Affinage

SLX4

Structure-specific endonuclease subunit SLX4 · UniProt Q8IY92

Length
1834 aa
Mass
200.0 kDa
Annotated
2026-04-28
100 papers in source corpus 42 papers cited in narrative 42 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SLX4 is a multidomain scaffold protein that coordinates genome maintenance by assembling and regulating distinct structure-specific endonucleases—SLX1, XPF-ERCC1, and MUS81-EME1—at sites of DNA damage, stalled replication forks, and telomeres (PMID:19596235, PMID:19596236, PMID:24012755). SLX4 stimulates SLX1 endonuclease activity up to 500-fold, enhances XPF-ERCC1 activity up to 100-fold to perform dual incisions during interstrand crosslink unhooking, and forms a CDK1-phosphorylation-dependent SLX-MUS holoenzyme that resolves Holliday junctions at G2/M (PMID:12832395, PMID:24726326, PMID:24076221, PMID:36288699). Recruitment to ICL sites requires UBZ domain-mediated recognition of ubiquitylated FANCD2 and RNF168-dependent ubiquitylation, while SUMO-interacting motifs direct SLX4 to ALT telomeres, fragile sites, and TopBP1 foci for mitotic DNA synthesis; SLX4 also functions as a SUMO E3 ligase and forms phase-separated condensates that compartmentalize the SUMO-RNF4 pathway to control nucleolytic processing and chromatin extraction of DNA-protein crosslinks (PMID:21464321, PMID:25533185, PMID:25533188, PMID:37059091, PMID:40615546). Biallelic loss-of-function mutations in SLX4 (FANCP) cause Fanconi anemia, characterized by cellular hypersensitivity to crosslinking agents and developmental abnormalities (PMID:21240276).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2003 High

    The foundational question of what enzymatic activity Slx1-Slx4 possesses was answered: yeast Slx1-Slx4 is a heteromeric structure-specific endonuclease that cleaves branched DNA substrates, with Slx4 stimulating Slx1 catalytic activity ~500-fold, establishing SLX4 as an activating partner rather than a catalytic subunit.

    Evidence In vitro endonuclease assays on defined branched substrates in S. cerevisiae and S. pombe, with mutagenesis of the Slx1 PHD finger and genetic epistasis with SGS1/Rqh1 helicases

    PMID:12832395 PMID:14528010

    Open questions at the time
    • Human ortholog function not yet characterized
    • No structural basis for Slx4-mediated activation of Slx1
    • Substrate specificity in vivo unknown
  2. 2007 High

    The question of whether Slx4 scaffolds multiple nucleases was first addressed in yeast: Slx4 binds two structure-specific endonucleases (Rad1 and Slx1) in a mutually exclusive manner, and checkpoint kinase phosphorylation of Slx4 by Mec1/Tel1 is required for Rad1-dependent single-strand annealing repair.

    Evidence Mutually exclusive co-IP of Rad1 and Slx1 with Slx4, phosphosite mapping, SSA repair assays with phosphomutants in S. cerevisiae

    PMID:17636031

    Open questions at the time
    • Whether mutually exclusive binding applies to the human system
    • Structural basis for exclusive binding not determined
  3. 2009 High

    The central question of human SLX4 function was resolved: three independent studies simultaneously demonstrated that human SLX4 (BTBD12) scaffolds XPF-ERCC1, MUS81-EME1, and SLX1 endonucleases and that SLX1-SLX4 is a Holliday junction resolvase required for ICL repair and homologous recombination.

    Evidence Co-IP/mass spectrometry interactome, in vitro nuclease assays on branched DNA, siRNA depletion with MMC sensitivity and HR reporter assays in human cells

    PMID:19595721 PMID:19596235 PMID:19596236

    Open questions at the time
    • How SLX4 distinguishes between substrates in vivo
    • Whether all three nucleases act simultaneously or are independently regulated
  4. 2010 High

    The regulatory logic connecting replication stress signaling to SLX4 complex assembly was established in yeast: Mec1 (ATR) phosphorylation of Slx4 and histone H2A nucleates recruitment of Slx4-Rtt107 behind stressed forks and promotes Dpb11 interaction, linking checkpoint signaling to scaffold complex assembly.

    Evidence Co-IP with phosphomutants, ChIP-seq at stressed forks, phosphosite mapping at defined DSBs in S. cerevisiae

    PMID:20382573 PMID:20670896

    Open questions at the time
    • Whether analogous checkpoint-dependent recruitment occurs in human cells
    • Structural basis for phospho-dependent interactions
  5. 2011 High

    How SLX4 is recruited to ICL damage sites was answered: the UBZ domain of SLX4 binds ubiquitylated FANCD2 to recruit SLX4 to ICL-induced foci, and the SLX4-XPF interaction is specifically required for crosslink repair, establishing SLX4 as FANCP in the Fanconi anemia pathway.

    Evidence UBZ mutant complementation in DT40 cells, co-IP with ubiquitylated FANCD2, Btbd12 knockout mice recapitulating FA phenotypes

    PMID:21240276 PMID:21464321

    Open questions at the time
    • Whether UBZ domains have additional ubiquitin-independent functions
    • Precise step at which SLX4-XPF acts during ICL unhooking
  6. 2013 High

    Two key questions were resolved simultaneously: how SLX4 resolves HJs in vivo through a coordinated SLX-MUS holoenzyme activated by CDK phosphorylation at G2/M, and how SLX4 accesses telomeres via direct TRF2 binding through a structurally characterized HxLxP motif.

