ERCC4 Antibody, Biotin conjugated

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Product Specs

Buffer
Preservative: 0.03% Proclin 300
Constituents: 50% Glycerol, 0.01M PBS, pH 7.4
Form
Liquid
Lead Time
Typically, we can ship the products within 1-3 business days after receiving your order. Delivery time may vary depending on the purchase method or location. Please consult your local distributors for specific delivery details.
Synonyms
DNA excision repair protein ERCC 4 antibody; DNA excision repair protein ERCC-4 antibody; DNA excision repair protein ERCC4 antibody; DNA repair endonuclease XPF antibody; DNA repair protein complementing XP F cells antibody; DNA repair protein complementing XP-F cells antibody; ERCC 11 antibody; ERCC 4 antibody; ERCC11 antibody; ERCC4 antibody; Excision repair complementing defective in Chinese hamster antibody; Excision repair cross complementing rodent repair deficiency complementation group 4 antibody; excision repair cross-complementation group 4 antibody; FANCQ antibody; RAD 1 antibody; RAD1 antibody; Xeroderma pigmentosum complementation group F antibody; Xeroderma pigmentosum group F complementing protein antibody; Xeroderma pigmentosum group F-complementing protein antibody; Xeroderma pigmentosum VI antibody; XP; group G antibody; XP6 antibody; XPF_HUMAN antibody
Target Names
Uniprot No.

