Affinage

POLE4

DNA polymerase epsilon subunit 4 · UniProt Q9NR33

Length
117 aa
Mass
12.2 kDa
Annotated
2026-06-10
33 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLE4 is an accessory subunit of the leading-strand DNA polymerase epsilon (Polε) that, together with POLE3, constitutes a histone H3–H4 chaperone module coupling DNA replication to chromatin assembly and inheritance (PMID:30217558). The POLE3–POLE4 subcomplex selectively binds both newly synthesized and parental H3–H4, promotes tetrasome formation and DNA supercoiling in vitro, and at replication forks supports helicase unwinding, chromatin PCNA unloading, and coordinated retention of parental histones with deposition of new histones (PMID:30217558). This chaperone activity carries epigenetic information across replication: POLE3–POLE4 acts as an effector of the HUSH complex to enforce asymmetric segregation of H3K9me3 onto leading strands and silence LINE-1 retrotransposons (PMID:37938774), mediates transfer of parental H3.1 and H3.3 in a manner required for faithful chromosome segregation (PMID:35523900), and—together with the lagging-strand MCM2 pathway—ensures balanced parental histone transmission needed for proper H3K27me3 patterning, differentiation, and viability in embryonic stem cells (PMID:39970210). Beyond histone handling, POLE4 also mediates 'gripping' of newly synthesized dsDNA as one of two tiers of Polε processivity regulation (PMID:41339636). Loss of POLE4 destabilizes the entire Polε complex and triggers replication stress with inefficient origin firing and p53 activation, which is the cause of embryonic lethality in Pole4-null mice (PMID:29754823). POLE4 loss creates several genetic dependencies, including synthetic lethality with RTEL1 (PMID:32460026) and with the CHTF18-RFC2/5 PCNA loader (PMID:41339636), hypersensitivity to ATR inhibition (PMID:31506018), and—through PRIMPOL-dependent accumulation of single-stranded DNA gaps behind forks and elevated ATR/DNA-PK signaling—sensitization to PARP inhibitors that is independent of homologous recombination and acts in a pathway parallel to BRCA1 (PMID:38753485, PMID:38828775).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2006 Medium

    Established the structural basis for POLE3–POLE4 association, showing the partners heterodimerize through a histone-like domain and that the subcomplex is transcriptionally tied to S-phase entry.

    Evidence Histone-fold domain mutagenesis, reporter assays, and ChIP for E2F1/4 and MYC at the Pole3 promoter

    PMID:16403426

    Open questions at the time
    • Did not demonstrate chaperone or replication function
    • Functional consequence of cell-cycle regulation not tested at the protein level
  2. 2008 Medium

    Placed POLE4 within a chromatin-modifying context by identifying it as a component of the histone acetyltransferase ATAC complex.

    Evidence Affinity purification and mass spectrometry of the human ATAC complex

    PMID:18838386

    Open questions at the time
    • No functional dissection of POLE4's role within ATAC
    • Relationship between ATAC membership and Polε function unresolved
  3. 2018 High

    Defined the in vivo requirement for POLE4 by showing its loss destabilizes the whole Polε complex and drives a p53-dependent replication-stress phenotype, ordering POLE4 upstream of p53.

    Evidence Pole4-knockout mouse with Pole4-/-p53-/- epistasis rescue and origin-firing/p53 activation readouts

    PMID:29754823

    Open questions at the time
    • Molecular cause of impaired origin firing not resolved at this stage
    • Did not address chromatin/histone functions
  4. 2018 High

    Resolved the biochemical identity of POLE3–POLE4 as a histone H3–H4 chaperone that operates at replication forks, connecting Polε to nucleosome dynamics.

    Evidence HDX-MS domain mapping, in vitro tetrasome assembly and supercoiling assays, Co-IP, and depletion readouts of PCNA unloading and histone dynamics

    PMID:30217558

    Open questions at the time
    • Strand specificity of histone deposition not directly shown here
    • Link to epigenetic inheritance not yet established
  5. 2019 Medium

    Identified a therapeutically relevant dependency, showing POLE3/POLE4-deficient cells are hypersensitive to ATR inhibition.