    Evidence In vitro reconstitution of SLX-MUS holoenzyme with CDK phosphorylation, crystal structure of SLX4 TBM-TRF2 TRFH complex, telomere ChIP and IF, synthetic lethality with BLM/GEN1

    PMID:23994477 PMID:24012755 PMID:24076221 PMID:24080495

    Open questions at the time
    • How cells choose between SLX-MUS and GEN1 pathways
    • Whether telomeric SLX4 uses all three nucleases simultaneously
  7. 2014 High

    Multiple mechanistic advances established how SLX4 directs nuclease specificity and added new functions: SLX4 enhances XPF-ERCC1 activity 100-fold for dual ICL incisions, UBZ-1 preferentially binds K63-linked ubiquitin chains for ICL recruitment while UBZ-2 supports HJ resolution, and SLX4 functions as a SUMO E3 ligase via its BTB domain and SIMs, SUMOylating XPF and itself to prevent mitotic catastrophe at fragile sites.

    Evidence Recombinant mini-SLX4 biochemistry with synthetic fork substrates, Xenopus egg extract ICL repair, in vitro SUMO E3 ligase assays, SIM mutant complementation, ubiquitin chain specificity assays

    PMID:24726325 PMID:24726326 PMID:24794496 PMID:25533185 PMID:25533188

    Open questions at the time
    • Structural basis for 100-fold XPF stimulation
    • How SUMO E3 ligase activity is coordinated with nuclease scaffolding
    • In vivo substrates of SLX4-dependent SUMOylation beyond XPF
  8. 2015 High

    Structural studies revealed the activation mechanism of SLX1 by SLX4: Slx1 forms an auto-inhibitory homodimer occluding its active site, and Slx4 binding disrupts this dimer to activate Slx1, while the SAP domain of SLX4 positions the substrate for accurate 5'-flap cleavage.

    Evidence Crystal structures of C. glabrata Slx1 homodimer and Slx1-Slx4 complex, biochemical validation of dimerization-activation switch

    PMID:25753413 PMID:34181713

    Open questions at the time
    • Whether the homodimer-to-heterodimer switch is conserved in human SLX1
    • Full-length SLX4 structure remains undetermined
  9. 2016 High

    The structural basis for SLX4 dimerization was established: the BTB domain mediates SLX4 homodimerization through F681/F708 contacts, and dimerization is required for nuclear foci formation, telomeric localization of associated nucleases, and ICL repair.

    Evidence Crystal structure of SLX4 BTB domain, dimerization-disrupting mutations with IF, telomere localization, and MMC sensitivity readouts

    PMID:27131364

    Open questions at the time
    • Whether BTB dimerization is regulated by post-translational modifications
    • How dimerization relates to SUMO E3 ligase activity
  10. 2019 High

    SLX4's role expanded beyond DNA repair to replication-transcription conflict resolution: SLX4 directly interacts with the helicase RTEL1 at nascent DNA to prevent replication-transcription conflicts, while WRNIP1 was shown to protect reversed forks from SLX4-mediated nucleolytic degradation.

    Evidence Co-IP, iPOND, PLA for SLX4-RTEL1 interaction at active replication; DNA fiber assay with WRNIP1 KO and SLX4 epistasis

    PMID:31654852 PMID:32398829

    Open questions at the time
    • Structural basis of SLX4-RTEL1 interaction
    • Which SLX4-associated nuclease degrades reversed forks
    • Whether SLX4-RTEL1 function is cell-cycle regulated
  11. 2022 High

    The precise phosphoregulation of SLX4-MUS81 interaction was structurally resolved: CDK1-cyclin B phosphorylates three SLX4 residues (T1544/T1561/T1571) to fold an SAP domain that drives high-affinity MUS81 binding and relaxes MUS81 substrate specificity for resolution of recombination and replication intermediates.

    Evidence In vitro CDK1 phosphorylation, NMR/structural analysis of phosphorylated SLX4 MUS81-binding region, nuclease assays with phosphomimetic mutants

    PMID:36288699

    Open questions at the time
    • Whether phosphatases actively reverse this activation
    • In vivo validation of the phospho-dependent SAP domain folding
  12. 2023 High

    SLX4 was discovered to form biomolecular condensates through BTB-mediated dimerization and SUMO-SIM interactions, compartmentalizing the SUMO-RNF4 pathway to promote ubiquitylation and chromatin extraction of TOP1 DNA-protein crosslinks and nucleolytic degradation of nascent DNA.

    Evidence Super-resolution microscopy, live imaging of condensate dynamics, SUMO/ubiquitin proteomics, SIM and dimerization mutant analysis

    PMID:37059091

    Open questions at the time
    • Whether condensates form at all SLX4 functional sites (ICLs, telomeres, fragile sites)
    • How condensate dissolution is regulated beyond SENP6/RNF4
    • Whether nuclease activity occurs preferentially within condensates
  13. 2025 High

    Two recent advances extended SLX4 function: SLX4-XPF-ERCC1 performs precise dual incisions to excise acetaldehyde-induced ICLs, and TopBP1 recruits SLX4 via a SUMO-dependent interaction to promote mitotic DNA synthesis at under-replicated loci.

    Evidence In vitro incision of site-specific AA-ICL substrates by reconstituted SXE complex; TopBP1-SLX4 interaction-deficient mutants with MiDAS assays and DNA damage transmission analysis

    PMID:40615546 PMID:41006773

    Open questions at the time
    • In vivo relevance of AA-ICL repair by SXE in alcohol-exposed tissues
    • Whether TopBP1-SLX4 interaction is the primary MiDAS recruitment pathway