Target Background

Function
This antibody targets the ERCC4 protein, a key component of a structure-specific DNA repair endonuclease. ERCC4 plays a crucial role in 5-prime incision during DNA repair and is involved in homologous recombination, which helps remove interstrand cross-links.
Gene References Into Functions
  1. For the 11985 A>G polymorphism, lung cancer patients treated with irinotecan cisplatin/carboplatin regimen exhibiting a heterozygous genotype (AG) showed a significantly higher mortality risk (p = 0.0001). Additionally, the 673 C>T polymorphism was linked to an increased risk of lung cancer. PMID: 29741112
  2. Our research confirms that biallelic ERCC4 mutations lead to a dominant cerebellar ataxia phenotype with mild cutaneous symptoms, potentially accounting for a substantial proportion of the genetic causes of ARCA in Japan, where XP-F is prevalent. PMID: 29403087
  3. Silencing XPF significantly enhanced the sensitivity and survival following treatment with cisplatin in xenograft mice bearing renal cell tumors. PMID: 27542841
  4. The C allele of the 30028T/C polymorphism was associated with a significantly increased risk of ischemic stroke. PMID: 26888738
  5. Polymorphisms in the XPF gene have been linked to gastrointestinal stromal tumors. PMID: 27460091
  6. Inherited abnormalities in the DNA repair pathway, particularly XPF 30028C and TP53 Arg72Pro polymorphisms, act as prognostic factors for progression-free survival and overall survival in cutaneous melanoma patients. PMID: 26427666
  7. Based on our findings, we conclude that the XPF gene polymorphism Ser835Ser might be associated with a decreased risk of colorectal cancer. PMID: 26146099
  8. Polymorphisms within the ERCC4 gene have been associated with HPV-positive cervical cancer. PMID: 25812040
  9. Helicobacter Pylori induces double-stranded DNA breaks through the nucleotide excision repair endonucleases XPF and XPG. These enzymes, along with RelA, are recruited to chromatin in a highly coordinated manner, dependent on the type IV secretion system. PMID: 26411687
  10. SLX4 (FANCP) and XPF (FANCQ) proteins interact with each other and play a crucial role in the Fanconi anemia (FA) DNA repair pathway. PMID: 26453996
  11. Mus81-deficient cells fail to recover from exposure to low doses of replication inhibitors. Cell viability in these cells is dependent on the XPF endonuclease. PMID: 25879486
  12. Genotypes of ERCC1 (rs11615, rs3212986, and rs2298881) and XPF (rs2276465 and rs6498486) were determined using the Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) assay. PMID: 26045829
  13. XPF and XPC expression may be a potential predictive factor for bladder cancer. Smoking not only influences the recurrence of bladder cancer as a single factor but also exacerbates the effects of XPF and XPC defects. PMID: 25535740
  14. Low XPF expression in head and neck squamous cell carcinoma patients is associated with a better response to induction chemoradiotherapy, while high XPF expression correlates with a worse response. PMID: 25019640
  15. ERCC4 is located on human chromosome 16p13.12 and consists of 11 exons spanning approximately 28.2 kb. The broad tissue expression pattern of ERCC4 is similar to that of ERCC1. ERCC1 and ERCC4 genes encode the two subunits of the ERCC1-XPF nuclease. This enzyme plays a critical role in DNA damage repair and maintaining genomic stability. [Review] PMID: 26074087
  16. This meta-analysis suggests that the 3 common XPF polymorphisms rs744154, rs6498486, and rs1799801 are not associated with gastric cancer risk. PMID: 25342505
  17. ERCC4 rs1800067 polymorphism is not associated with cancer risk. PMID: 25292041
  18. Our study suggests that the rs1800067 genetic variant of XPF plays a role in the development of glioma. PMID: 24938470
  19. Genetic variants in XPF might contribute to the susceptibility to ESCC. PMID: 24709955
  20. The contribution of ERCC4/FANCQ coding mutations to hereditary breast cancer in Central and Eastern Europe is likely to be small. PMID: 24465539
  21. No significant associations were found between XPF polymorphisms in rs2276466 or rs6498486 and the risk of colorectal cancer in a Chinese population. PMID: 24861646
  22. The C2169A nonsense mutation in the XPF protein is closely associated with gastric carcinogenesis in the Chinese population. The XPF mutation is largely monoallelic, suggesting haplo-insufficiency of XPF. PMID: 24412486
  23. The frequency of Spanish individuals heterozygous for pathogenic mutations in the ERCC4 gene is approximately 0.3% and does not differ between familial breast/ovarian cancer patients and healthy controls. PMID: 24027083
  24. The rs1800067 G and rs2276466 G allele frequencies in Xeroderma pigmentosum complementation group f polymorphisms influence the risk of glioma. PMID: 23991957
  25. Overexpression of XPF decreased drug sensitivity in malignant melanoma. PMID: 23982883
  26. ERCC4 rs1800124 and MBD4 rs10342 non-synonymous single nucleotide polymorphism variants were associated with DNA repair capacity. PMID: 24004570
  27. Polymorphisms in rs180067, rs1799801, rs2276466, and rs744154 in XPF are associated with gastric cancer. PMID: 23679285
  28. A significantly decreased risk of gastric cancer was associated with the ERCC4 rs744154 GC/CC genotypes in a Chinese population. PMID: 23537993
  29. Frameshift mutation XP11BE not only eliminates the XPF-interaction motif, impairing DNA repair, but also reduces XPB solubility, leading to a lower intracellular level of transcription factor TFIIH and deficient transcription. PMID: 23385459
  30. Mutations in ERCC4, encoding the DNA-repair endonuclease XPF, cause Fanconi anemia. PMID: 23623386
  31. The ERCC4 tagSNPs, rs6498486 and rs254942, may play protective roles in gastric carcinogenesis, particularly in the development of atrophic gastritis. PMID: 23415627
  32. Two SNPs (rs2276466 and rs3136038) in ERCC4 may be functional and contribute to SCCHN susceptibility. PMID: 22848636
  33. XPG endonuclease promotes DNA breaks and DNA demethylation at promoters, enabling the recruitment of CTCF and gene looping, which is further stabilized by XPF. PMID: 22771116
  34. This meta-analysis suggests a lack of statistical evidence for the association between the four XPF SNPs and the overall risk of cancers. PMID: 22768293
  35. There is no evidence that the G1244A and T2505 single nucleotide polymorphisms in XPF affect the expression of ERCC1. PMID: 22609620
  36. XPF Arg415Gln may be a low-penetrant risk factor in the Caucasian ethnicity for developing breast cancer. PMID: 21424776
  37. These results indicate that the interaction between XPF and Eg5 plays a role in mitosis and DNA repair, providing new insights into the pathogenesis of XP-F and XFE. PMID: 22353549
  38. Data show that high XPF expression correlated with early time to progression, both by univariate and multivariate analysis. PMID: 21737503
  39. The gene polymorphism at the ERCC4 gene had no effects on the DNA damage of lymphocytes in coke oven workers. PMID: 17945097
  40. Results indicated that the Arg399Gln polymorphism of the XRCC1 gene and the Arg415Gln polymorphism of the ERCC4 gene may not be associated with smoking- and drinking-related larynx cancer in the Polish population. PMID: 21423097
  41. The association of MPM with DNA repair genes supports the hypothesis that increased susceptibility to DNA damage may favor asbestos carcinogenicity. PMID: 21277872
  42. Squamous cell carcinoma metastases of the head and neck exhibit increased levels of nucleotide excision repair protein XPF in vivo, which correlate with increased chemoresistance ex vivo. PMID: 20372803
  43. Studies indicate that a marginally statistically significant association was found for XRCC1 codon 399, XPD Asp312Asn, and XRCC1 codon 194 variants and head and neck cancer. PMID: 20429839
  44. The XPF promoter -357A>C polymorphism may regulate the expression of XPF and thereby contribute to susceptibility to and prognosis of bladder cancer. PMID: 20062074
  45. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator) PMID: 20201926
  46. XPF protein plays significant roles in psoralen ICL-mediated DNA repair and mutagenesis. PMID: 14728600
  47. The ternary complex of hRad52 and XPF/ERCC1 is the active species that processes recombination intermediates generated during the repair of DNA double-strand breaks and in homology-dependent gene targeting events. PMID: 14734547
  48. We demonstrate that RAD1 is an essential gene for sustained cell proliferation, and that loss of Rad1 causes destabilization of Rad9 and Hus1, consequently leading to disintegration of the sliding-clamp complex. PMID: 15184880
  49. XPF is required to form gamma-H2AX and likely double-strand breaks in response to interstrand crosslinks in human cells. PMID: 16678501
  50. A SNP (rs744154) in intron 1 was associated with recessive protection from breast cancer after adjustment for multiple testing in stage 2. This SNP is located in the first intron, within a region that is highly conserved across species, and could be causal. PMID: 17018596

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Database Links

HGNC: 3436

OMIM: 133520

KEGG: hsa:2072

STRING: 9606.ENSP00000310520

UniGene: Hs.567265

Involvement In Disease
Xeroderma pigmentosum complementation group F (XP-F); XFE progeroid syndrome (XFEPS); Xeroderma pigmentosum type F/Cockayne syndrome (XPF/CS); Fanconi anemia complementation group Q (FANCQ)
Protein Families
XPF family
Subcellular Location
Nucleus.