    Evidence Genome-scale CRISPR/Cas9 screens with experimental validation of ATRi hypersensitivity

    PMID:31506018

    Open questions at the time
    • Mechanism linking POLE4 loss to ATR dependence not dissected
    • Single lab without deep pathway analysis
  6. 2020 High

    Uncovered a synthetic-lethal relationship between Polε accessory function and RTEL1-mediated fork progression, revealing how POLE4 loss is tolerated only when fork resolution is intact.

    Evidence Genome-wide synthetic lethal screen in C. elegans and Rtel1 loss in Pole4-/- mouse cells, with HR-intermediate and replication-completion assays

    PMID:32460026

    Open questions at the time
    • Precise molecular substrate driving HR-intermediate accumulation unclear
    • Whether chaperone activity is required for this interaction not separated
  7. 2022 High

    Connected the chaperone function to genome stability by showing POLE3–POLE4 transfers parental H3.1/H3.3 and that transfer-defective mutants mis-segregate chromosomes.

    Evidence SNAP-tag pulse-chase histone tracking, histone-binding mutants, and chromosome segregation assays

    PMID:35523900

    Open questions at the time
    • Coordination with lagging-strand recycling not addressed
    • How histone transfer defects cause segregation errors mechanistically not defined
  8. 2023 High

    Established POLE3–POLE4 as effectors of epigenetic inheritance by linking them to HUSH-directed asymmetric H3K9me3 segregation and retrotransposon silencing.

    Evidence Reciprocal Co-IP of HUSH with Polε, strand-specific H3K9me3 asymmetry assays, and LINE-1 expression analysis in POLE3/POLE4-deficient cells

    PMID:37938774

    Open questions at the time
    • Mechanism of HUSH recruitment to Polε not defined
    • How asymmetry is biochemically enforced unresolved
  9. 2024 High

    Defined POLE4 loss as a PARPi-sensitizing vulnerability acting through PRIMPOL-dependent ssDNA gaps rather than HR deficiency, in a pathway parallel to BRCA1.

    Evidence POLE3-POLE4 and POLE4 CRISPR knockouts with RAD51 foci, ssDNA gap detection, PRIMPOL and 53BP1 epistasis, fork-speed and ATR/DNA-PK signaling assays

    PMID:38753485 PMID:38828775

    Open questions at the time
    • How POLE4 loss promotes PRIMPOL repriming not mechanistically resolved
    • Why 53BP1 loss fails to rescue not fully explained
  10. 2025 High

    Integrated POLE4's functions by defining its leading-strand dsDNA 'gripping' role in Polε processivity, its synthetic lethality with the CHTF18-RFC2/5 loader, and the requirement for iron metabolism to sustain Polε activity when POLE4 is absent.

    Evidence CRISPR genetic screens in POLE4-null cells, structural modelling, biochemical reconstitution, and leading-strand synthesis assays

    PMID:41339636

    Open questions at the time
    • Structural detail of the gripping mechanism is modelled rather than solved
    • Link between ISC/iron metabolism and Polε activity not fully dissected
  11. 2025 High

    Showed that leading- and lagging-strand parental histone recycling are jointly required by demonstrating that combined POLE4/MCM2-2A loss disrupts histone transmission, perturbs H3K27me3, and compromises ESC differentiation.

    Evidence Inducible POLE4 and MCM2-2A double mutants with parental histone tracking, H3K27me3 ChIP, expression profiling, and differentiation assays

    PMID:39970210

    Open questions at the time
    • Causal chain from histone mislocalization to H3K27me3 gain not fully mapped
    • Tissue-specificity beyond ESCs not tested
  12. 2025 Low

    Reported a candidate physical link between POLE4 and WWOX-associated DNA damage repair.

    Evidence Co-immunoprecipitation of POLE4 with WWOX wild-type versus P282A mutant

    PMID:41124647

    Open questions at the time
    • Single Co-IP without functional validation
    • POLE4's role in WWOX-mediated repair not dissected
    • No reciprocal or in vitro confirmation

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the chaperone, dsDNA-gripping, and processivity functions of POLE4 are mechanistically partitioned, and how POLE4 loss is sensed to trigger PRIMPOL repriming and replication-stress signaling, remain unresolved.
  • No high-resolution structure of POLE3-POLE4 engaging dsDNA in the holoenzyme
  • Direct trigger linking POLE4 loss to PRIMPOL gap formation undefined
  • Human Mendelian disease association not established in the corpus