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include: the full-length structure of human SLX4 and how it simultaneously or sequentially coordinates multiple nuclease modules; the in vivo decision logic that determines which nuclease is activated at a given lesion; and whether SLX4 condensate formation is functionally required at all damage contexts or is specific to certain repair pathways.
  • No full-length structure of human SLX4
  • Decision logic for nuclease selection at different lesion types in vivo unknown
  • In vivo relevance of condensate formation across different damage types untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 5 GO:0098772 molecular function regulator activity 4 GO:0016874 ligase activity 1
Localization
GO:0005694 chromosome 3 GO:0005634 nucleus 2
Pathway
R-HSA-73894 DNA Repair 8 R-HSA-1640170 Cell Cycle 4 R-HSA-1852241 Organelle biogenesis and maintenance 3
Partners
EME1ERCC1FANCD2MUS81RTEL1SLX1TRF2XPF
Complex memberships
SLX-MUS holoenzyme (SLX1-SLX4-MUS81-EME1)SLX4-SLX4IP-XPF-ERCC1SLX4-XPF-ERCC1

Evidence

Reading pass · 42 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 Human SLX4 (BTBD12) was identified as a scaffold protein that assembles a multiprotein complex with three structure-specific endonucleases: XPF-ERCC1, MUS81-EME1, and SLX1. The SLX1-SLX4 module promotes symmetrical cleavage of static and migrating Holliday junctions, identifying it as a HJ resolvase. SLX4 complexes also cleave 3' flap, 5' flap, and replication fork structures. Co-immunoprecipitation, mass spectrometry, in vitro nuclease assays on branched DNA substrates, siRNA knockdown with sensitivity phenotypes Cell High 19595721 19596235 19596236
2009 Human SLX1-SLX4 displays robust Holliday junction resolvase activity in addition to 5' flap endonuclease activity. SLX4 binds the XPF(ERCC4) and MUS81 subunits of the XPF-ERCC1 and MUS81-EME1 endonucleases and is required for DNA interstrand crosslink repair. SLX4 acts as a docking platform for multiple structure-specific endonucleases. Affinity purification, in vitro HJ cleavage assays, siRNA depletion with MMC hypersensitivity and 53BP1/H2AX foci readouts Cell High 19596236
2009 SLX4 acts as a regulator and enhancer of the nuclease activity of SLX1, MUS81, and XPF. SLX4 immunoprecipitates show SLX1-dependent nuclease activity toward Holliday junctions and MUS81-dependent activity toward other branched DNA structures. Depletion of SLX4 causes defects in DSB-induced homologous recombination. Immunoprecipitation followed by nuclease activity assays, siRNA depletion, HR reporter assays Molecular cell High 19595721
2003 Yeast Slx1-Slx4 encodes a heteromeric structure-specific endonuclease active on branched DNA substrates (simple-Y, 5'-flap, replication fork structures), cleaving the strand bearing the 5' nonhomologous arm at the branch junction. Slx1 displays weak endonuclease activity alone and is stimulated ~500-fold by Slx4; the PHD finger of Slx1 is required for activity in vitro and in vivo. In vitro endonuclease assays on defined branched DNA substrates, mutagenesis of PHD finger, genetic epistasis with SGS1/TOP3 Genes & development High 12832395
2013 SLX1-SLX4 and MUS81-EME1 define a second HJ resolution pathway (SLX-MUS) distinct from GEN1 in human cells. In response to CDK-mediated phosphorylation at G2/M, SLX1-SLX4 and MUS81-EME1 associate to form a stable SLX-MUS holoenzyme that can be reconstituted in vitro and acts as a more efficient HJ resolvase than SLX1-SLX4 alone, coordinating the active sites of two distinct endonucleases. Co-immunoprecipitation, in vitro reconstitution of SLX-MUS holoenzyme, biochemical HJ cleavage assays, CDK phosphorylation, siRNA depletion with chromosome segregation readouts Molecular cell High 24076221
2014 XPF-ERCC1 cooperates with SLX4/FANCP to carry out the unhooking incisions during replication-coupled ICL repair in Xenopus egg extracts. Efficient recruitment of XPF-ERCC1 and SLX4 to the ICL depends on FANCD2 and its ubiquitylation. Xenopus egg extract ICL repair assay, immunodepletion, add-back experiments, monitoring of incision products Molecular cell High 24726325
2014 The N-terminal domain of mouse SLX4 (mini-SLX4) that binds only XPF-ERCC1 is sufficient to confer resistance to DNA crosslinking agents. Recombinant mini-SLX4 enhances XPF-ERCC1 nuclease activity up to 100-fold and directs its specificity toward DNA forks, including stimulating dual incisions around a DNA crosslink in a synthetic replication fork. Recombinant protein biochemistry, in vitro nuclease stimulation assays, complementation of Slx4-deficient mouse cells, synthetic replication fork substrates Molecular cell High 24726326
2011 The UBZ (ubiquitin-binding zinc finger) domain of SLX4 is required for interaction with ubiquitylated FANCD2 and for recruitment of SLX4 to ICL-induced DNA damage foci. UBZ-deficient SLX4 cells are selectively sensitive to ICL-inducing agents, indicating ubiquitylated FANCD2 recruits SLX4 to damage sites for ICL repair. SLX4 knockout in DT40 cells, complementation with UBZ mutants, Co-IP of SLX4 with ubiquitylated FANCD2, immunofluorescence foci assays Proceedings of the National Academy of Sciences of the United States of America High 21464321
2012 SLX4-dependent XPF-ERCC1 activity is essential for ICL repair but dispensable for repairing TOP1 inhibitor-induced lesions. Conversely, MUS81-SLX4 interaction is critical for resistance to TOP1 inhibitors but less important for ICL repair. SLX1-SLX4 interaction contributes partially to resistance to both agents. Complementation of SLX4-null FA-P cells with SLX4 mutants lacking specific nuclease interactions; sensitivity assays to MMC and camptothecin Blood High 23093618
