Affinage

Showing ERCC4 — XPF is a alias.

ERCC4

DNA repair endonuclease XPF · UniProt Q92889

Length
916 aa
Mass
104.5 kDa
Annotated
2026-06-09
100 papers in source corpus 41 papers cited in narrative 40 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 8/8 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ERCC4 (XPF) is the catalytic subunit of a structure-specific endonuclease that operates as an obligate heterodimer with ERCC1 to incise DNA at single-strand/double-strand junctions across multiple genome-maintenance pathways (PMID:8253090, PMID:8253091, PMID:7559382, PMID:9525876). The purified heterodimer cleaves bubble, splayed-arm, and flap substrates on the 5' side of ss/ds junctions, requiring divalent cations and a minimal stretch of unpaired nucleotides (PMID:9525876), with the nuclease active site mapping to XPF residues 670–740 where point mutations abolish catalysis without affecting DNA binding (PMID:11953324). Structural work resolves the basis for substrate engagement: ERCC1 and XPF contribute non-equivalent (HhH)₂ and central domains that bind ssDNA and dsDNA asymmetrically (PMID:16076955, PMID:22483113), and cryo-EM shows the DNA-free complex adopts an auto-inhibited conformation that masks the active site until junction engagement couples the ERCC1 (HhH)₂ to the nuclease domains (PMID:32111838). In nucleotide excision repair, the complex is recruited through direct ERCC1–XPA interaction to execute the 5' incision (PMID:8197175, PMID:17948053), and its participation is distributive, with damage-induced transient immobilization at lesions (PMID:10320375). Beyond NER, XPF-ERCC1 carries out interstrand crosslink unhooking downstream of FANCD2 ubiquitylation and SLX4 recruitment, with RPA activating incision at replication-fork ICL structures and SNM1A loading from the resulting nicks (PMID:19805513, PMID:24726325, PMID:28607004, PMID:28292785), and it functions in double-strand break end-joining and single-strand annealing (PMID:18541667, PMID:17962301). The complex additionally maintains telomeres (PMID:18812185), processes R-loops in association with XAB2 (PMID:34039990), drives ALT telomere synthesis via TERRA R-loops (PMID:36184605), and supports CTCF/cohesin-dependent chromatin looping for transcriptional regulation and imprinted-gene silencing independent of repair, a role requiring its catalytic activity (PMID:22771116, PMID:28368372). Heterodimerization governs the complex's integrity and compartmentalization: XPF stability requires ERCC1 (PMID:20418188), nuclear import of ERCC1 requires XPF (PMID:28130555), and USP45-mediated deubiquitylation of ERCC1 promotes recruitment to damage sites (PMID:25538220). Biallelic ERCC4 mutations cause Fanconi anemia, and the spectrum of XP, XFE progeroid, and FA phenotypes reflects mutations that separably impair NER, ICL repair, or proper localization (PMID:20221251, PMID:23623386, PMID:30165384).

Mechanistic history

Synthesis pass · year-by-year structured walk · 19 steps
  1. 1993 High

    Established that ERCC4/XPF and ERCC1 are not independent repair factors but a single functional complex, unifying multiple complementation groups.

    Evidence In vitro NER complementation, immunodepletion, and native gel fractionation showing co-purification as a ~100 kDa complex

    PMID:8253090 PMID:8253091

    Open questions at the time
    • Did not define the catalytic mechanism or substrate specificity
    • Stoichiometry and direct biochemical activity not yet characterized
  2. 1994 High

    Connected the ERCC1-XPF complex to the broader NER machinery by demonstrating a direct interaction with the damage-recognition factor XPA.

    Evidence XPA affinity column pulldown from HeLa extract plus in vitro complementation

    PMID:8197175

    Open questions at the time
    • Did not map the interaction interface
    • Functional consequence of the interaction for incision not established
  3. 1995 High

    Showed the purified heterodimer is itself the endonuclease and is stimulated by RPA, identifying XPF and ERCC4 as the same protein.

    Evidence Purification to homogeneity from HeLa and endonuclease assays on model substrates

    PMID:7559382

    Open questions at the time
    • Polarity and precise cleavage position not yet defined
    • Which subunit carries the active site unknown
  4. 1998 High

    Defined the structure-specific cleavage rule: incision on the 5' side of ss/ds junctions with a minimal unpaired-nucleotide requirement.

    Evidence Recombinant ERCC1-XPF endonuclease assays with systematic substrate variation and divalent cation requirements

    PMID:9525876

    Open questions at the time
    • Active-site residues not yet localized
    • Did not address regulation in cells
  5. 2002 High

    Localized the nuclease active site to XPF residues 670–740 and separated catalysis from substrate binding.

    Evidence Affinity cleavage, site-directed mutagenesis, and parallel nuclease/DNA-binding assays

    PMID:11953324

    Open questions at the time
    • Conformational regulation of the active site not addressed
    • Role of ERCC1 in catalysis not defined
  6. 1999 High

    Determined that the complex participates in NER distributively, transiently immobilizing at lesions rather than acting as a preassembled processive machine.

    Evidence Live-cell FRAP of GFP-tagged ERCC1/XPF in CHO cells after UV

    PMID:10320375

    Open questions at the time
    • Molecular trigger of immobilization not defined
    • Did not address non-NER mobility behavior
  7. 2007 High

    Established at atomic resolution why the ERCC1-XPA interaction is essential for recruiting the complex to NER sites.

    Evidence Crystal structure of ERCC1-XPA peptide complex, SPR, and peptide-mediated cell-free NER inhibition

    PMID:17948053

    Open questions at the time
    • Did not define recruitment dynamics in living cells
    • Interface relevance to ICL repair not addressed
  8. 2005 High

    Provided the structural basis for asymmetric branched-DNA recognition by the heterodimer's HhH and central domains.