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0042393 histone binding 4 GO:0003677 DNA binding 2 GO:0060090 molecular adaptor activity 1
Localization
GO:0005634 nucleus 3 GO:0000228 nuclear chromosome 2
Pathway
R-HSA-4839726 Chromatin organization 4 R-HSA-69306 DNA Replication 3 R-HSA-73894 DNA Repair 2 R-HSA-8953897 Cellular responses to stimuli 2
Partners
HUSH COMPLEXPOLE1POLE3WWOX
Complex memberships
ATAC complexDNA polymerase epsilon (Polε)POLE3-POLE4 histone H3-H4 chaperone subcomplex

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2018 POLE3-POLE4 forms a subcomplex of DNA polymerase epsilon (Polε) that selectively binds histones H3-H4. Using hydrogen/deuterium exchange mass spectrometry and physical domain mapping, minimal interaction domains were defined. Biochemically, POLE3-POLE4 promotes tetrasome formation and DNA supercoiling in vitro, establishing it as a histone H3-H4 chaperone. In cells, POLE3-POLE4 binds both newly synthesized and parental histones, and its depletion hinders helicase unwinding, chromatin PCNA unloading, and compromises coordinated parental histone retention and new histone deposition at replication forks. Hydrogen/deuterium exchange mass spectrometry, physical domain mapping, in vitro tetrasome assembly assay, DNA supercoiling assay, Co-IP, cellular depletion with readouts of PCNA unloading and histone dynamics Molecular cell High 30217558
2018 POLE4 deficiency in mice destabilizes the entire Polε complex (POLE1-POLE4), leading to embryonic lethality in inbred strains and developmental abnormalities in outbred strains. POLE4 loss is associated with replication stress, p53 activation, and inefficient replication origin firing. Genetic removal of p53 rescues embryonic lethality and developmental abnormalities in Pole4-null mice, placing POLE4 upstream of p53 in a replication stress pathway. Pole4 knockout mouse model, genetic epistasis (Pole4-/-p53-/- double knockout rescue), replication origin firing assays, p53 activation measurements Molecular cell High 29754823
2023 The HUSH complex interacts with the leading-strand DNA polymerase Polε (including POLE3 and POLE4 subunits) and contributes to asymmetric segregation of H3K9me3 onto leading strands at replication forks. Cells deficient in POLE3 and POLE4 show compromised H3K9me3 asymmetry and increased LINE-1 retrotransposon expression, placing POLE3-POLE4 as effectors of HUSH-mediated epigenetic inheritance. Co-IP (HUSH-Polε interaction), POLE3/POLE4 knockdown/knockout with H3K9me3 strand-specific asymmetry assays, LINE-1 expression analysis Nature High 37938774
2022 POLE3 and POLE4 participate in the transfer of parental histones H3.1 and H3.3 following DNA replication. Pole3 and Pole4 mutants defective in parental histone transfer show defects in chromosome segregation, linking the histone chaperone function of POLE3-POLE4 to chromosome stability. SNAP-tag pulse-chase tracking of parental histones, Pole3/Pole4 histone-binding mutants, chromosome segregation assays Nature communications High 35523900
2020 Loss of POLE4 (the C. elegans ortholog POLE-4) has no overt phenotype alone in worms, but combined loss of POLE-4 and RTEL-1 results in synthetic lethality, embryonic lethality, accumulation of HR intermediates, genome instability, and cessation of DNA replication. Similarly, loss of Rtel1 in Pole4-/- mouse cells inhibits cellular proliferation with persistent HR intermediates and incomplete DNA replication, establishing a synthetic lethal genetic interaction between Polε accessory function and RTEL1-mediated fork progression. Genome-wide synthetic lethal screen in C. elegans, Pole4-/- mouse cells with Rtel1 loss, HR intermediate accumulation assay, DNA replication completion assays Cell reports High 32460026