Q&A

What is ERCC4 and what biological pathways involve this protein?

ERCC4 (Excision Repair Cross-Complementing 4), also known as XPF, is a structure-specific endonuclease that forms a complex with ERCC1 to participate in multiple DNA repair pathways. This protein plays critical roles in nucleotide excision repair (NER) and interstrand crosslink (ICL) repair mechanisms . ERCC4's biological significance is underscored by the fact that mutations in this gene can lead to three distinct clinical disorders depending on the mutation type: Fanconi anemia (FA-Q subtype), xeroderma pigmentosum (XP-F), or XFE progeroid syndrome . The ERCC4-ERCC1 complex functions as a 5' endonuclease that makes incisions during DNA repair processes, acting downstream of FANCD2 monoubiquitination in the Fanconi anemia pathway .

What experimental applications are validated for ERCC4 antibodies?

ERCC4 antibodies have been validated across multiple experimental applications with specific dilution recommendations:

ApplicationValidated Dilution RangePositive Detection Systems
Western Blot (WB)1:500-1:5000HeLa cells, human kidney tissue, MCF-7 cells, SKOV-3 cells, T-47D cells
Immunoprecipitation (IP)0.5-4.0 μg per 1-3 mg protein lysateMCF-7 cells
Immunohistochemistry (IHC)1:20-1:200Human testis, brain, ovary, skin, and spleen tissues
Immunofluorescence (IF/ICC)1:50-1:500MCF-7 cells, COS7 cells
Flow Cytometry1:100HEK293T cells with overexpressed ERCC4

When using these antibodies, researchers should optimize conditions for their specific experimental systems, as antibody performance can be sample-dependent .

What are the advantages of biotin-conjugated ERCC4 antibodies over unconjugated variants?

Biotin-conjugated ERCC4 antibodies offer several methodological advantages:

  • Enhanced signal amplification: The biotin-streptavidin system provides one of the strongest non-covalent interactions in biology (Kd ≈ 10^-15 M), allowing for superior signal amplification in detection systems.

  • Versatile detection options: Compatible with various streptavidin-conjugated reporter molecules (fluorophores, enzymes, quantum dots), enabling flexible experimental design.

  • Multi-labeling capability: Facilitates simultaneous detection of multiple targets in co-localization studies, particularly valuable when examining ERCC4 interactions with other DNA repair proteins.

  • Reduced background in certain tissues: The biotin-streptavidin system can provide cleaner results in tissues with high endogenous immunoglobulin levels.

  • Stability advantage: Biotin conjugation can increase antibody shelf-life and resistance to denaturation during experimental procedures.

When using biotin-conjugated antibodies, researchers should block endogenous biotin (particularly in tissues like liver, kidney, and brain) using streptavidin/avidin blocking kits to minimize background signal.

What are the optimal sample preparation conditions for ERCC4 detection?

Optimal conditions for ERCC4 detection vary by application:

For Immunohistochemistry:

  • Antigen retrieval: TE buffer (pH 9.0) is recommended; citrate buffer (pH 6.0) can be used as an alternative

  • Fixation: 10% neutral buffered formalin for FFPE tissues

For Immunofluorescence:

  • Fixation: 4% paraformaldehyde (10-15 minutes) for cultured cells

  • Permeabilization: 0.1-0.5% Triton X-100 (5-10 minutes) for nuclear protein access

For Western Blotting:

  • Lysis buffers containing protease inhibitors are essential

  • Sample heating at 95°C for 5 minutes in reducing sample buffer

  • Expected molecular weight: Approximately 104 kDa (calculated), though observed at ~38 kDa in some systems

Since ERCC4 is primarily nuclear and associates with chromatin during DNA repair, nuclear extraction protocols may yield better results for certain applications.

What control samples are essential when using ERCC4 antibodies?

A robust experimental design requires these controls:

Positive Controls:

  • HEK293T cells transfected with ERCC4 expression vectors

  • HeLa cells (endogenous expression)

  • MCF-7 cells (endogenous expression)

Negative Controls:

  • ERCC4 knockdown/knockout cell lines

  • Isotype control (matched IgG class with no specific target)

  • Secondary antibody-only control

Specificity Controls:

  • Pre-absorption with immunizing peptide/protein

  • For biotin-conjugated antibodies: streptavidin-only control to assess endogenous biotin

These controls help distinguish specific signal from background and validate antibody specificity, particularly important when studying proteins involved in complex repair pathways.

How can ERCC4 antibodies be used to investigate the functional consequences of ERCC4 mutations?

ERCC4 antibodies provide powerful tools for investigating mutation consequences through multiple methodological approaches:

  • Protein Expression Analysis: Western blotting can reveal if mutations affect protein stability or expression levels. Research has shown that certain mutations like p.Arg689Ser maintain protein expression while others lead to truncated or unstable protein products .

  • Subcellular Localization Studies: Immunofluorescence can determine if mutations alter nuclear localization or chromatin association. Studies have demonstrated that some XP-F causing mutations result in cytoplasmic aggregation, while FA-causing mutations maintain nuclear localization .

  • Functional Complementation Assays: Using ERCC4 antibodies to monitor protein expression in genetic complementation studies where wild-type or mutant ERCC4 is introduced into deficient cells. This approach has been used to confirm that p.Leu230Pro and p.Arg689Ser mutations fail to complement MMC sensitivity in ERCC4-null cells .