2014 The SLX4 complex functions as a SUMO E3 ligase that SUMOylates SLX4 itself and the XPF subunit of XPF-ERCC1. This activity is mediated by a specific interaction between SLX4 and the SUMO-charged E2 conjugating enzyme UBC9 and requires SUMO-interacting motifs (SIMs) and the BTB domain of SLX4. SLX4 SIMs are dispensable for ICL repair but critical to prevent mitotic catastrophe following common fragile site expression. In vitro SUMO E3 ligase assay, identification of SUMOylated substrates by MS, SIM mutant complementation, fragile site induction assays Molecular cell High 25533188
2013 SLX4 localizes to telomeres in human cells via a direct interaction with the shelterin subunit TRF2. The crystal structure of the SLX4 TRF2-binding motif (TBM) in complex with TRF2 TRFH domain reveals that TRF2 recognizes a unique HxLxP motif on SLX4. SLX4 assembles SLX1, XPF, and MUS81 at telomeres and negatively regulates telomere length via SLX1-catalyzed nucleolytic resolution of telomere DNA structures. Crystal structure determination, domain mapping by Co-IP/pulldown, telomere localization by ChIP and immunofluorescence, in vitro nuclease assays on telomeric substrates Cell reports High 24012755
2013 SLX4 is recruited to telomeres via a TRF2-binding motif, and this recruitment requires the SLX4-TRF2 interaction. SLX1 is recruited to telomeres by SLX4. TRF2-dependent recruitment of SLX4 prevents telomere damage, and SLX4 prevents telomere lengthening and fragility through mechanisms that are partly independent of telomere localization. Immunofluorescence co-localization, TRF2-binding motif mutagenesis, telomere damage foci assays, telomere length measurement Cell reports High 23994477
2014 HIV-1 Vpr causes G2/M cell cycle arrest through untimely activation of the SLX4 complex. Vpr directly interacts with SLX4, inducing recruitment of VPRBP (DCAF1) and kinase-active PLK1, and enhancing cleavage of DNA by SLX4-associated MUS81-EME1 endonucleases. Knockdown of SLX4, MUS81, or EME1 inhibits Vpr-induced G2/M arrest. The SLX4 complex also suppresses spontaneous and HIV-1-mediated induction of type I interferon. Co-immunoprecipitation, siRNA knockdown with G2/M flow cytometry, Vpr interaction mapping, cell cycle arrest assays Cell High 24412650
2014 SLX4 binds SUMO-2/3 chains via SUMO-interacting motifs (SIMs). SLX4 SIMs are dispensable for ICL repair but important for processing CPT-induced replication intermediates, suppressing fragile site instability, and localizing SLX4 to ALT telomeres. SUMO binding of SLX4 enhances its interaction with DNA-damage sensors or telomere-binding proteins including RPA, MRE11-RAD50-NBS1, and TRF2. SIM mutagenesis, SUMO chain binding assays, localization to laser-induced damage and ALT telomeres, functional complementation assays Molecular cell High 25533185
2015 The crystal structure of Candida glabrata Slx1 alone and in complex with the C-terminal region of Slx4 reveals that Slx1 forms a stable homodimer that blocks its active site. Slx1-Slx4 interaction is mutually exclusive with Slx1 homodimerization, providing a structural mechanism for Slx1 activation by Slx4. X-ray crystallography of Slx1 and Slx1-Slx4 C-terminal complex, biochemical validation of dimerization and activation Cell reports High 25753413
2014 SLX4 UBZ-1 domain (but not UBZ-2) binds ubiquitin polymers with preference for K63-linked chains, and UBZ-1 is required for SLX4 recruitment to ICL sites and for efficient ICL repair. UBZ-2 does not bind ubiquitin but is required for Holliday junction resolution in vivo. SLX4 is recruited to sites of ICL induction, but the UBZ-deleted FA patient form of SLX4 is not. In vitro ubiquitin-binding assays, immunofluorescence foci assays at ICL sites, murine cell complementation with UBZ mutants, Holliday junction resolution assay Journal of cell science High 24794496
2022 CDK1-cyclin B phosphorylates SLX4 residues T1544, T1561, and T1571 in the MUS81-binding region (SLX4MBR). Phosphorylated SLX4MBR drives folding of an SAP domain, underpinning high-affinity interaction with MUS81. This phosphorylation relaxes the substrate specificity of MUS81-EME1 and stimulates cleavage of replication and recombination structures. The structure of phosphorylated SLX4MBR and MUS81-binding interface were determined. In vitro CDK1-cyclin B phosphorylation, NMR/structural analysis of phosphorylated SLX4MBR, in vitro nuclease activity assays with phosphomimetic mutants, domain mapping Cell reports High 36288699
2015 The SAP domain of SLX4 is critical for efficient and accurate processing of 5'-flap DNA. The SAP domain binds the minor groove of DNA approximately one turn from the flap junction, and the 5'-flap interacts with the core domain of SLX1, accounting for specific recognition of 5'-flap DNA and specification of the cleavage site by SLX1-SLX4. Structural analysis (crystal structure of Slx1-Slx4 with DNA), biochemical assays, computational modeling Nucleic acids research High 34181713
2016 SLX4 dimerizes via its BTB domain. The crystal structure of the SLX4 BTB dimer was solved, identifying key contacts (F681 and F708) mediating dimerization. Disruption of BTB dimerization abrogates nuclear foci formation, telomeric localization of SLX4 and associated nucleases, and causes defective responses to ICL-inducing agents and telomere maintenance. Crystal structure of SLX4 BTB domain, BTB dimerization mutagenesis, immunofluorescence foci/telomere localization, MMC sensitivity assays Nucleic acids research High 27131364