    Evidence X-ray crystallography of ERCC1 domains and the XPF-ERCC1 (HhH)₂ heterodimer with ssDNA binding assays, plus archaeal XPF apo/DNA-bound structures

    PMID:15719018 PMID:16076955

    Open questions at the time
    • Full-length complex architecture not resolved
    • Coupling between DNA binding and catalysis incompletely defined
  9. 2012 High

    Refined the DNA-recognition model with atomic XPF HhH-ssDNA contacts and demonstrated cooperative, multi-domain DNA binding governs NER versus ICL repair.

    Evidence NMR structure of XPF HhH bound to ssDNA and mutagenesis across multiple DNA-binding domains with NER/ICL functional readouts

    PMID:22483113 PMID:22547097

    Open questions at the time
    • Did not capture the auto-inhibited full-length conformation
    • Quantitative affinity differences between pathways not fully mapped
  10. 2008 Medium

    Extended the complex's repertoire beyond NER to double-strand break end-joining, single-strand annealing, retrotransposition control, and telomere maintenance.

    Evidence Mouse double-mutant genetics and in vitro DSB repair; SSA/gene-conversion reporters; retrotransposition reporters; telomere length and TRF2 ChIP with nuclease-dead mutants

    PMID:17962301 PMID:18396111 PMID:18541667 PMID:18812185

    Open questions at the time
    • Mechanistic step at which XPF acts in each pathway not fully defined
    • Nuclease-independent telomere role mechanism unresolved
    • Some readouts from single labs
  11. 2004 Medium

    Placed XPF-ERCC1 in recombination intermediate processing via direct interaction with hRad52.

    Evidence Co-IP from cell-free extracts plus endonuclease and strand-annealing activity assays

    PMID:14734547

    Open questions at the time
    • Single lab without reciprocal in vivo validation
    • Physiological context of the ternary complex not established
  12. 2014 High

    Ordered the interstrand crosslink repair pathway: FANCD2 ubiquitylation licenses SLX4/XPF-ERCC1 recruitment for unhooking incisions, with FANCD2 foci themselves requiring upstream unhooking.

    Evidence Xenopus egg-extract replication-coupled ICL repair with immunodepletion and FANCD2 ubiquitylation/incision assays; chromatin fractionation and foci counting across species

    PMID:19805513 PMID:24726325

    Open questions at the time
    • Did not define the conformational activation of the nuclease
    • Spatial positioning of incisions relative to the crosslink not fully resolved
  13. 2017 High

    Dissected ICL repair into separable recruitment, positioning, and catalysis steps and identified RPA and SNM1A as activators/partners of the incision reaction.

    Evidence Xenopus extract structure-function mutagenesis of XPF helicase-like and nuclease domains; in vitro RPA-activated incision and SNM1A loading on defined ICL fork substrates

    PMID:21896658 PMID:28292785 PMID:28607004

    Open questions at the time
    • In vivo dynamics of the transient XPF-SLX4 interactions not visualized
    • Regulation of RPA-dependent activation in cells not established
  14. 2019 Medium

    Identified accessory factors and substrate contexts expanding XPF-ERCC1 function to secondary-structure DSBs and stabilization of the SLX4 complex.

    Evidence SLX4IP co-IP/GST pulldown with depletion phenotypes; CRISPR/siRNA XPF-FANCM synthetic lethality with HR reporters and G4 drug sensitivity

    PMID:31153042 PMID:31495888

    Open questions at the time
    • Direct structural role of SLX4IP unresolved
    • Single-lab studies without orthogonal confirmation
  15. 2012 High

    Revealed a non-repair function in chromatin organization, showing XPF catalytic activity is required for CTCF-dependent chromatin looping and transcription, later extended to cohesin-dependent imprinted-gene silencing in vivo.

    Evidence 3C, ChIP, and catalytic-site mutagenesis at RARβ2; in vivo biotinylation tagging, mass spectrometry, and Ercc1 knockout mouse liver chromatin analysis

    PMID:22771116 PMID:28368372

    Open questions at the time
    • Substrate cleaved during looping not identified
    • Generality across other loci incompletely defined
  16. 2021 Medium

    Connected XPF-ERCC1 to R-loop biology through XAB2 association, ALT telomere synthesis, and mis-repair deletions at transcribed loci.

    Evidence IP-MS and RNA:DNA hybrid binding with XAB2; TERRA interactome, telomeric XPF ChIP, and ALT readouts; reporter deletion assays with Senataxin/RNaseH1 perturbation and DRIP

    PMID:29497062 PMID:34039990 PMID:36184605

    Open questions at the time
    • Direct catalytic action on R-loops not biochemically reconstituted
    • Single-lab studies for several novel functions
  17. 2020 High

    Captured the regulatory switch of the complex: an auto-inhibited DNA-free conformation relieved by junction engagement, and showed FA mutations resist SLX4-dependent activation.

    Evidence Cryo-EM of DNA-free and DNA-bound human XPF-ERCC1 with mutagenesis and SLX4-stimulated activation assays

    PMID:32111838

    Open questions at the time
    • Dynamics of the conformational transition in cells not measured
    • Activation by NER-specific factors not structurally resolved
  18. 2014 High

    Established that complex integrity and localization are regulated post-translationally and by heterodimerization, with disease mutations acting through mislocalization.

    Evidence USP45 deubiquitylation assays and KO phenotypes; XPF/ERCC1 reciprocal stability and nuclear-import dependence; XFE patient cell mislocalization with nuclear-microinjection rescue

    PMID:20221251 PMID:20418188 PMID:25538220 PMID:28130555

    Open questions at the time
    • Ubiquitin ligase opposing USP45 not identified
    • Import machinery mediating XPF-dependent ERCC1 nuclear entry not defined
  19. 2021 Medium

    Demonstrated tissue- and pathway-specific deployment of XPF in NER, with cell type dictating global-genome versus transcription-coupled subpathway usage.