  • Protein-Protein Interaction Analysis: Co-immunoprecipitation studies can assess if mutations disrupt the ERCC4-ERCC1 complex formation, essential for nuclease activity .

  • DNA Damage Response Pathway Analysis: Combined with markers of DNA damage (γH2AX) or repair intermediates (RAD51 foci), ERCC4 antibodies can help determine how mutations affect response to specific DNA damaging agents .

This multi-faceted approach has revealed that FA-causing ERCC4 mutations specifically compromise ICL repair without severely affecting nucleotide excision repair, explaining the distinct clinical presentation .

What methodological approaches can resolve contradictory ERCC4 antibody results across different experimental systems?

When facing contradictory results with ERCC4 antibodies, researchers should consider these methodological approaches:

  • Antibody Validation Hierarchy:

    • Genetic approach: Test in ERCC4 knockout/knockdown systems

    • Biochemical approach: Immunoprecipitation followed by mass spectrometry

    • Independent antibody approach: Use multiple antibodies targeting different epitopes

  • Epitope Accessibility Analysis:

    • ERCC4 undergoes conformational changes when bound to DNA or ERCC1

    • Some epitopes may be masked in certain protein complexes

    • Consider native versus denatured conditions in your experimental system

  • Cell-Type Specific Considerations:

    • ERCC4 expression levels vary across tissues and cell lines

    • Post-translational modifications may differ between cell types

    • DNA damage status affects ERCC4 localization and complex formation

  • Technical Optimization Matrix:

ParameterVariables to TestMeasurement Method
Antibody concentrationSerial dilutionsSignal-to-noise ratio
Blocking reagentsBSA vs. serum vs. commercial blockersBackground reduction
Incubation conditionsTime, temperature, buffer compositionSignal intensity and specificity
Detection systemsDirect vs. indirect, enzyme vs. fluorophoreSensitivity and resolution
  • Quantitative Validation Metrics:

    • Establish minimum acceptable specificity ratios

    • Implement statistical analysis of reproducibility

    • Consider absolute quantification using recombinant protein standards

By systematically addressing these factors, researchers can resolve contradictory results and establish reliable ERCC4 detection protocols.

How can researchers optimize ChIP-seq experiments using biotin-conjugated ERCC4 antibodies?

Chromatin immunoprecipitation sequencing (ChIP-seq) with biotin-conjugated ERCC4 antibodies requires specific optimization:

  • DNA Damage Induction Protocols:

    • ERCC4 binding to chromatin is enhanced following DNA damage

    • Consider treatment with cisplatin (interstrand crosslinks) or UV (for NER substrates)

    • Time course experiments to capture transient interactions

  • Crosslinking Optimization:

    • Standard formaldehyde (1%) may be insufficient for transient interactions

    • Test dual crosslinkers (formaldehyde plus disuccinimidyl glutarate)

    • Crosslinking time should be optimized (5-15 minutes) to prevent over-crosslinking

  • Sonication Parameters:

    • Target fragment size: 200-300bp for high-resolution binding site identification

    • Verify fragmentation efficiency by agarose gel electrophoresis

    • Consider enzymatic fragmentation alternatives for specific chromatin environments

  • Biotin-Streptavidin Capture Strategy:

    • Pre-clear lysates with streptavidin beads to reduce background

    • Block endogenous biotin with free avidin before adding antibody

    • Consider sequential ChIP for interacting protein complexes (e.g., ERCC4-ERCC1)

  • Bioinformatic Analysis Considerations:

    • Use appropriate peak calling algorithms sensitive to repair protein binding patterns

    • Compare damage-induced versus constitutive binding sites

    • Integrate with DNA damage mapping data (e.g., XR-seq) for functional correlation

This approach has successfully identified ERCC4 binding at sites of DNA damage and revealed unexpected roles in regulating gene expression at promoter regions.

What are the best strategies for multiplexed detection of ERCC4 and other DNA repair proteins?

Multiplexed detection of ERCC4 alongside other DNA repair proteins requires careful experimental design:

  • Antibody Selection Criteria:

    • Choose antibodies raised in different host species

    • Verify no cross-reactivity between detection systems

    • Ensure compatible fixation/permeabilization requirements

  • Biotin-Conjugated ERCC4 Advantage:

    • The biotin-streptavidin system provides flexible detection options

    • Can be visualized last in sequential staining protocols

    • Compatible with tyramide signal amplification for low-abundance detection

  • Recommended Multiplex Panel for DNA Repair Studies:

ProteinFunctionRecommended LabelingSubcellular Localization
ERCC4 (XPF)EndonucleaseBiotin-conjugated + streptavidin-fluorophoreNuclear
ERCC1ERCC4 binding partnerDirect fluorophore conjugateNuclear
FANCD2FA pathway markerDirect fluorophore conjugateNuclear foci
γH2AXDNA damage markerDirect fluorophore conjugateNuclear foci
RAD51Homologous recombinationDirect fluorophore conjugateNuclear foci
  • Sequential Staining Protocol:

    • Start with lowest abundance target first

    • Include stringent washing steps between antibodies

    • Consider antibody stripping for highly multiplexed panels

    • Validate each antibody individually before combining

  • Advanced Imaging Considerations:

    • Spectral unmixing for overlapping fluorophores

    • Super-resolution techniques for co-localization studies

    • Live-cell compatible tags for real-time dynamics

This approach has successfully demonstrated the sequential recruitment of repair factors and temporal dynamics of ERCC4 function in response to DNA damage.

