3' exonuclease and flap structure-specific endonuclease activities. The Journal of biological chemistry 156 10608837
1994 Structural and functional conservation of the human homolog of the Schizosaccharomyces pombe rad2 gene, which is required for chromosome segregation and recovery from DNA damage. Molecular and cellular biology 149 8007985
1999 Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Molecular cell 148 10635332
1999 A role for FEN-1 in nonhomologous DNA end joining: the order of strand annealing and nucleolytic processing events. Proceedings of the National Academy of Sciences of the United States of America 147 9990019
1999 Roles for the winged helix transcription factors MF1 and MFH1 in cardiovascular development revealed by nonallelic noncomplementation of null alleles. Developmental biology 145 10479458
1999 The forkhead/winged-helix gene, Mf1, is necessary for the normal development of the cornea and formation of the anterior chamber in the mouse eye. Developmental biology 142 10395790
2000 Two modes of FEN1 binding to PCNA regulated by DNA. The EMBO journal 134 10899134
1993 Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature 130 8247134
2020 IGF2BP2 Promotes Liver Cancer Growth Through an m6A-FEN1-Dependent Mechanism. Frontiers in oncology 128 33224879
2005 Multiple but dissectible functions of FEN-1 nucleases in nucleic acid processing, genome stability and diseases. BioEssays : news and reviews in molecular, cellular and developmental biology 123 15954100
2010 Methylation of FEN1 suppresses nearby phosphorylation and facilitates PCNA binding. Nature chemical biology 115 20729856
2003 CRN-1, a Caenorhabditis elegans FEN-1 homologue, cooperates with CPS-6/EndoG to promote apoptotic DNA degradation. The EMBO journal 105 12840007
2009 Coordination between polymerase beta and FEN1 can modulate CAG repeat expansion. The Journal of biological chemistry 101 19674974
1998 Hex1: a new human Rad2 nuclease family member with homology to yeast exonuclease 1. Nucleic acids research 100 9685493
1986 Nucleotide sequence, transcript mapping, and regulation of the RAD2 gene of Saccharomyces cerevisiae. Journal of bacteriology 91 3011752
2017 FEN1 promotes tumor progression and confers cisplatin resistance in non-small-cell lung cancer. Molecular oncology 89 28371273
2012 Sequential posttranslational modifications program FEN1 degradation during cell-cycle progression. Molecular cell 87 22749529
1999 Pleiotropic skeletal and ocular phenotypes of the mouse mutation congenital hydrocephalus (ch/Mf1) arise from a winged helix/forkhead transcriptionfactor gene. Human molecular genetics 85 10072431
1995 DNA structural elements required for FEN-1 binding. The Journal of biological chemistry 84 7876218
2019 MicroRNA-140 impedes DNA repair by targeting FEN1 and enhances chemotherapeutic response in breast cancer. Oncogene 83 31471584
2020 FEN1 endonuclease as a therapeutic target for human cancers with defects in homologous recombination. Proceedings of the National Academy of Sciences of the United States of America 76 32719125
2002 Requirement of yeast RAD2, a homolog of human XPG gene, for efficient RNA polymerase II transcription. implications for Cockayne syndrome. Cell 75 12110180
2009 Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk. Human mutation 71 19618370
2003 Increased expression and no mutation of the Flap endonuclease (FEN1) gene in human lung cancer. Oncogene 65 14562054
1994 Yeast nucleotide excision repair proteins Rad2 and Rad4 interact with RNA polymerase II basal transcription factor b (TFIIH). Molecular and cellular biology 65 8196602
2010 FEN1 ensures telomere stability by facilitating replication fork re-initiation. The Journal of biological chemistry 64 20551483
1995 Sequence of human FEN-1, a structure-specific endonuclease, and chromosomal localization of the gene (FEN1) in mouse and human. Genomics 63 7774922
2003 Nuclease-deficient FEN-1 blocks Rad51/BRCA1-mediated repair and causes trinucleotide repeat instability. Molecular and cellular biology 62 12917330
2002 Biochemical characterization of the WRN-FEN-1 functional interaction. Biochemistry 62 12356323
2005 Fen-1 facilitates homologous recombination by removing divergent sequences at DNA break ends. Molecular and cellular biology 61 16055708