    Evidence In vivo imaging of tagged XPF-1 in C. elegans with tissue-specific NER and loss-of-function genetics

    PMID:33440146

    Open questions at the time
    • Molecular determinant of subpathway choice not identified
    • Conservation of tissue specificity in mammals not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the diverse non-canonical roles (chromatin looping, R-loop processing, ALT synthesis) are coordinated with classical repair, and what determines pathway choice at a given substrate, remains unresolved.
  • No unified model linking conformational activation to non-repair substrate engagement
  • Regulatory hierarchy among partners (SLX4, XAB2, CTCF, USP45) not integrated
  • Substrates cleaved during transcriptional/looping functions not biochemically defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0016787 hydrolase activity 3 GO:0140097 catalytic activity, acting on DNA 3 GO:0003723 RNA binding 2
Localization
GO:0000228 nuclear chromosome 3 GO:0005634 nucleus 3
Pathway
R-HSA-73894 DNA Repair 4 R-HSA-1643685 Disease 3 R-HSA-4839726 Chromatin organization 2
Partners
ERCC1RAD52RPASLX4SLX4IPUSP45XAB2XPA
Complex memberships
ERCC1-XPF heterodimerSLX4-XPF-ERCC1 complexXAB2-ERCC1-XPF-XPG complex

Evidence

Reading pass · 40 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 XPA forms a ternary complex with the ERCC1/XPF (ERCC4) heterodimer; XPA affinity column retained ERCC1 and ERCC4(XPF) correcting activities from HeLa cell-free extract, establishing a direct protein-protein interaction between XPA and the ERCC1-XPF complex. XPA affinity column pulldown from HeLa cell-free extract; in vitro complementation assay Proceedings of the National Academy of Sciences of the United States of America High 8197175
1993 ERCC1 co-purifies with XPF/ERCC4 as a ~100 kDa complex; extracts from ERCC1, ERCC4 (group 4), and XP-F cells all fail to complement each other in vitro, and depletion of ERCC1 simultaneously removes correcting activities for groups 4, 11, and XP-F, indicating ERCC1 and XPF form a functional repair complex. In vitro NER complementation assay; immunodepletion; native gel fractionation; immunoblotting The EMBO journal High 8253090 8253091
1995 Purified XPF-ERCC1 heterodimer (ERCC1 38 kDa + XPF 112 kDa) from HeLa cells possesses endonuclease activity with preference for single-stranded DNA and bubble-structured duplex DNA; this activity is stimulated by RPA in the presence of UV-damaged DNA. XPF and ERCC4 are biochemically confirmed to be identical proteins. Purification from HeLa cells to homogeneity; endonuclease assay on model DNA substrates; in vitro NER complementation The Journal of biological chemistry High 7559382
1998 Recombinant ERCC1-XPF purified from insect cells cleaves at single-strand/double-strand DNA junctions (5' side of junction) in the absence of other NER factors, requiring divalent cations (optimal at 0.2 mM Mn²⁺). A minimum of 4–8 unpaired nucleotides is required; the complex cuts splayed arm and flap substrates to remove 3' single-stranded arms, 2–8 nt from the junction. In vitro endonuclease assay with recombinant protein on defined DNA substrates; mutational analysis of substrate structure The Journal of biological chemistry High 9525876
1999 In living CHO cells, GFP-tagged ERCC1/XPF moves freely through the nucleus (diffusion coefficient ~15 µm²/s) consistent with free complex rather than preassembled holocomplexes. UV-induced DNA damage causes transient, dose-dependent immobilization of ERCC1/XPF for ~4 minutes per repair event, consistent with distributive (not processive) participation in NER. GFP-tagging and live-cell fluorescence microscopy (FRAP) in CHO cells; UV irradiation Science High 10320375
2002 The nuclease active site of the XPF-ERCC1 heterodimer resides within residues 670–740 of XPF. Point mutations of acidic and basic residues in this region abolish nuclease activity but not DNA binding, separating catalysis from substrate recognition. Seven residues are absolutely conserved with Mus81 and archaeal RNA helicase families, defining a shared nuclease motif. Affinity cleavage assay; site-directed mutagenesis; nuclease activity assays; DNA binding assays The EMBO journal High 11953324
2004 XPF-ERCC1 is required for repair of DNA double-strand breaks (DSBs) in mammals via a Ku86-independent end-joining mechanism. XPF-deficient fibroblasts are hypersensitive to γ-irradiation and accumulate persistent γH2AX foci; Ercc1−/− Ku86−/− cells show additive hypersensitivity and chromosomal aberrations; in vitro repair of DSBs with 3' overhangs produces large deletions in absence of ERCC1-XPF. Cell viability assay; γH2AX foci immunostaining; double-mutant mouse genetics (Ercc1−/− × Ku86−/−); in vitro DSB repair assay Molecular and cellular biology High 18541667
2004 XPF physically interacts with hRad52 via the N-terminal domain of hRad52 and the XPF protein. This interaction is stable in human cell-free extracts and stimulates XPF-ERCC1 endonuclease activity while attenuating hRad52 strand annealing activity, placing XPF-ERCC1 in a ternary complex that processes recombination intermediates. Co-immunoprecipitation from cell-free extracts; direct protein interaction assay; endonuclease activity assay; strand annealing assay The Journal of biological chemistry Medium 14734547