How can ERCC4 antibodies be employed to study pathway-specific functions in different disease models?

ERCC4 antibodies can differentiate pathway-specific functions through these methodological approaches:

  • Disease-Specific Model Systems:

    • Fanconi anemia patient-derived cells: Study ICL repair function

    • XP-F patient-derived cells: Focus on NER function

    • Cancer cell lines with altered ERCC4: Examine chemoresistance mechanisms

  • Pathway-Specific DNA Damage Induction:

DNA Damaging AgentPrimary PathwayERCC4 RoleDetection Method
UV radiationNucleotide excision repairMake 5' incision with ERCC1Measure repair capacity by unscheduled DNA synthesis
Mitomycin CInterstrand crosslink repairProcess unhooking intermediatesChromosome breakage analysis, cell survival
CisplatinICL repair + NERBoth pathwaysAssess differential sensitivity patterns
CamptothecinTopoisomerase I inhibitorMinimal involvementNegative control (FA cells show normal response)
  • Functional Separation Methods:

    • Chromatin fractionation to isolate DNA-bound ERCC4

    • Immunoprecipitation with pathway-specific partners

    • CRISPR-induced mutations affecting specific domains

  • Quantitative Analysis Approaches:

    • Microscopy-based repair kinetics measurements

    • Repair capacity correlation with ERCC4 expression levels

    • Structure-function analysis using domain-specific antibodies

  • Therapeutic Response Applications:

    • Monitor ERCC4 as a biomarker for chemotherapy response

    • Target pathway-specific functions for synthetic lethality

    • Evaluate ERCC4 status in personalized medicine approaches

Studies have demonstrated that specific ERCC4 mutations like p.Arg689Ser disrupt ICL repair while preserving NER activity, explaining the Fanconi anemia phenotype without the photosensitivity typical of XP . This type of pathway-specific dysfunction analysis has significant implications for understanding disease mechanisms and developing targeted therapies.

What are the critical factors for successful western blot detection of ERCC4?

Western blot detection of ERCC4 requires attention to several technical factors:

  • Sample Preparation Considerations:

    • Nuclear extraction protocols improve detection of chromatin-bound ERCC4

    • Gentle lysis conditions help preserve protein-protein interactions

    • Protease inhibitors are essential to prevent degradation

  • Protein Size and Detection Parameters:

    • Calculated molecular weight: 104.5 kDa

    • Observed molecular weight: May appear at ~38 kDa in some systems

    • This discrepancy may represent detection of processed forms or alternative splice variants

  • Gel/Transfer Optimization:

    • 8% SDS-PAGE gels provide optimal resolution in the 100 kDa range

    • Extended transfer times (overnight at low voltage) improve high-molecular-weight protein transfer

    • PVDF membranes offer better protein retention than nitrocellulose for large proteins

  • Antibody Dilution Optimization:

    • Primary antibody: 1:1000-1:5000 for most applications

    • For biotin-conjugated antibodies: 1:500-1:2000

    • Streptavidin-HRP: Typically 1:10,000-1:50,000 depending on manufacturer

  • Signal Development Strategies:

    • Enhanced chemiluminescence (ECL) provides good sensitivity

    • For low abundance detection, consider fluorescent detection systems

    • Quantitative analysis requires linear range determination

For reproducible results, standardize protein loading (25-50 μg per lane) and include appropriate positive controls like HeLa or MCF-7 cells .

How should researchers optimize immunofluorescence protocols for ERCC4 detection in different experimental contexts?

Immunofluorescence protocols for ERCC4 require optimization based on experimental context:

  • Fixation Method Selection:

    • Paraformaldehyde (4%) preserves structural integrity

    • Methanol fixation can improve nuclear protein accessibility

    • Avoid glutaraldehyde which increases autofluorescence

  • Nuclear Antigen Accessibility:

    • Triton X-100 (0.1-0.5%) permeabilization is essential

    • Consider additional permeabilization with 0.5% saponin for dense chromatin

    • Pre-extraction with CSK buffer can reveal chromatin-bound fraction

  • Signal Enhancement Strategies:

    • For biotin-conjugated antibodies: Fluorescent streptavidin conjugates provide flexibility

    • Tyramide signal amplification can detect low abundance ERCC4

    • Anti-fading mounting media essential for quantitative imaging

  • Damage-Induced Foci Visualization:

    • Pre-treatment with DNA damaging agents (UV, MMC, cisplatin) induces foci formation

    • Time course experiments (0.5-24 hours post-damage) capture dynamic responses

    • Co-staining with γH2AX confirms DNA damage localization

  • Dilution Optimization by Context:

Experimental ContextSuggested Dilution RangeSpecial Considerations
Cultured cell lines1:100-1:200Pre-extraction may help visualize chromatin-bound fraction
Primary cells1:50-1:100Lower antibody concentration reduces background
Tissue sections1:20-1:50Requires stringent antigen retrieval
DNA damage-induced1:100-1:200Optimize timepoint for maximum foci visualization

Successful immunofluorescence has shown that ERCC4 forms discrete nuclear foci that co-localize with other repair factors following DNA damage .

What approaches can resolve detection challenges when studying ERCC4 in specific tissue types?