2024 Loss of POLE3-POLE4 sensitizes cancer cells to PARP inhibitors in a Polε level-independent manner. This sensitization is not due to defective RAD51 foci formation (homologous recombination is intact). Instead, PARPi treatment triggers PRIMPOL-dependent replicative gap accumulation in POLE3-POLE4 knockout cells. Knockdown of 53BP1 does not rescue PARPi sensitivity in POLE3-POLE4 KO cells, bypassing a common PARPi resistance mechanism. POLE3-POLE4 CRISPR knockout, RAD51 foci assay (negative for HR defect), replicative gap detection, PRIMPOL epistasis experiments, 53BP1 knockdown epistasis Cell reports High 38753485
2024 POLE4 loss affects replication fork speed and leads to accumulation of single-stranded DNA gaps behind replication forks upon PARPi treatment due to impaired post-replicative repair. POLE4 knockouts elicit elevated replication stress signaling via ATR and DNA-PK. POLE4 acts in a pathway parallel to BRCA1 in mediating PARPi sensitivity, and POLE4 loss can counteract acquired PARPi resistance associated with restoration of homologous recombination. POLE4 CRISPR knockout, replication speed assays, ssDNA gap detection, ATR/DNA-PK signaling analysis, genetic epistasis with BRCA1 silencing and HR restoration Nucleic acids research High 38828775
2025 POLE3-POLE4 mediates leading strand 'gripping' of newly synthesised dsDNA, constituting one of two tiers of Polε processivity regulation. The combined loss of POLE3-POLE4 and the CHTF18-RFC2/5 PCNA loader is incompatible with leading strand synthesis and cell viability, defining a synthetic lethal interaction. Iron metabolism genes are required to sustain ISC-dependent Polε activity in the absence of POLE4. CRISPR genetic screens in POLE4-null cells, structural modelling, biochemical reconstitution, cell biology assays for leading strand synthesis Nature communications High 41339636
2025 Simultaneous disruption of leading strand parental histone recycling (POLE4) and lagging strand recycling (MCM2-2A) impairs transmission of parental histones to newly synthesized DNA and releases parental histones to the soluble pool. This causes aberrant H3K27me3 accumulation during chromatin restoration preceding gene expression changes, and ultimately compromises differentiation programs and cell viability in embryonic stem cells. Inducible POLE4 mutant and MCM2-2A double mutant, parental histone tracking, H3K27me3 ChIP, gene expression profiling, differentiation assays Science advances High 39970210
2019 Loss of POLE3/POLE4, the accessory subunits of DNA polymerase epsilon, results in marked hypersensitivity to ATR inhibition in genome-scale CRISPR/Cas9 screens, validated experimentally, placing POLE3/POLE4 function as genetically required for cell survival when ATR kinase activity is suppressed. Genome-scale CRISPR/Cas9 screens, validation of ATR inhibitor hypersensitivity in POLE3/POLE4 loss cells Open biology Medium 31506018
2008 POLE4 (along with POLE3/CHRAC17) is incorporated into the vertebrate ATAC (Ada Two-A containing) complex, which also contains GCN5/PCAF acetyltransferases, ADA2-A, ADA3, and other chromatin assembly/remodeling cofactors, physically linking POLE4 to a histone acetyltransferase complex. Affinity purification and mass spectrometry of human ATAC complex; POLE3/POLE4 identified as components The Journal of biological chemistry Medium 18838386
2006 POLE3 (DPB4/YBL1/CHRAC17) contains a histone-like domain required for heterodimerization with its POLE4 (DPB3) partner. The Pole3 promoter is cell-cycle regulated, with peaks at S-phase entry driven by E2F1/4 and MYC binding, as shown by mutagenesis and chromatin immunoprecipitation. Domain mutagenesis (histone-fold domain), reporter assays, ChIP for E2F1/4 and MYC binding to Pole3 promoter Gene Medium 16403426
2025 POLE4 was identified as a binding partner of WWOX by Co-IP, but this interaction is disrupted by the WWOXP282A mutant, suggesting POLE4 participates in nucleotide excision repair-related functions through WWOX. The interaction links POLE4 to WWOX-mediated DNA damage repair. Co-immunoprecipitation of POLE4 with WWOX wild-type vs. P282A mutant Advanced science Low 41124647