2005 Crystal structure of ERCC1 central domain reveals it adopts a fold similar to archaeal Mus81/XPF nuclease domains despite low sequence identity; ERCC1 central domain and C-terminal HhH₂ domain both bind ssDNA. Crystal structure of the XPF-ERCC1 HhH₂ heterodimer reveals two independent ssDNA-binding surfaces. ERCC1 central domain preferentially binds 5' single-stranded overhangs at ssDNA/dsDNA junctions. A model is proposed in which XPF-ERCC1 recognizes branched DNA using HhH₂ domains of both subunits plus the ERCC1 central domain. X-ray crystallography; ssDNA binding assays; NER reconstitution with truncated XPF-ERCC1 Proceedings of the National Academy of Sciences of the United States of America High 16076955
2005 Crystal structure of an archaeal XPF homodimer alone and bound to dsDNA reveals large domain movement upon DNA binding, coupling the (HhH)₂ domain and nuclease domain for recognition of ds/ssDNA junctions; two non-equivalent DNA-binding sites are identified, and a model is proposed in which XPF distorts a 3' flap substrate to engage both sites for cleavage. X-ray crystallography (apo and DNA-bound structures); structural comparison The EMBO journal High 15719018
2007 ERCC1 directly binds XPA via a small region (peptide) of XPA with submicromolar affinity; crystal structure of ERCC1 in complex with an XPA peptide reveals the binding interface. This XPA peptide potently inhibits NER in cell-free assay, blocking excision of a cisplatin adduct, establishing that XPA-ERCC1 interaction is essential for ERCC1-XPF recruitment to NER complexes. X-ray crystallography of ERCC1-XPA peptide complex; surface plasmon resonance; cell-free NER inhibition assay The EMBO journal High 17948053
2007 ERCC1-XPF endonuclease is required for single-strand annealing (SSA) and also gene conversion in mammalian cells, supporting a role in synthesis-dependent strand annealing during DSB repair. Reporter gene assay for SSA and gene conversion; ERCC1-deficient cell lines; cell cycle arrest experiments Nucleic acids research Medium 17962301
2008 ERCC1/XPF limits LINE-1 retrotransposition: XPF knockdown in human cells increases retrotransposition frequency, and ERCC1 complementation in ERCC1-deficient hamster cells reduces it, revealing that ERCC1-XPF processes flap intermediates generated during retrotransposon insertion. RNAi knockdown of XPF; genetic complementation in ERCC1-deficient cells; retrotransposition reporter assay DNA repair Medium 18396111
2008 XPF controls TRF2 association with telomeric DNA and telomere length maintenance through two distinct mechanisms: (1) nuclease-activity-dependent control of TRF2 binding to telomeres; (2) nuclease-activity-independent regulation of telomere length. Overexpression of XPF induces telomere shortening in XPF-proficient cells; XPF complementation suppresses telomere lengthening in XPF-deficient cells. XPF overexpression and complementation; telomere length analysis; ChIP for TRF2; nuclease-dead XPF mutant Mechanisms of ageing and development Medium 18812185
2009 XPF-ERCC1 unhooking of ICLs is required for stable chromatin loading and FANCD2 foci formation at ICLs: in XPF-ERCC1-deficient cells, FANCD2 is monoubiquitinated but chromatin-bound FANCD2 levels are dramatically reduced and ICL-induced foci are significantly lower, establishing that ICL unhooking by XPF-ERCC1 is required for downstream FA pathway activation and homologous recombination. Chromatin fractionation; FANCD2 ubiquitination assay; immunofluorescence foci counting in XPF-deficient human, mouse, and hamster cells Molecular and cellular biology High 19805513
2010 XPF protein stability depends on ERCC1: siRNA knockdown of ERCC1 significantly reduces XPF protein levels (but not mRNA), while ERCC1 knockdown by XPF does not reciprocally destabilize ERCC1, indicating XPF protein stability requires its heterodimer partner. RNAi knockdown; immunoblotting; RT-PCR for transcript levels DNA repair Medium 20418188
2010 Missense mutations in XPF can cause cytoplasmic mislocalization of XPF-ERCC1: cells from XFE progeroid patients show XPF-ERCC1 accumulation in the cytoplasm. Microinjection of XPF(R153P)-ERCC1 into the nucleus of XPF-deficient human cells restores NER of UV damage, demonstrating that mislocalization (not catalytic inactivity) accounts for part of the DNA repair defect in XFE syndrome. Immunofluorescence; cell fractionation; YFP-tagged XPF live imaging; nuclear microinjection of recombinant protein; NER assay PLoS genetics High 20221251
2011 SNM1A (hSNM1A) collaborates with XPF-ERCC1 to initiate ICL repair in replicating human cells: SNM1A 5'-3' exonuclease loads from XPF-ERCC1-induced nicks and digests past the ICL. Depletion of hSNM1A or ERCC1 each causes ICL sensitivity and accumulation of Mus81-dependent replication-associated DSBs. Purified protein biochemistry (exonuclease assay on ICL substrates); siRNA depletion; γH2AX foci; epistasis with Mus81 Genes & development High 21896658
2012 XPF (and XPG) endonuclease activity is required for CTCF-dependent chromatin looping between promoter and terminator of the RARβ2 gene: siRNA silencing or catalytic-site mutations in XPF prevent CTCF recruitment, chromatin loop formation, and optimal transcription, establishing a non-repair transcriptional role for XPF. RNAi; catalytic-site mutagenesis; chromosome conformation capture (3C); ChIP; transcription assays Molecular cell High 22771116