Tissue-specific detection of ERCC4 presents unique challenges requiring specialized approaches:

  • Tissue-Specific Fixation Optimization:

    • Brain tissue: Shorter fixation times (6-12 hours) prevent overfixation

    • Skin samples: Required for XP studies, needs minimal fixation (4-6 hours)

    • Bone marrow: Critical for FA studies, requires specialized fixatives

  • Antigen Retrieval Requirements:

    • TE buffer (pH 9.0) is generally recommended

    • Alternative: citrate buffer (pH 6.0)

    • Heat-induced epitope retrieval (95-100°C, 20 minutes) typically needed

  • Endogenous Biotin Blocking:

    • Critical for biotin-conjugated antibodies

    • Particularly important in biotin-rich tissues (liver, kidney, brain)

    • Implement avidin/biotin blocking kit before antibody incubation

  • Background Reduction Strategies:

Tissue TypeCommon ChallengeRecommended Solution
SkinHigh keratin backgroundExtended blocking (2+ hours), 0.1% Tween-20 in wash buffers
Bone marrowBlood cell autofluorescenceSudan Black B treatment (0.1-0.3%)
BrainLipofuscin autofluorescence0.1% Sudan Black B or TrueBlack® treatment
LiverEndogenous biotinAvidin-biotin blocking system, consider alternative conjugation
  • Signal Amplification Options:

    • Tyramide signal amplification for low abundance detection

    • Multi-layer detection systems (biotin-streptavidin-tertiary enhancement)

    • Quantum dots for multiplexed detection with improved signal-to-noise ratio

These approaches have successfully detected ERCC4 in human tissues including testis, brain, ovary, skin, and spleen , enabling studies of pathway-specific functions in disease-relevant tissues.

How can flow cytometry protocols with biotin-conjugated ERCC4 antibodies be optimized?

Flow cytometry with biotin-conjugated ERCC4 antibodies requires specific optimization steps:

  • Cell Preparation Protocol:

    • Fixation: 2-4% paraformaldehyde (10-15 minutes)

    • Permeabilization: 90% ice-cold methanol or 0.1% Triton X-100

    • Critical: Gentle cell handling to maintain nuclear integrity

  • Antibody Titration Strategy:

    • Starting dilution: 1:100 for ERCC4 antibodies

    • Serial dilutions (1:50, 1:100, 1:200, 1:400)

    • Determine optimal concentration by signal-to-noise ratio

  • Detection System Options:

    • Streptavidin-fluorophore conjugates (PE, APC, FITC)

    • Consider bright fluorophores (PE, PE-Cy7) for low-abundance targets

    • Tandem dyes provide flexible panel design options

  • Controls for Biotin-Based Systems:

    • Unstained cells

    • Secondary-only (streptavidin-fluorophore only)

    • Isotype control with biotin conjugation

    • Positive control: ERCC4-overexpressing cells

  • Data Analysis Considerations:

    • Gating strategy: Exclude debris, select single cells, then viable cells

    • Compare mean fluorescence intensity (MFI) rather than percent positive

    • For inducible systems: Calculate fold change in MFI after DNA damage

This approach has successfully detected ERCC4 expression in transfected HEK293T cells and can be adapted to study endogenous expression in various cell types and experimental conditions.

What considerations are important when designing immunoprecipitation experiments with ERCC4 antibodies?

Immunoprecipitation (IP) experiments with ERCC4 antibodies require careful design:

Interaction PartnerFunctionDetection StrategySpecial Considerations
ERCC1Essential cofactorCo-IP with ERCC4 antibodyPrimary interaction to validate
SLX4 (FANCP)Scaffold proteinCo-IP with ERCC4 antibodyMay require gentle lysis conditions
XPANER pathwayCo-IP after UV damageDamage-induced interaction
FANCD2FA pathwayCo-IP after ICL damageMonoubiquitinated form interaction
  • Elution and Detection Strategies:

    • For biotin-conjugated antibodies: Biotin competition elution preserves protein integrity

    • Standard elution: Gentle (native) or denaturing conditions depending on downstream applications

    • Western blot detection: Use clean detection systems to avoid antibody cross-reactivity

This approach has been successfully used to detect ERCC4 interaction partners in MCF-7 cells and can reveal damage-specific protein complexes when combined with appropriate DNA damaging agents.

How can ERCC4 antibodies contribute to precision medicine approaches in cancer therapy?

ERCC4 antibodies can play crucial roles in personalizing cancer treatments:

  • Biomarker Development Applications:

    • Expression level analysis in tumor biopsies

    • Localization patterns as predictive indicators

    • Post-translational modification status assessment

  • Chemotherapy Response Prediction:

    • ERCC4 levels correlate with cisplatin resistance in multiple cancer types

    • Functional assays measuring repair capacity can guide therapy selection

    • Monitoring dynamic changes during treatment can predict acquired resistance

  • Synthetic Lethality Approaches:

    • Identify tumors with specific ERCC4 pathway defects

    • Match with complementary targeted therapies

    • Monitor pathway status during treatment

  • Methodological Integration in Clinical Workflows:

ApplicationMethodologyClinical Utility
Expression screeningIHC on tissue microarraysPatient stratification
Functional assessmentRepair capacity assays in patient-derived modelsTherapy selection
Mutation impactAntibodies specific to common variantsPersonalized dosing
Treatment monitoringSerial liquid biopsies with ERCC4 detectionResistance prediction
  • Companion Diagnostic Development:

    • Standardized ERCC4 detection assays

    • Threshold determination for clinical decision-making

    • Validation in prospective clinical trials

These approaches leverage our understanding that FA-causing ERCC4 mutations specifically compromise ICL repair functions , potentially creating exploitable vulnerabilities in tumors with similar pathway alterations.