2010 In budding yeast, Mec1 (ATR) mediates a key interaction between the fork protein Dpb11 and the DNA repair scaffolds Slx4-Rtt107 during replication stress. Slx4 phosphorylation by Mec1 is required for its interaction with Dpb11. Mutation of Mec1 phosphorylation sites in Slx4 disrupts Dpb11 interaction and compromises the cellular response to blocked replisomes. Co-immunoprecipitation, phosphorylation site mapping, phosphomutant complementation, MMS sensitivity assays Molecular cell High 20670896
2014 In yeast, cell cycle-dependent phosphorylation of Slx4 by Cdk1 promotes the Dpb11-Slx4 interaction. In mitosis, additional phosphorylation of Mms4 by Polo-like kinase Cdc5 promotes association of Mus81-Mms4 with the Dpb11-Slx4 complex, activating Mus81-Mms4 for resolution of sister chromatid joint molecules. The DNA damage checkpoint counteracts Mus81-Mms4 binding to the Dpb11-Slx4 complex. Phosphorylation site mapping, genetic epistasis, Co-IP of complex assembly, joint molecule resolution assays Genes & development High 25030699
2007 In budding yeast, Slx4 is phosphorylated by Mec1 and Tel1 kinases after DNA damage. Slx4 associates physically, in a mutually exclusive manner, with two structure-specific endonucleases Rad1 and Slx1. Rad1-dependent DNA repair by single-strand annealing (SSA) requires Slx4. Phosphorylation of Slx4 by Mec1/Tel1 is essential for SSA but not for resistance to MMS. Phosphosite mapping, mutually exclusive Co-IP with Rad1 and Slx1, SSA repair assay, phosphomutant complementation Molecular and cellular biology High 17636031
2010 Phosphorylation of yeast Slx4 at Thr113 by Mec1/Tel1 is required for efficient cleavage of 3' non-homologous DNA tails by Rad1-Rad10 during single-strand annealing and homologous recombination. Slx4 is recruited to 3' non-homologous tails during DSB repair independently of its phosphorylation. Deletion of both Mec1 and Tel1 severely reduces non-homologous DNA tail cleavage. Phosphosite mapping at a specific DSB, Slx4 ChIP at 3' NH tails, phosphomutant complementation of SSA efficiency, genetic deletion of Mec1/Tel1 DNA repair High 20382573
2005 In budding yeast, Slx4 forms a complex with Rtt107 (Esc4). Slx4 is required for phosphorylation of Rtt107 by the checkpoint kinase Mec1 in vivo, acting as a mediator of DNA damage-dependent phosphorylation. Slx4, but not Slx1, is required for repair of DNA alkylation damage and for recovery from checkpoint activation. Co-IP of Slx4 with Rtt107, checkpoint kinase assays, DNA damage sensitivity assays, epistasis with Slx1 Molecular biology of the cell High 16267268
2011 Genetic complementation of Btbd12 (mouse SLX4) knockout cells reveals a crucial requirement for Slx4 to interact with XPF-ERCC1 to promote crosslink repair. Btbd12 knockout mice recapitulate features of Fanconi anemia including reduced fertility, developmental defects, and cellular sensitivity to crosslinking agents. Btbd12 knockout mouse generation, genetic complementation with interaction-deficient SLX4 mutants, MMC sensitivity assays, chromosomal analysis Nature genetics High 21240276
2013 Lack of BLM and SLX4 or GEN1 and SLX4 is synthetically lethal in human cells in the absence of exogenous DNA damage, due to dysfunctional mitosis with unprocessed Holliday junctions. In vivo HJ resolution depends on both SLX4-associated MUS81-EME1 and SLX1, suggesting they act in concert in the context of SLX4. SLX4-null human cell lines, epistatic synthetic lethality analysis, chromosome segregation and mitotic phenotype assays, genetic rescue experiments Cell reports High 24080495
2014 SLX4 MUS81-binding interface point mutations were identified in MUS81 that abolish SLX4 interaction. These mutations fully rescued MMC hypersensitivity in MUS81 knockout murine cells but not in human cells, supporting an SLX4-dependent role for MUS81 in ICL-induced DSB repair specifically in human cells. Mutagenesis of MUS81-SLX4 interaction interface, Co-IP, complementation of MUS81 knockout cells from two species DNA repair Medium 25224045
2019 SLX4 directly interacts with the DNA helicase RTEL1. SLX4 and RTEL1 are recruited to nascent DNA and co-localize with active RNA pol II. SLX4 in complex with RTEL1 promotes FANCD2/RNA pol II co-localization. Disrupting the SLX4-RTEL1 interaction causes DNA replication defects in unstressed cells rescued by transcription inhibition, indicating the complex prevents replication-transcription conflicts. Co-immunoprecipitation, proximity ligation assay, iPOND (isolation of proteins on nascent DNA), interaction-deficient mutant complementation, DNA fiber assay Nature structural & molecular biology High 32398829
2019 SLX4IP binds to SLX4 and XPF-ERCC1 simultaneously, and disruption of one interaction also disrupts the other. SLX4IP binding to both partners maintains SLX4IP stability and promotes the SLX4-XPF-ERCC1 interaction, especially after DNA damage. SLX4IP depletion sensitizes cells to ICL-inducing agents. Co-immunoprecipitation, domain interaction mapping, protein stability assays, ICL sensitivity assays Nucleic acids research Medium 31495888
2021 SLX4 interacts with MSH2 via an MSH2-interacting peptide (SHIP box), which drives interaction with both MutSβ (MSH2-MSH3) and MutSα (MSH2-MSH6). The MSH2-binding domain of SLX4 is dispensable for ICL repair but mediates inhibition of MutSα-dependent mismatch repair by SLX4. Domain mapping by Co-IP, MMR activity assays, SLX4 SHIP box mutant complementation in MMR reporter assays Nucleic acids research Medium 35166826