2012 Multiple DNA-binding domains of ERCC1-XPF cooperate for NER function: mutations in the HhH domain of ERCC1 or the nuclease domain of XPF abolish cleavage of model substrates. Mutations in multiple DNA-binding domains are required to significantly diminish NER activity in vitro and in vivo, and ICL repair requires tighter substrate binding than NER. Site-directed mutagenesis; in vitro NER reconstitution; cleavage assays on model substrates; cellular sensitivity to UV and MMC The Journal of biological chemistry High 22547097
2012 The XPF C-terminal HhH domain directly contacts ssDNA phosphate backbone (NMR structure); a guanine base is flipped into a pocket contacting residues from both HhH motifs; a one-residue deletion in XPF's second HhH motif permits ssDNA interactions distinct from ERCC1's dsDNA binding, establishing asymmetric DNA recognition by the XPF-ERCC1 heterodimer at ss/ds junctions. NMR structure determination of XPF HhH domain bound to ssDNA; comparison with ERCC1 structural data Structure High 22483113
2013 Biallelic germline mutations in ERCC4 (XPF) cause Fanconi anemia (FA-Q subtype). FA-causing ERCC4 mutations strongly disrupt ICL repair function without severely compromising NER, demonstrating that ERCC4/XPF has separable NER and ICL repair activities, and that the type of mutation determines which disease (XP, XFE progeroid, or FA) manifests. Whole-exome and Sanger sequencing; genetic complementation with wild-type ERCC4 cDNA; cellular ICL and NER repair assays; chromosomal fragility assays American journal of human genetics High 23623386
2014 XPF-ERCC1 cooperates with SLX4/FANCP to carry out ICL unhooking incisions in replication-coupled ICL repair. Efficient recruitment of XPF-ERCC1 and SLX4 to the ICL requires FANCD2 and its ubiquitylation, establishing the pathway order: FANCD2 ubiquitylation → SLX4/XPF-ERCC1 recruitment → unhooking. Xenopus egg extract replication-coupled ICL repair assay; immunodepletion of XPF-ERCC1 and SLX4; FANCD2 ubiquitylation assay; DNA repair incision assay Molecular cell High 24726325
2014 USP45 deubiquitylase directly binds ERCC1 (via an acidic motif outside the USP45 catalytic domain), deubiquitylates ERCC1 in vitro, and promotes ERCC1-XPF translocation to UV-induced DNA damage foci. Loss of USP45 causes elevated ubiquitylated ERCC1, impaired ERCC1-XPF foci formation, and hypersensitivity to UV and ICL agents similar to ERCC1-deficient cells. Co-immunoprecipitation; in vitro deubiquitylation assay; USP45 knockout cells; UV sensitivity assay; immunofluorescence foci The EMBO journal High 25538220
2017 RPA activates XPF-ERCC1 endonuclease activity at ICL-containing replication fork structures: a nascent leading strand inhibits XPF-ERCC1 incision on model fork substrates, but addition of RPA selectively restores activity. SNM1A can load from XPF-ERCC1-RPA-induced incisions and digest past the crosslink to complete unhooking. In vitro endonuclease assay with purified XPF-ERCC1, RPA, and defined ICL fork substrates; exonuclease loading assay The EMBO journal High 28607004
2017 The helicase-like domain of XPF mediates binding to SLX4 for ICL-specific recruitment; a mutation in this domain disrupts SLX4 binding and recruitment to ICL but not to NER substrates. A second transient XPF-SLX4 interaction is required for positioning/unhooking. Nuclease domain mutations prevent incisions without affecting ICL localization, defining three separable steps: recruitment, positioning, and catalysis. Xenopus egg extract ICL and NER repair assays; site-directed mutagenesis; XPF localization to ICL by IP; separation-of-function mutants The EMBO journal High 28292785
2017 ERCC1-XPF cooperates with the insulator protein CTCF and cohesin (SMC1A, SMC3) to facilitate developmental silencing of imprinted genes. In vivo biotinylation tagging shows ERCC1-XPF co-localizes with CTCF, cohesin, MBD2, and ATRX at imprinted gene promoters and ICRs during postnatal hepatic development. Loss of Ercc1 dissociates CTCF-cohesin from promoters and alters histone marks without changing DNA methylation. In vivo biotinylation tagging in mice; mass spectrometry; ChIP; gene expression analysis; Ercc1 knockout mouse liver Nature cell biology High 28368372
2019 SLX4IP binds both SLX4 and XPF-ERCC1 simultaneously, stabilizing the SLX4-XPF-ERCC1 complex; disruption of one interaction destabilizes both. SLX4IP depletion sensitizes cells to ICL agents and causes G2/M accumulation, promoting the interaction between SLX4 and XPF-ERCC1 particularly after DNA damage. Co-immunoprecipitation; GST pulldown; siRNA depletion; cell viability and cell cycle analysis; DNA damage induction Nucleic acids research Medium 31495888
2019 ERCC1/XPF is required for repair of DSBs containing DNA secondary structures (AT-rich sequences from common fragile sites and G-quadruplexes). XPF inactivation is synthetically lethal with FANCM deficiency (which removes DNA secondary structures), and XPF sensitizes FANCM-deficient cells to G4-interacting compounds. CRISPR/siRNA-mediated XPF and FANCM inactivation; HR reporter assay; cytogenetic analysis; drug sensitivity assays iScience Medium 31153042