What methodological innovations are emerging for studying ERCC4 in chromatin contexts?

Advanced methodologies for studying ERCC4 in chromatin contexts include:

  • Proximity Ligation Assays (PLA):

    • Visualize ERCC4 interactions with specific partners in situ

    • Detect transient repair complexes at damage sites

    • Quantify interaction dynamics during repair progression

  • Chromatin Immunoprecipitation Innovations:

    • CUT&RUN: Improved signal-to-noise ratio over traditional ChIP

    • ChIP-SICAP: Identifies chromatin-bound protein complexes

    • HiChIP: Maps long-range chromatin interactions involving ERCC4

  • Single-Cell Approaches:

    • scCUT&Tag: Maps ERCC4 binding in individual cells

    • Single-cell protein analysis: Measures ERCC4 levels in heterogeneous populations

    • Spatial transcriptomics correlation with ERCC4 localization

  • Live-Cell Imaging Technologies:

    • CRISPR-based tagging of endogenous ERCC4

    • Split-fluorescent protein complementation for interaction visualization

    • Optogenetic control of ERCC4 recruitment

  • Integrated Multi-Omics Approaches:

    • Correlate ERCC4 binding with DNA damage locations

    • Map repair outcomes at ERCC4-bound sites

    • Link to transcriptional regulation and chromatin structure

These methodologies address the challenge of studying dynamic, low-abundance repair factors like ERCC4 in their native chromatin context, providing insights into the spatio-temporal organization of DNA repair processes.

How can ERCC4 antibodies be used to study the relationship between DNA repair and cellular aging?

ERCC4 antibodies provide valuable tools for investigating repair-aging connections:

  • Aging-Related ERCC4 Alterations:

    • Expression level changes during replicative and organismal aging

    • Post-translational modifications affecting function

    • Protein-protein interaction dynamics in aged cells

  • Progeroid Syndrome Research Applications:

    • XFE progeroid syndrome involves severe ERCC4 mutations

    • Compare molecular phenotypes across mutation spectrum

    • Correlate repair capacity with aging acceleration

  • Methodological Approaches for Senescence Studies:

TechniqueApplicationMeasurement Outcome
ImmunofluorescenceCo-localization with senescence markersAssociation with persistent DNA damage
ChIP-seqGenome-wide binding changesAge-related redistribution patterns
Protein interaction studiesCo-IP followed by mass spectrometryAltered repair complex formation
Functional repair assaysUnscheduled DNA synthesis, ICL repairAge-dependent repair capacity
  • Intervention Testing Models:

    • Monitor ERCC4 status during senolytic treatments

    • Assess impact of caloric restriction on ERCC4 function

    • Evaluate ERCC4 pathway activation by anti-aging compounds

  • Translational Applications:

    • Biomarkers of DNA repair capacity in aging

    • Therapeutic targets to enhance repair in aged tissues

    • Predictors of age-related disease susceptibility

Research has demonstrated that ERCC4 mutations can cause accelerated aging phenotypes , making this protein a critical node connecting DNA repair efficiency with aging processes and a valuable target for intervention development.

What considerations are important when developing highly multiplexed imaging approaches involving ERCC4?

Highly multiplexed imaging with ERCC4 antibodies requires specialized methodological approaches:

  • Panel Design Principles:

    • Include markers for different repair pathways

    • Add cell cycle phase indicators

    • Incorporate damage type-specific markers

  • Cyclic Immunofluorescence Methods:

    • Sequential staining-imaging-bleaching cycles

    • Biotin-conjugated ERCC4 antibodies as anchoring markers

    • Careful validation of epitope stability through cycles

  • Advanced Imaging Technologies:

TechnologyAdvantageERCC4 Application
CODEX40+ markers in single sampleComprehensive repair pathway mapping
Imaging Mass Cytometry40+ proteins at subcellular resolutionMetal-labeled antibodies for quantitative analysis
4i (iterative immunofluorescence)Repeated cycles on same sampleTemporal dynamics of repair complex assembly
Super-resolution microscopyNanoscale resolutionFine structure of repair foci
  • Data Analysis Challenges:

    • Image registration across cycles

    • Segmentation of nuclear structures

    • Quantification of co-localization events

    • Machine learning for pattern recognition

  • Validation Requirements:

    • Single-stain controls for each marker

    • Spillover compensation matrices

    • Comparison with orthogonal methods

    • Reproducibility across experimental conditions

These approaches enable unprecedented insights into the spatial organization of DNA repair processes, revealing how ERCC4 coordinates with other factors in complex repair pathways and how these interactions are altered in disease states.

How can researchers integrate ERCC4 antibody-based methods with genomic approaches for comprehensive pathway analysis?