2023 SLX4 dimerization and SUMO-SIM interactions drive the assembly of SLX4 membraneless compartments (condensates/nanocondensates) in the nucleus. SLX4 compartmentalizes the SUMO-RNF4 signaling pathway; SENP6 and RNF4 regulate assembly and disassembly of SLX4 condensates. SLX4 condensation induces ubiquitylation and chromatin extraction of topoisomerase 1 DNA-protein cross-links and induces nucleolytic degradation of newly replicated DNA. Super-resolution microscopy, live imaging, condensate formation assays, SUMO/ubiquitin proteomics, SIM and dimerization mutants Molecular cell High 37059091
2015 RNF168 E3 ubiquitin ligase is required for mitomycin C-induced SLX4 foci formation and recruitment of SLX4 to ICL sites. RNF168 and SLX4 colocalize in MMC-induced ubiquitin foci. RNF168 is epistatic with SLX4 in promoting MMC tolerance. siRNA screen for SLX4 recruitment factors, immunofluorescence at ICL tracks, epistasis assays Cell reports Medium 34706224
2019 Polyubiquitinated PCNA (polyUb-PCNA) at telomeres accumulates SLX4 through its ubiquitin-binding domain (UBZ) and increases telomere damage and BIR in ALT cancer cells. APB (ALT-associated PML body) increase induced by Ub-PCNA depends on SLX4 and structure-specific endonucleases. RAD18/USP1/ATAD5 perturbation, SLX4 UBZ mutants, Co-IP, telomere immunofluorescence, APB assays Nucleic acids research Medium 39291733
2025 Human TopBP1 promotes mitotic DNA synthesis (MiDAS) through recruitment of the nuclease scaffold SLX4. The interaction requires TopBP1-K704, SLX4-T1260, and SUMO-interaction motifs in SLX4. SLX4 recruitment to TopBP1 foci in mitosis prevents transmission of DNA damage to daughter cells. Immunofluorescence at FANCD2-marked sites, interaction-deficient mutants (TopBP1-K704, SLX4-T1260), MiDAS assays, DNA damage transmission analysis Communications biology Medium 40615546
2015 In budding yeast, Slx4 is recruited to chromatin behind stressed replication forks in a region distinct from the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes promote full activity of Mec1. ChIP-seq of Slx4 at stressed replication forks, genetic epistasis with H2A phosphorylation mutants, Mec1 activity assays The EMBO journal Medium 26113155
2016 The crystal structure of S. pombe Slx1 C-terminal zinc finger domain in complex with the C-terminal helix-turn-helix domain of Slx4 reveals a conserved binding mechanism. The Slx1 C-terminal domain is an atypical C4HC3-type RING finger required for Slx1 interaction with Slx4. S. pombe Slx1 C-terminal tail contains a SUMO-interacting motif that can recognize SUMO (Pmt3), suggesting recruitment by SUMOylated targets. X-ray crystallography at 2.0 Å, sequence analysis, SUMO binding assays Scientific reports High 26787556
2022 SLX4-XPF is required for homologous recombination triggered by Tus-Ter DNA-protein replication fork barriers in mouse cells. SLX4-XPF promotes error-prone long-tract gene conversion during DSB-induced HR and processes DNA-protein replication fork barriers for HR, operating distinctly from error-free HR at replication-independent DSBs. Site-specific Tus-Ter chromosomal barriers in mouse cells, Slx4 and Xpf mutant analysis, HR assay (Southern blot of recombination products), ICL sensitivity assays Nature structural & molecular biology High 35941380
2021 SLX4 cooperates with MUS81 to introduce DSBs after replication stress and counteracts pathological targeting of demised forks by GEN1. SLX4 physically prevents unscheduled GEN1-mediated fork cleavage independently of its nuclease-binding function. Ectopic expression of the Holliday junction-binding protein RuvA inhibits DSBs in SLX4-deficient cells by preventing GEN1 chromatin association. RNAi, FA-P cells complemented with SLX4 mutants abolishing MUS81/SLX1 interactions, GEN1 chromatin association assays, DSB quantification Scientific reports Medium 28290553
2015 Physical interaction between SLX4 and XPF has been mapped to a specific SLX4 region; the SLX4(Y546C) and SLX4(L530Q) missense variants are defective in XPF interaction and cannot complement Fancp knockout mouse cells for MMC-induced cytotoxicity or chromosomal aberrations. Immunoprecipitation interaction mapping, complementation of Fancp knockout mouse cells, MMC cytotoxicity and chromosomal aberration assays DNA repair Medium 26453996
2003 Fission yeast Slx1-Slx4 is a structure-specific endonuclease that introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA and maintains rDNA copy number. Slx1 associates with chromatin at rDNA loci. Simultaneous elimination of Slx1-Slx4 endonuclease and Rqh1 helicase is lethal. In vitro endonuclease assays on defined substrates, chromatin immunofluorescence, genetic deletion epistasis Molecular biology of the cell High 14528010
2025 The Slx4-Xpf-Ercc1 (SXE) nuclease complex specifically excises acetaldehyde-induced interstrand DNA crosslinks (AA-ICL) by performing two precise incisions flanking the AA-ICL in a synthetic replication fork substrate, demonstrating a direct role for SXE in repair of alcohol-induced DNA damage. In vitro nuclease incision assays on site-specific AA-ICL-containing replication fork substrates, biochemical characterization of dual incision products Communications biology High 41006773
2019 WRNIP1 protects reversed replication forks from SLX4-mediated endonucleolytic degradation, acting downstream of fork reversal. WRNIP1 protection is mechanistically distinct from BRCA2-dependent fork protection and is specific to the shorter variant of WRNIP1. WRNIP1 KO and complementation with variants, DNA fiber assay, SLX4 genetic epistasis, reversed fork substrate protection assay iScience Medium 31654852