2015 YY1 suppresses FEN1 over-expression and drug resistance in breast cancer. BMC cancer 57 25885449
2018 Curcumin increases breast cancer cell sensitivity to cisplatin by decreasing FEN1 expression. Oncotarget 55 29541412
1999 Expression of the Mf1 gene in developing mouse hearts: implication in the development of human congenital heart defects. Developmental dynamics : an official publication of the American Association of Anatomists 55 10474162
2002 Vertebrate cells lacking FEN-1 endonuclease are viable but hypersensitive to methylating agents and H2O2. Nucleic acids research 53 12136109
1992 Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1 and the BAF1 loci and reveals one tRNA gene and several new open reading frames including homologs to RAD2 and kinases. Yeast (Chichester, England) 51 1561835
1996 Transcription factor TFIIH and DNA endonuclease Rad2 constitute yeast nucleotide excision repair factor 3: implications for nucleotide excision repair and Cockayne syndrome. Proceedings of the National Academy of Sciences of the United States of America 49 8855246
2012 Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proceedings of the National Academy of Sciences of the United States of America 48 22586102
2011 Fen1 mutations that specifically disrupt its interaction with PCNA cause aneuploidy-associated cancer. Cell research 48 21383776
1994 A conserved 5' to 3' exonuclease activity in the yeast and human nucleotide excision repair proteins RAD2 and XPG. The Journal of biological chemistry 48 7989298
1995 Structure-specific nuclease activity in yeast nucleotide excision repair protein Rad2. The Journal of biological chemistry 47 8530429
1984 Saccharomyces cerevisiae RAD2 gene: isolation, subcloning, and partial characterization. Molecular and cellular biology 45 6366519
2002 DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro. The Journal of biological chemistry 44 11948189
1996 Mechanism of tracking and cleavage of adduct-damaged DNA substrates by the mammalian 5'- to 3'-exonuclease/endonuclease RAD2 homologue 1 or flap endonuclease 1. The Journal of biological chemistry 44 8939893
1989 Regulation of the RAD2 gene of Saccharomyces cerevisiae. Molecular microbiology 44 2695743
2022 Small-Molecule Inhibitors Targeting FEN1 for Cancer Therapy. Biomolecules 43 35883563
2001 Minimal ischaemic neuronal damage and HSP70 expression in MF1 strain mice following bilateral common carotid artery occlusion. Brain research 43 11578611
2019 FEN1 mediates miR-200a methylation and promotes breast cancer cell growth via MET and EGFR signaling. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 41 31266372
2004 Processing and joining of DNA ends coordinated by interactions among Dnl4/Lif1, Pol4, and FEN-1. The Journal of biological chemistry 40 15342630
1985 The RAD2 gene of Saccharomyces cerevisiae: nucleotide sequence and transcript mapping. Gene 40 3000874
2006 The DNA-protein interaction modes of FEN-1 with gap substrates and their implication in preventing duplication mutations. Nucleic acids research 39 16582103
2021 Dual-Mode FEN1 Activity Detection Based on Nt.BstNBI-Induced Tandem Signal Amplification. Analytical chemistry 38 33847477
2021 Precision Spherical Nucleic Acids Enable Sensitive FEN1 Imaging and Controllable Drug Delivery for Cancer-Specific Therapy. Analytical chemistry 38 34342424
1998 Expression of the mouse Fkh1/Mf1 and Mfh1 genes in late gestation embryos is restricted to mesoderm derivatives. Mechanisms of development 38 9545561
2016 The FEN1 L209P mutation interferes with long-patch base excision repair and induces cellular transformation. Oncogene 37 27270424
2023 Down-regulation of DNA key protein-FEN1 inhibits OSCC growth by affecting immunosuppressive phenotypes via IFN-γ/JAK/STAT-1. International journal of oral science 35 37185662
2020 PRMT1 is critical to FEN1 expression and drug resistance in lung cancer cells. DNA repair 33 32861926
2013 Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic acids research 33 24234453
2003 Role of the Mf1-1 pheromone precursor gene of the filamentous ascomycete Cryphonectria parasitica. Fungal genetics and biology : FG & B 33 14599892
2019 FEN1 inhibitor increases sensitivity of radiotherapy in cervical cancer cells. Cancer medicine 32 31670906