Integrating antibody-based detection with genomic methods provides powerful insights:

  • Multi-Modal Data Integration Strategies:

    • Correlate ERCC4 binding sites (ChIP-seq) with mutation patterns (whole-genome sequencing)

    • Link protein levels (immunoblot) with expression profiles (RNA-seq)

    • Connect repair complex formation (IP-MS) with epigenetic landscapes (ATAC-seq)

  • Sequential Workflow Approaches:

Genomic MethodAntibody-Based Follow-upIntegrated Insight
DNA damage mappingERCC4 ChIP at damage sitesRepair efficiency correlation
CRISPR screensImmunoblot of pathway componentsCompensatory mechanism identification
RNA-seq after damageERCC4 ChIP-seq in same conditionsTranscription-repair coupling
Mutation signature analysisERCC4 functional assaysRepair deficiency biomarkers
  • Single-Cell Multi-Omics Integration:

    • Combine protein detection (ERCC4) with transcriptomics

    • Correlate repair capacity with cellular states

    • Track clonal evolution of repair-deficient cells

  • Spatial Biology Applications:

    • Multiplex imaging with spatial transcriptomics

    • Map repair centers relative to nuclear architecture

    • Correlate with 3D genome organization

  • Computational Framework Requirements:

    • Data normalization across platforms

    • Feature selection for cross-modal correlation

    • Network analysis to identify regulatory relationships

    • Machine learning integration of multi-modal data

This integrated approach has revealed that ERCC4 functions extend beyond canonical repair roles to include influences on gene expression and chromosome architecture, particularly at sites where transcription and repair pathways intersect.

What are the critical quality control measures for validating ERCC4 antibodies?

Comprehensive validation of ERCC4 antibodies should include:

  • Specificity Verification:

    • Testing in knockout/knockdown systems

    • Pre-absorption with immunizing antigen

    • Detecting expected molecular weight (~104 kDa)

    • Cross-validation with multiple antibodies to different epitopes

  • Application-Specific Validation Tests:

ApplicationValidation TestSuccess Criteria
Western BlotDetect single band at expected MWClear band at ~104 kDa with minimal background
ImmunoprecipitationPull down ERCC4 and known partnersEnrichment of ERCC4 and ERCC1
ImmunofluorescenceNuclear localization patternNuclear staining with damage-induced foci
ChIPEnrichment at known binding sitesSignal at damage sites or regulatory regions
Flow CytometryDetection in positive control cellsShift in positive versus negative populations
  • Reproducibility Assessment:

    • Inter-lot comparison

    • Inter-laboratory validation

    • Performance in multiple cell types/tissues

  • Functional Correlation Tests:

    • Antibody detection correlates with repair capacity

    • Signal changes appropriately after damage induction

    • Detection of mutant forms matches functional defects

  • Documentation Standards:

    • Detailed methods for each validation experiment

    • Raw data preservation and accessibility

    • Transparent reporting of limitations

These rigorous validation measures ensure reliable research outcomes when using ERCC4 antibodies across multiple experimental systems and applications.

What best practices should researchers follow when publishing studies using ERCC4 antibodies?

Researchers should adhere to these best practices for transparency and reproducibility:

  • Comprehensive Antibody Reporting:

    • Full product details: manufacturer, catalog number, lot number

    • Clone information for monoclonals (e.g., OTI2A1)

    • Host species and antibody class/isotype

    • For biotin-conjugated antibodies: conjugation method and ratio

  • Detailed Methodology Documentation:

    • Complete protocol with all buffer compositions

    • Incubation conditions (time, temperature, concentration)

    • Critical steps (blocking, washing stringency)

    • Image acquisition parameters or flow cytometry settings

  • Controls Disclosure:

    • Positive and negative controls used

    • Validation in relevant experimental system

    • Supporting data demonstrating specificity

    • Limitation acknowledgments

  • Data Presentation Standards:

Data TypeRequired InformationBest Practice
Western BlotFull blots with molecular weight markersShow biologically relevant replicates
ImmunofluorescenceRaw and processed imagesInclude scale bars and colocalization metrics
Flow CytometryGating strategy and controlsShow both histogram and statistical analysis
ChIP dataInput normalization methodInclude known targets as positive controls
  • Resource Sharing Commitments:

    • Detailed protocols deposition

    • Raw data availability statement

    • Reagent sharing policies

    • Analysis code/pipeline access

Adherence to these practices enhances research reproducibility and facilitates building upon existing knowledge in ERCC4 biology and DNA repair mechanisms.

What future directions are emerging for ERCC4 antibody development and application?

Emerging directions in ERCC4 antibody technology include:

  • Next-Generation Antibody Formats:

    • Recombinant antibody fragments for improved penetration

    • Nanobodies for super-resolution imaging applications

    • Bi-specific antibodies for proximity detection

    • Conditionally active antibodies for damage-induced detection

  • Advanced Conjugation Strategies:

    • Site-specific biotin conjugation for optimal orientation

    • Click chemistry-compatible antibodies for modular detection

    • Photoactivatable crosslinkers for capturing transient interactions

    • Degradation-resistant linkers for long-term imaging

  • Mutation-Specific Antibody Development:

    • Antibodies recognizing common pathogenic variants

    • Conformational-state specific antibodies

    • Post-translational modification status detection

    • Functional activity-reporting antibodies

  • Technological Integration Opportunities:

TechnologyApplication to ERCC4Potential Impact
CRISPR-based taggingEndogenous labelingNative context visualization
Spatial proteomicsRepair complex mappingComprehensive pathway organization
Deep learning analysisPattern recognition in repair fociPredictive biomarkers
Organ-on-chip modelsTissue-specific repair dynamicsPersonalized intervention testing
  • Translational Development Pathways:

    • Standardized diagnostic assays

    • Companion diagnostics for DNA repair-targeted therapies

    • Screening tools for chemical modulators of ERCC4 function

    • Non-invasive detection methods for clinical monitoring

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