2020 Cryo-EM structures of human XPF-ERCC1 reveal that the DNA-free form adopts an auto-inhibited conformation in which the XPF helical domain masks the ERCC1 (HhH)₂ domain and restricts access to the XPF catalytic site. DNA junction engagement releases this auto-inhibition, coupling ERCC1 (HhH)₂ with the nuclease domains. FA patient mutations in XPF are resistant to activation by the ICLR recruitment factor SLX4 despite retaining in vitro activity. Cryo-electron microscopy (DNA-free and DNA-bound); structure-function mutagenesis; SLX4-stimulated activation assay Nature communications High 32111838
2017 XPF protein requires heterodimerization with ERCC1 for nuclear import: in CRISPR/Cas9 XPF knockout cells, ERCC1 is retained in the cytoplasm and not detectable in the nucleus; overexpression of wild-type XPF restores ERCC1 nuclear localization, showing that XPF is required for nuclear entry of ERCC1. CRISPR/Cas9 XPF knockout; immunofluorescence; nuclear/cytoplasmic fractionation; XPF overexpression rescue Cellular and molecular life sciences High 28130555
2021 The splicing factor XAB2 interacts with ERCC1-XPF (and XPG) outside of canonical NER; the trimeric XAB2-ERCC1-XPF-XPG complex binds RNA:DNA hybrids (R-loops). XAB2 depletion causes aberrant intron retention, R-loop formation, and DNA damage, linking spliceosomal function to R-loop processing by ERCC1-XPF. In vivo biotinylation tagging (IP-MS); immunoprecipitation; RNA:DNA hybrid binding assay; siRNA depletion; R-loop detection Nature communications Medium 34039990
2021 In C. elegans, tissue-specific NER activity differs: in oocytes XPF-1 functions in global genome NER for rapid genome-wide lesion removal, whereas in post-mitotic neurons and muscles XPF-1 participates only in transcription-coupled NER of transcribed genes, establishing that XPF-1 NER subpathway usage is determined by cell type. In vivo imaging of tagged XPF-1 in C. elegans; tissue-specific NER analysis; loss-of-function genetics Cell reports Medium 33440146
2022 XPF is recruited to ALT telomeres by telomeric RNA:DNA R-loops (TERRA R-loops) and induces DNA damage response (DDR) independently of CSB and SLX4, triggering break-induced telomere synthesis (ALT). XPF recruitment requires BRCA1 and RAD51 in FANCM-deficient cells that accumulate telomeric R-loops. TERRA depletion (RNA-targeting Cas9); TERRA interactome (mass spectrometry); XPF ChIP at telomeres; ALT-associated PML body analysis; telomere length assay; epistasis with CSB and SLX4 Nature communications Medium 36184605
2001 Functional ERCC1-XPF heterodimer can be reconstituted from separately produced subunits (expressed in E. coli). ERCC1 alone can confer partial NER activity to ERCC1-deficient extracts only when endogenous XPF is present; adding ERCC1 to XPF-deficient extracts requires co-addition of XPF. Sequence comparison reveals similarity between ERCC1 and the C-terminal region of XPF, suggesting ancient gene duplication gave rise to both subunits. Recombinant protein expression in E. coli; NER complementation assay; immunoassays; protein sequence analysis Nucleic acids research Medium 11160918
2015 ERCC1-XPF participates in repair of Topoisomerase 1-attached nick DNA lesions (Tyr-nick DNA): ERCC1-XPF shows nuclease activity on Tyr-nick substrates in the presence of RPA in vitro; ERCC1-XPF and RPA co-localize in CPT-treated cells in vivo; repair synthesis of Tyr-nick DNA requires ERCC1-XPF, RPA, DNA polymerase delta, FEN1, and DNA ligase 1. In vitro nuclease assay on Tyr-nick substrates; EMSA; co-localization immunofluorescence; in vitro repair synthesis assay Carcinogenesis Medium 26025908
2018 XP-causing XPF mutations (e.g. R799W) diminish XPF recruitment to DNA damage and mildly affect GG-NER, whereas an XPCS-complex-specific mutation causes persistent recruitment of XPF and upstream NER machinery to DNA damage, severely impairing both GG-NER and TC-NER. Persistent NER factor engagement at DNA damage is identified as a hallmark of XPCS-complex cells. Live-cell imaging of GFP-tagged XPF; FRAP; NER activity assays (host-cell reactivation, UDS); patient-derived cell lines Nucleic acids research High 30165384
2018 XPF-ERCC1 mediates large deletions at DSBs associated with DNA:RNA hybrids (R-loops): XPF-dependent kilobase deletions are increased by Senataxin knockdown and reduced by RNaseH1 overexpression, and DNA:RNA hybrids are detected at DSB sites, establishing XPF as a mediator of mis-repair deletions at transcribed loci. Reporter gene deletion assay; Senataxin siRNA knockdown; RNaseH1 overexpression; DRIP (DNA:RNA immunoprecipitation); XPF knockdown Scientific reports Medium 29497062
2018 XPF and ARTEMIS independently cleave stalled DNA replication forks through non-epistatic pathways during S and G2 phases. Both nucleases are recruited to chromatin to promote replication fork restart; their rapid fork cleavage activity prevents mitotic segregation defects. Endonuclease knockdown/inhibition; chromosomal breakage analysis; cell cycle analysis; chromatin fractionation; genetic epistasis PLoS genetics Medium 30059501
2019 TGFβ signaling enhances NER by increasing ERCC1-XPF and ERCC1-XPA protein interactions and promoting their nuclear co-localization; the effect requires intact TGFβ/Smad4 signaling and ERCC1, and is cell-cycle independent. Co-immunoprecipitation; immunofluorescence co-localization; siRNA of Smad4 and ERCC1; NER activity assays Carcinogenesis Medium 30418489