2013 Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment. Genes & development 32 24298055
2005 Fen1 is induced p53 dependently and involved in the recovery from UV-light-induced replication inhibition. Oncogene 32 16103874
2012 Structural and functional characterization of interactions involving the Tfb1 subunit of TFIIH and the NER factor Rad2. Nucleic acids research 30 22373916
2012 Kinetics of endogenous mouse FEN1 in base excision repair. Nucleic acids research 30 22810208
2003 OsSEND-1: a new RAD2 nuclease family member in higher plants. Plant molecular biology 30 12602891
1984 Isolation and characterization of the RAD2 gene of Saccharomyces cerevisiae. Gene 30 6392021
2005 Genetic and physical interactions between Schizosaccharomyces pombe Mcl1 and Rad2, Dna2 and DNA polymerase alpha: evidence for a multifunctional role of Mcl1 in DNA replication and repair. Current genetics 29 15915339
1995 The yeast RAD2, but not RAD1, gene is involved in the transcription-coupled repair of thymine glycols. Mutation research 29 7491120
2020 Endonuclease FEN1 Coregulates ERα Activity and Provides a Novel Drug Interface in Tamoxifen-Resistant Breast Cancer. Cancer research 27 32193286
1998 Fen1 expression: a novel marker for cell proliferation. The Journal of pathology 27 10211123
1997 Characterization of a novel DNA damage-inducible gene of Saccharomyces cerevisiae, DIN7, which is a structural homolog of the RAD2 and RAD27 DNA repair genes. Molecular & general genetics : MGG 27 9079876
1992 Regulation of the yeast RAD2 gene: DNA damage-dependent induction correlates with protein binding to regulatory sequences and their deletion influences survival. Molecular & general genetics : MGG 26 1557031
2022 Programmable CRISPR-Cas12a and self-recruiting crRNA assisted dual biosensing platform for simultaneous detection of lung cancer biomarkers hOGG1 and FEN1. Analytica chimica acta 25 36641157
2003 Complementary functions of the Saccharomyces cerevisiae Rad2 family nucleases in Okazaki fragment maturation, mutation avoidance, and chromosome stability. DNA repair 25 12893088
1998 Characterization of Schizosaccharomyces pombe Rad2 protein, a FEN-1 homolog. Nucleic acids research 24 9685478
2011 Bacterial genotoxin triggers FEN1-dependent RhoA activation, cytoskeleton remodeling and cell survival. Journal of cell science 23 21807938
2014 The FEN1 E359K germline mutation disrupts the FEN1-WRN interaction and FEN1 GEN activity, causing aneuploidy-associated cancers. Oncogene 22 24608430
2014 Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic acids research 22 25120270
2021 FEN1 Blockade for Platinum Chemo-Sensitization and Synthetic Lethality in Epithelial Ovarian Cancers. Cancers 21 33919707
2017 The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis. Journal of bacteriology 20 28416706
2016 Association between Single-Nucleotide Polymorphisms of the hOGG1,NEIL1,APEX1, FEN1,LIG1, and LIG3 Genes and Alzheimer's Disease Risk. Neuropsychobiology 20 27010693
2014 Association of functional FEN1 genetic variants and haplotypes and breast cancer risk. Gene 20 24440783
2024 PARG-deficient tumor cells have an increased dependence on EXO1/FEN1-mediated DNA repair. The EMBO journal 19 38360994
1987 Overexpression of the RAD2 gene of S. cerevisiae: identification and preliminary characterization of Rad2 protein. Yeast (Chichester, England) 19 3332971
2023 FEN1-aided recombinase polymerase amplification (FARPA) for one-pot and multiplex detection of nucleic acids with an ultra-high specificity and sensitivity. Biosensors & bioelectronics 18 37354713
2022 miR-4324 inhibits ovarian cancer progression by targeting FEN1. Journal of ovarian research 18 35246224
2004 DmGEN, a novel RAD2 family endo-exonuclease from Drosophila melanogaster. Nucleic acids research 18 15576351
1989 The Saccharomyces cerevisiae RAD2 gene complements a Schizosaccharomyces pombe repair mutation. Current genetics 18 2663184
2001 Role of the DNA repair nucleases Rad13, Rad2 and Uve1 of Schizosaccharomyces pombe in mismatch correction. Journal of molecular biology 17 11800554

Missed literature

Know a paper Affinage missed for FEN1? Flag it for the maintainers and the community.

No submissions yet.