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Cell 374 19596235
2009 Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell 341 19596236
2011 Mutations of the SLX4 gene in Fanconi anemia. Nature genetics 277 21240275
2009 Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. Molecular cell 272 19595721
2013 Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells. Molecular cell 255 24076221
2014 XPF-ERCC1 acts in Unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4. Molecular cell 254 24726325
2011 SLX4, a coordinator of structure-specific endonucleases, is mutated in a new Fanconi anemia subtype. Nature genetics 241 21240277
2014 Premature activation of the SLX4 complex by Vpr promotes G2/M arrest and escape from innate immune sensing. Cell 177 24412650
2003 Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3. Genes & development 173 12832395
2011 Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia. Nature genetics 170 21240276
2011 Involvement of SLX4 in interstrand cross-link repair is regulated by the Fanconi anemia pathway. Proceedings of the National Academy of Sciences of the United States of America 167 21464321
2009 Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. Molecular cell 144 19595722
2012 Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Blood 142 23093618
2017 BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres. The EMBO journal 137 28877996
2014 Mouse SLX4 is a tumor suppressor that stimulates the activity of the nuclease XPF-ERCC1 in DNA crosslink repair. Molecular cell 119 24726326
2013 Human GEN1 and the SLX4-associated nucleases MUS81 and SLX1 are essential for the resolution of replication-induced Holliday junctions. Cell reports 119 24080495
2014 The SLX4 complex is a SUMO E3 ligase that impacts on replication stress outcome and genome stability. Molecular cell 115 25533188
2014 Roles of SLX1-SLX4, MUS81-EME1, and GEN1 in avoiding genome instability and mitotic catastrophe. Genes & development 114 24831703
2003 Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Molecular biology of the cell 104 14528010
2013 SLX4 assembles a telomere maintenance toolkit by bridging multiple endonucleases with telomeres. Cell reports 99 24012755
2019 RAD52 and SLX4 act nonepistatically to ensure telomere stability during alternative telomere lengthening. Genes & development 98 30692206
2007 Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand annealing mode of DNA repair in budding yeast. Molecular and cellular biology 86 17636031
2010 DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Molecular cell 83 20670896
2014 A cell cycle-regulated Slx4-Dpb11 complex promotes the resolution of DNA repair intermediates linked to stalled replication. Genes & development 80 25030699
2013 Combinatorial regulation of meiotic holliday junction resolution in C. elegans by HIM-6 (BLM) helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases. PLoS genetics 80 23901331
2013 Localization-dependent and -independent roles of SLX4 in regulating telomeres. Cell reports 77 23994477
2010 GEN1/Yen1 and the SLX4 complex: Solutions to the problem of Holliday junction resolution. Genes & development 76 20203129
2005 Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Molecular biology of the cell 74 16267268
2014 Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance. Molecular cell 71 25533185
2011 Mammalian BTBD12 (SLX4) protects against genomic instability during mammalian spermatogenesis. PLoS genetics 65 21655083
2002 Role of SGS1 and SLX4 in maintaining rDNA structure in Saccharomyces cerevisiae. Current genetics 61 12228808
2015 SLX4 contributes to telomere preservation and regulated processing of telomeric joint molecule intermediates. Nucleic acids research 59 25990736
2012 Distinct roles of Mus81, Yen1, Slx1-Slx4, and Rad1 nucleases in the repair of replication-born double-strand breaks by sister chromatid exchange. Molecular and cellular biology 58 22354996
2015 SUMOylation and PARylation cooperate to recruit and stabilize SLX4 at DNA damage sites. EMBO reports 55 25722289
2010 Mec1/Tel1-dependent phosphorylation of Slx4 stimulates Rad1-Rad10-dependent cleavage of non-homologous DNA tails. DNA repair 46 20382573
2014 Distinct functional roles for the two SLX4 ubiquitin-binding UBZ domains mutated in Fanconi anemia. Journal of cell science 45 24794496
2023 Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair. Molecular cell 44 37059091
2018 SLX4: multitasking to maintain genome stability. Critical reviews in biochemistry and molecular biology 44 30284473
2005 Slx4 becomes phosphorylated after DNA damage in a Mec1/Tel1-dependent manner and is required for repair of DNA alkylation damage. The Biochemical journal 44 15975089
2011 FANCP/SLX4: a Swiss army knife of DNA interstrand crosslink repair. Cell cycle (Georgetown, Tex.) 43 21527828
2020 SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations. Nature structural & molecular biology 41 32398829
2014 G2/M cell cycle arrest correlates with primate lentiviral Vpr interaction with the SLX4 complex. Journal of virology 38 25320300
2016 Activation of the DNA Damage Response Is a Conserved Function of HIV-1 and HIV-2 Vpr That Is Independent of SLX4 Recruitment. mBio 37 27624129
2015 Assembly of Slx4 signaling complexes behind DNA replication forks. The EMBO journal 37 26113155
2015 Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic acids research 37 26490958
2015 Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease. Cell reports 36 25753413
2016 SLX4-SLX1 Protein-independent Down-regulation of MUS81-EME1 Protein by HIV-1 Viral Protein R (Vpr). The Journal of biological chemistry 34 27354282
2013 Assessment of SLX4 Mutations in Hereditary Breast Cancers. PloS one 34 23840564
2006 Rad22Rad52-dependent repair of ribosomal DNA repeats cleaved by Slx1-Slx4 endonuclease. Molecular biology of the cell 33 16467377
2016 Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation. International journal of radiation oncology, biology, physics 32 27084631
2019 SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic acids research 31 31495888
2008 Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae. Genetics 29 18579504