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 Action of DNA repair endonuclease ERCC1/XPF in living cells. Science (New York, N.Y.) 291 10320375
2013 Mutations in ERCC4, encoding the DNA-repair endonuclease XPF, cause Fanconi anemia. American journal of human genetics 259 23623386
2014 XPF-ERCC1 acts in Unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4. Molecular cell 255 24726325
2008 ERCC1-XPF endonuclease facilitates DNA double-strand break repair. Molecular and cellular biology 246 18541667
2008 Structural and functional relationships of the XPF/MUS81 family of proteins. Annual review of biochemistry 231 18518821
1998 DNA structural elements required for ERCC1-XPF endonuclease activity. The Journal of biological chemistry 191 9525876
1994 Formation of a ternary complex by human XPA, ERCC1, and ERCC4(XPF) excision repair proteins. Proceedings of the National Academy of Sciences of the United States of America 183 8197175
2002 The active site of the DNA repair endonuclease XPF-ERCC1 forms a highly conserved nuclease motif. The EMBO journal 166 11953324
1993 Co-correction of the ERCC1, ERCC4 and xeroderma pigmentosum group F DNA repair defects in vitro. The EMBO journal 160 8253090
2012 DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy. Nucleic acids research 158 22941649
1993 Evidence for a repair enzyme complex involving ERCC1 and complementing activities of ERCC4, ERCC11 and xeroderma pigmentosum group F. The EMBO journal 157 8253091
2010 Downregulation of XPF-ERCC1 enhances cisplatin efficacy in cancer cells. DNA repair 144 20418188
2005 Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proceedings of the National Academy of Sciences of the United States of America 141 16076955
2011 Physiological consequences of defects in ERCC1-XPF DNA repair endonuclease. DNA repair 135 21612988
2007 The ERCC1/XPF endonuclease is required for efficient single-strand annealing and gene conversion in mammalian cells. Nucleic acids research 134 17962301
2004 Growth retardation, early death, and DNA repair defects in mice deficient for the nucleotide excision repair enzyme XPF. Molecular and cellular biology 132 14729965
2010 Cisplatin sensitivity of testis tumour cells is due to deficiency in interstrand-crosslink repair and low ERCC1-XPF expression. Molecular cancer 130 20846399
2007 Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. The EMBO journal 129 17948053
2010 Multiple roles of the ERCC1-XPF endonuclease in DNA repair and resistance to anticancer drugs. Anticancer research 123 20944091
2011 Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair. Genes & development 122 21896658
2009 XPF-ERCC1 participates in the Fanconi anemia pathway of cross-link repair. Molecular and cellular biology 119 19805513
2015 The ERCC1 and ERCC4 (XPF) genes and gene products. Gene 112 26074087
1995 Purification and characterization of the XPF-ERCC1 complex of human DNA repair excision nuclease. The Journal of biological chemistry 112 7559382
1996 ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs. Molecular and cellular biology 109 8887684
2008 Interstrand crosslink repair: can XPF-ERCC1 be let off the hook? Trends in genetics : TIG 94 18192062
2005 Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition. The EMBO journal 93 15719018
2012 XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes. Molecular cell 89 22771116
2008 ERCC1/XPF limits L1 retrotransposition. DNA repair 84 18396111
2001 Activity of individual ERCC1 and XPF subunits in DNA nucleotide excision repair. Nucleic acids research 84 11160918
2009 Immunodetection of DNA repair endonuclease ERCC1-XPF in human tissue. Cancer research 83 19723666
2004 Physical and functional interaction between the XPF/ERCC1 endonuclease and hRad52. The Journal of biological chemistry 83 14734547
2018 Functional Polymorphisms at ERCC1/XPF Genes Confer Neuroblastoma Risk in Chinese Children. EBioMedicine 80 29544698
2018 A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation. Genes & development 78 29440262
2018 Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules (Basel, Switzerland) 73 30563071
2013 Small molecule inhibitors of ERCC1-XPF protein-protein interaction synergize alkylating agents in cancer cells. Molecular pharmacology 69 23580445
2003 An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA. Molecular microbiology 67 12675797
2015 Inhibition of the ERCC1-XPF structure-specific endonuclease to overcome cancer chemoresistance. DNA repair 64 25956741
2010 Mislocalization of XPF-ERCC1 nuclease contributes to reduced DNA repair in XP-F patients. PLoS genetics 63 20221251
2005 The XPF-ERCC1 endonuclease and homologous recombination contribute to the repair of minor groove DNA interstrand crosslinks in mammalian cells produced by the pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136. Nucleic acids research 60 15944449
2014 Laryngeal cancer risk and common single nucleotide polymorphisms in nucleotide excision repair pathway genes ERCC1, ERCC2, ERCC3, ERCC4, ERCC5 and XPA. Gene 57 24582975
2006 Increased expression and activity of repair genes TDP1 and XPF in non-small cell lung cancer. Lung cancer (Amsterdam, Netherlands) 55 17118488
2017 RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks. The EMBO journal 53 28607004
2014 USP45 deubiquitylase controls ERCC1-XPF endonuclease-mediated DNA damage responses. The EMBO journal 51 25538220
2016 Identification of small molecule inhibitors of ERCC1-XPF that inhibit DNA repair and potentiate cisplatin efficacy in cancer cells. Oncotarget 50 27650543
2008 Human XPF controls TRF2 and telomere length maintenance through distinctive mechanisms. Mechanisms of ageing and development 48 18812185
2021 The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing. Nature communications 47 34039990
2009 Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideum. PLoS genetics 47 19763158
2005 Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms. Structure (London, England : 1993) 47 16084390
2018 SHOC1 is a ERCC4-(HhH)2-like protein, integral to the formation of crossover recombination intermediates during mammalian meiosis. PLoS genetics 46 29742103
2020 Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation. Nature communications 45 32111838
1994 Molecular cloning of the human nucleotide-excision-repair gene ERCC4. Proceedings of the National Academy of Sciences of the United States of America 45 8041709
2017 Recruitment and positioning determine the specific role of the XPF-ERCC1 endonuclease in interstrand crosslink repair. The EMBO journal 44 28292785