Source papers

Stage 0 corpus · 33 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2008 Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. The Journal of biological chemistry 176 18838386
2015 Frequency and phenotypic spectrum of germline mutations in POLE and seven other polymerase genes in 266 patients with colorectal adenomas and carcinomas. International journal of cancer 119 25529843
2018 POLE3-POLE4 Is a Histone H3-H4 Chaperone that Maintains Chromatin Integrity during DNA Replication. Molecular cell 116 30217558
2018 Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers. Genome research 110 29636374
2019 A consensus set of genetic vulnerabilities to ATR inhibition. Open biology 88 31506018
2018 Polε Instability Drives Replication Stress, Abnormal Development, and Tumorigenesis. Molecular cell 69 29754823
2012 Growth inhibition by miR-519 via multiple p21-inducing pathways. Molecular and cellular biology 61 22547681
2023 Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements. Nature 37 37938774
2014 MicroRNA and messenger RNA profiling reveals new biomarkers and mechanisms for RDX induced neurotoxicity. BMC genomics 24 25559034
2022 Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. Nature communications 20 35523900
2021 Novel LRRK2 mutations and other rare, non-BAP1-related candidate tumor predisposition gene variants in high-risk cancer families with mesothelioma and other tumors. Human molecular genetics 16 34008015
2021 Role of Amygdalin in Blocking DNA Replication in Breast Cancer In Vitro. Current pharmaceutical biotechnology 15 33535947
2021 Transcriptome sequencing reveals Gastrodia elata Blume could increase the cell viability of eNPCs under hypoxic condition by improving DNA damage repair ability. Journal of ethnopharmacology 13 34530095
2020 Personalized Assessment of Normal Tissue Radiosensitivity via Transcriptome Response to Photon, Proton and Carbon Irradiation in Patient-Derived Human Intestinal Organoids. Cancers 13 32085439
2023 Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer. Scientific reports 11 37950047
2022 Candidate Modifier Genes for the Penetrance of Leber's Hereditary Optic Neuropathy. International journal of molecular sciences 11 36233195
2006 The Pole3 bidirectional unit is regulated by MYC and E2Fs. Gene 11 16403426
2024 Loss of POLE3-POLE4 unleashes replicative gap accumulation upon treatment with PARP inhibitors. Cell reports 10 38753485
2023 Somatic Variants in DNA Damage Response Genes in Ovarian Cancer Patients Using Whole-exome Sequencing. Anticancer research 10 37097678
2020 Synthetic Lethality between DNA Polymerase Epsilon and RTEL1 in Metazoan DNA Replication. Cell reports 10 32460026
2023 Molecular landscapes of glioblastoma cell lines revealed a group of patients that do not benefit from WWOX tumor suppressor expression. Frontiers in neuroscience 8 37781246
2024 The loss of DNA polymerase epsilon accessory subunits POLE3-POLE4 leads to BRCA1-independent PARP inhibitor sensitivity. Nucleic acids research 7 38828775
2024 TET3 gene rs828867 G>A polymorphism reduces neuroblastoma risk in Chinese children. Heliyon 5 38509981
2025 'Where is my gap': mechanisms underpinning PARP inhibitor sensitivity in cancer. Biochemical Society transactions 4 39927794
2025 Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability. Science advances 3 39970210
2025 Proximal proteomics analysis reveals DNA polymerase δ subunit 3 is a new MCM2 binding partner and promotes parental histones inheritance in mammalian cells. Cell death and differentiation 3 41310184
2007 Human non-synonymous single nucleotide polymorphisms can influence ubiquitin-mediated protein degradation. Omics : a journal of integrative biology 2 17594238
2025 Genetic and Functional Evidence Links Germline Biallelic Inactivating Variants in WWOX to Histological Mixed-Type Thyroid Cancer. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 1 41124647
2025 Mitochondria-enriched nanovesicles: A novel approach for treating radiation-induced skin injury. Materials today. Bio 1 41142427
2025 Knockout of SIN3B modulates transcriptional programs and cell survival in cutaneous melanoma. Pharmacological research 0 40393534
2025 Unveiling Replication Timing-Dependent Mutational Biases: Mechanistic Insights from Gene Knockouts and Genotoxins Exposures. International journal of molecular sciences 0 40806440
2025 Comprehensive and In-Depth Molecular and Pathway Studies of the Hippocampus in Alzheimer's Disease. Cellular and molecular neurobiology 0 41317176
2025 The genetic and biochemical basis of human leading strand synthesis. Nature communications 0 41339636

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