2005 Indirect evidence from DNA sequence diversity for genetic degeneration of the Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs. Journal of evolutionary biology 29 15715840
2011 Mutation analysis of the SLX4/FANCP gene in hereditary breast cancer. Breast cancer research and treatment 26 21805310
2019 The role of SLX4 and its associated nucleases in DNA interstrand crosslink repair. Nucleic acids research 24 30576517
2012 The nuclease hSNM1B/Apollo is linked to the Fanconi anemia pathway via its interaction with FANCP/SLX4. Human molecular genetics 24 22907656
2021 Coordinated roles of SLX4 and MutSβ in DNA repair and the maintenance of genome stability. Critical reviews in biochemistry and molecular biology 23 33596761
2012 Whole exome sequencing reveals uncommon mutations in the recently identified Fanconi anemia gene SLX4/FANCP. Human mutation 23 23033263
2021 Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex. Nucleic acids research 21 34181713
2019 WRNIP1 Protects Reversed DNA Replication Forks from SLX4-Dependent Nucleolytic Cleavage. iScience 21 31654852
2016 Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma 21 27165041
2012 Analysis of the novel fanconi anemia gene SLX4/FANCP in familial breast cancer cases. Human mutation 21 22911665
2021 Exploring the Structures and Functions of Macromolecular SLX4-Nuclease Complexes in Genome Stability. Frontiers in genetics 19 34804132
2014 Nuclease delivery: versatile functions of SLX4/FANCP in genome maintenance. Molecules and cells 19 24938228
2022 Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell reports 18 36288699
2016 Dimerization of SLX4 contributes to functioning of the SLX4-nuclease complex. Nucleic acids research 18 27131364
2012 Low prevalence of SLX4 loss-of-function mutations in non-BRCA1/2 breast and/or ovarian cancer families. European journal of human genetics : EJHG 18 23211700
2022 The structure-specific endonuclease complex SLX4-XPF regulates Tus-Ter-induced homologous recombination. Nature structural & molecular biology 16 35941380
2021 Abraxas suppresses DNA end resection and limits break-induced replication by controlling SLX4/MUS81 chromatin loading in response to TOP1 inhibitor-induced DNA damage. Nature communications 16 34272385
2015 Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics 16 26362319
2014 Identification and characterization of MUS81 point mutations that abolish interaction with the SLX4 scaffold protein. DNA repair 16 25224045
2015 Physical interaction between SLX4 (FANCP) and XPF (FANCQ) proteins and biological consequences of interaction-defective missense mutations. DNA repair 14 26453996
2024 Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells. Nucleic acids research 13 39291733
2021 SLX4-XPF mediates DNA damage responses to replication stress induced by DNA-protein interactions. The Journal of cell biology 13 33347546
2019 Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Nucleic acids research 13 31584081
2016 Budding Yeast SLX4 Contributes to the Appropriate Distribution of Crossovers and Meiotic Double-Strand Break Formation on Bivalents During Meiosis. G3 (Bethesda, Md.) 13 27172214
2015 The Slx4-Dpb11 scaffold complex: coordinating the response to replication fork stalling in S-phase and the subsequent mitosis. Cell cycle (Georgetown, Tex.) 13 25496009
2012 Analysis of SLX4/FANCP in non-BRCA1/2-mutated breast cancer families. BMC cancer 13 22401137
2014 How SLX4 cuts through the mystery of HIV-1 Vpr-mediated cell cycle arrest. Retrovirology 12 25496524
2012 Sequencing analysis of SLX4/FANCP gene in Italian familial breast cancer cases. PloS one 12 22383991
2021 RNF168 E3 ligase participates in ubiquitin signaling and recruitment of SLX4 during DNA crosslink repair. Cell reports 11 34706224
2023 Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 Using Proximity Labeling and Affinity Purification. Journal of proteome research 10 37071664
2017 SLX4 Prevents GEN1-Dependent DSBs During DNA Replication Arrest Under Pathological Conditions in Human Cells. Scientific reports 10 28290553
2022 SLX4 dampens MutSα-dependent mismatch repair. Nucleic acids research 9 35166826
2014 Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae. G3 (Bethesda, Md.) 9 24700328
2023 PARP Inhibitors and Proteins Interacting with SLX4. Cancers 6 36765954
2014 Crossover recombination mediated by HIM-18/SLX4-associated nucleases. Worm 6 25057454
2023 Localization and expression of SLX4 in the testis of sterile male cattle-yak. Reproduction in domestic animals = Zuchthygiene 5 36880652
2021 PARP1 modulates telomere sister chromatid exchange and telomere length homeostasis by regulating telomere localization of SLX4 in U2OS cells. Life sciences 5 33945829
2020 Chromosome 16p13.3 Contiguous Gene Deletion Syndrome including the SLX4, DNASE1, TRAP1, and CREBBP Genes Presenting as a Relatively Mild Rubinstein-Taybi Syndrome Phenotype: A Case Report of a Saudi Boy. Case reports in genetics 5 32181026
2016 Crystal structure and SUMO binding of Slx1-Slx4 complex. Scientific reports 5 26787556
2025 TopBP1 coordinates DNA repair synthesis in mitosis via recruitment of the nuclease scaffold SLX4. Communications biology 4 40615546
2015 SLX4: not SIMply a nuclease scaffold? Molecular cell 4 25574947
2015 SLX4 gains weight with SUMO in genome maintenance. Molecular & cellular oncology 4 27308578
2024 In silico analysis of several frequent SLX4 mutations appearing in human cancers. microPublication biology 3 38828439
2017 A low-frequency haplotype spanning SLX4/FANCP constitutes a new risk locus for early-onset breast cancer (<60 years) and is associated with reduced DNA repair capacity. International journal of cancer 3 29044504
2011 Cancel all Hollidays for SLX4 mutations: identification of a new Fanconi anemia subtype, FANCP. Clinical genetics 2 21476996
2025 SLX1 silencing overcomes Olaparib resistance in metastatic castration-resistant prostate cancer by disrupting SLX4-mediated DNA repair complexes. Cancer biology & therapy 1 40789692
2025 Mechanistic insights into alcohol-induced DNA crosslink repair by Slx4-Xpf-Ercc1 nuclease complex in the Fanconi anaemia pathway. Communications biology 1 41006773
2023 Protocol for in vitro phosphorylation of the MUS81-binding region of SLX4 using CDK1-cyclin B. STAR protocols 1 36917604