1996 The importance of the ERCC1/ERCC4[XPF] complex for hypoxic-cell radioresistance does not appear to derive from its participation in the nucleotide excision repair pathway. Mutation research 44 8960133
2011 XPF expression correlates with clinical outcome in squamous cell carcinoma of the head and neck. Clinical cancer research : an official journal of the American Association for Cancer Research 43 21737503
2012 Polymorphisms in ERCC1 and XPF genes and risk of gastric cancer in an eastern Chinese population. PloS one 41 23166636
2010 Multiple roles of ERCC1-XPF in mammalian interstrand crosslink repair. Environmental and molecular mutagenesis 41 20658648
2011 Role of endonucleases XPF and XPG in nucleotide excision repair of platinated DNA and cisplatin/oxaliplatin cytotoxicity. Chembiochem : a European journal of chemical biology 39 21452186
2011 XPF-dependent DNA breaks and RNA polymerase II arrest induced by antitumor DNA interstrand crosslinking-mimetic alkaloids. Chemistry & biology 38 21867914
2005 Gastrostomy in oropharyngeal cancer patients with ERCC4 (XPF) germline variants. International journal of radiation oncology, biology, physics 38 15936543
2013 Decreased expression of DNA repair genes (XRCC1, ERCC1, ERCC2, and ERCC4) in squamous intraepithelial lesion and invasive squamous cell carcinoma of the cervix. Molecular and cellular biochemistry 36 23435956
2004 An archaeal endonuclease displays key properties of both eukaryal XPF-ERCC1 and Mus81. The Journal of biological chemistry 36 15591065
1999 Polymorphisms in the human DNA repair gene XPF. Mutation research 36 10479728
2021 The ZEB2-dependent EMT transcriptional programme drives therapy resistance by activating nucleotide excision repair genes ERCC1 and ERCC4 in colorectal cancer. Molecular oncology 35 33931939
2019 ERCC1-XPF deficiency is a predictor of olaparib induced synthetic lethality and platinum sensitivity in epithelial ovarian cancers. Gynecologic oncology 35 30797591
2019 ERCC1/XPF Is Important for Repair of DNA Double-Strand Breaks Containing Secondary Structures. iScience 35 31153042
2012 Multiple DNA binding domains mediate the function of the ERCC1-XPF protein in nucleotide excision repair. The Journal of biological chemistry 33 22547097
2012 Association between XPF polymorphisms and cancer risk: a meta-analysis. PloS one 33 22768293
2011 MiR-192 inhibits nucleotide excision repair by targeting ERCC3 and ERCC4 in HepG2.2.15 cells. Biochemical and biophysical research communications 33 21672525
2021 Tissue-Specific DNA Repair Activity of ERCC-1/XPF-1. Cell reports 32 33440146
2013 Polymorphisms in the ERCC1 and XPF genes and risk of breast cancer in a Chinese population. Genetic testing and molecular biomarkers 32 23909490
2019 SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic acids research 31 31495888
2019 MiR-192-5p reverses cisplatin resistance by targeting ERCC3 and ERCC4 in SGC7901/DDP cells. Journal of Cancer 30 30854110
2018 miR‑138‑5p modulates the expression of excision repair cross‑complementing proteins ERCC1 and ERCC4, and regulates the sensitivity of gastric cancer cells to cisplatin. Oncology reports 30 30535472
2017 ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes. Nature cell biology 30 28368372
1995 Partial characterization of the DNA repair protein complex, containing the ERCC1, ERCC4, ERCC11 and XPF correcting activities. Mutation research 30 7596355
2019 The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding. Nucleic acids research 29 30566683
2018 Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features. Nucleic acids research 29 30165384
2013 Evaluation of rare variants in the new fanconi anemia gene ERCC4 (FANCQ) as familial breast/ovarian cancer susceptibility alleles. Human mutation 29 24027083
1993 Regional mapping of human DNA excision repair gene ERCC4 to chromosome 16p13.13-p13.2. Mutagenesis 29 8332082
2011 Formaldehyde-induced genome instability is suppressed by an XPF-dependent pathway. DNA repair 28 22186232
2018 DNA replication stress triggers rapid DNA replication fork breakage by Artemis and XPF. PLoS genetics 27 30059501
2013 Structure-specific endonucleases xpf and mus81 play overlapping but essential roles in DNA repair by homologous recombination. Cancer research 27 23576554
2019 Targeting DNA Repair in Tumor Cells via Inhibition of ERCC1-XPF. Journal of medicinal chemistry 25 31369707
2018 Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin. Scientific reports 25 29497062
2015 Repair synthesis step involving ERCC1-XPF participates in DNA repair of the Top1-DNA damage complex. Carcinogenesis 25 26025908
2012 Association between single nucleotide polymorphisms in ERCC4 and risk of squamous cell carcinoma of the head and neck. PloS one 25 22848636
2011 Lack of association between XPG Asp1104His and XPF Arg415Gln polymorphism and breast cancer risk: a meta-analysis of case-control studies. Breast cancer research and treatment 25 21424776
2000 Differential processing of UV mimetic and interstrand crosslink damage by XPF cell extracts. Nucleic acids research 25 11095693
1996 Roles of XPG and XPF/ERCC1 endonucleases in UV-induced immunostaining of PCNA in fibroblasts. Experimental cell research 24 8660947
2020 Computer-aided drug design of small molecule inhibitors of the ERCC1-XPF protein-protein interaction. Chemical biology & drug design 23 31891209
2017 ERCC4 variants identified in a cohort of patients with segmental progeroid syndromes. Human mutation 23 29105242
2012 The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition. Structure (London, England : 1993) 23 22483113
2020 XPF-ERCC1 protects liver, kidney and blood homeostasis outside the canonical excision repair pathways. PLoS genetics 22 32271760
2022 XPF activates break-induced telomere synthesis. Nature communications 21 36184605
2006 Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides 21 16584298
2011 Polymorphisms of the DNA repair genes XRCC1 and ERCC4 are not associated with smoking- and drinking-dependent larynx cancer in a Polish population. Experimental oncology 20 21423097
2019 TGF beta promotes repair of bulky DNA damage through increased ERCC1/XPF and ERCC1/XPA interaction. Carcinogenesis 19 30418489
2017 XPF knockout via CRISPR/Cas9 reveals that ERCC1 is retained in the cytoplasm without its heterodimer partner XPF. Cellular and molecular life sciences : CMLS 19 28130555
2016 Higher expression of XPF is a critical factor in intrinsic chemotherapy resistance of human renal cell carcinoma. International journal of cancer 19 27542841
2009 PCNA and XPF cooperate to distort DNA substrates. Nucleic acids research 19 20008103

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