GTF2H2C Antibody

What is GTF2H2C and why is it important in research?

GTF2H2C (General Transcription Factor IIH, Polypeptide 2C) is a component of the TFIIH (BTF2) complex, which plays critical roles in both transcription initiation and DNA repair mechanisms. TFIIH is a multisubunit transcription/DNA repair factor with several enzymatic activities. The core of TFIIH consists of five subunits (p89/XPB/ERCC3, p62, p52, p44, and p34), with GTF2H2C functioning as part of this machinery . Its importance in research stems from its involvement in fundamental cellular processes including nucleotide excision repair and RNA polymerase II-mediated transcription, making it a valuable target for studies on transcriptional regulation, DNA damage response, and related pathologies .

How do I choose between monoclonal and polyclonal GTF2H2C antibodies for my research?

The choice between monoclonal and polyclonal GTF2H2C antibodies depends on your experimental objectives:

For critical quantitative experiments requiring high reproducibility, monoclonal antibodies are preferable. For initial characterization or when working with fixed tissues, polyclonal antibodies often provide better sensitivity. When epitope accessibility is uncertain, polyclonal antibodies targeting multiple regions can increase detection success .

What species reactivity should I consider when selecting a GTF2H2C antibody?

Species reactivity is a crucial consideration when selecting GTF2H2C antibodies. The available antibodies show varying cross-reactivity profiles:

When working with non-human models, select antibodies with confirmed reactivity to your species of interest. For novel species applications, consider sequence homology analysis of the epitope region—antibodies targeting highly conserved regions (like the N-terminal sequence HLYVVVDGSR TMEDQDLKPN in ABIN2792028) offer better cross-species performance . Validation experiments are strongly recommended when using antibodies in species not explicitly confirmed by the manufacturer.

What are the optimal conditions for Western blot detection of GTF2H2C?

Optimizing Western blot conditions for GTF2H2C (predicted MW: 44 kDa) requires attention to several parameters:

Sample Preparation:

• Use tissues with known GTF2H2C expression (human breast or prostate carcinoma have been validated)

• Thoroughly lyse cells in RIPA buffer supplemented with protease inhibitors

• Include phosphatase inhibitors if phosphorylation status is relevant

Electrophoresis and Transfer:

• Use 10-12% SDS-PAGE gels for optimal resolution of the 44 kDa target

• Transfer proteins to PVDF membrane (preferred over nitrocellulose for this target)

• Verify transfer efficiency with reversible protein stain

Antibody Incubation:

• Block with 5% non-fat milk in TBST (some epitopes may require BSA instead)

• Primary antibody dilutions:

  • ABIN7127037: 1:200-1:1000

  • ABIN2792028: 1:200-1:2000

  • A9684: 1:200-1:2000

  • NBP308896: 1-2 μg/mL

• Incubate primary antibody overnight at 4°C for maximum sensitivity

• Use HRP-conjugated secondary antibodies at 1:5000-1:10000

Detection:

• Enhanced chemiluminescence (ECL) systems are sufficient for most applications

• For low abundance detection, consider enhanced ECL substrates

• Include positive control (LO2 cell lysate has been verified)

For quantitative applications, establish a standard curve with recombinant GTF2H2C protein at known concentrations and ensure exposure times remain in the linear range of detection.

How should I optimize immunohistochemistry protocols for GTF2H2C detection in FFPE tissues?

For optimal immunohistochemical detection of GTF2H2C in formalin-fixed, paraffin-embedded (FFPE) tissues:

Antigen Retrieval:

• Heat-induced epitope retrieval is crucial due to cross-linking during fixation

• Use citrate buffer (pH 6.0) in pressure cooker (20 minutes)

• Alternative: EDTA buffer (pH 9.0) if citrate buffer yields weak signals

Blocking and Antibody Parameters:

• Block with 10% normal serum from the same species as the secondary antibody

• Add 0.3% Triton X-100 for membrane permeabilization

• Primary antibody dilutions:

  • A9684: 1:50-1:200 (validated for IHC-P)

  • NBP308896: 1-2 μg/mL (validated for IHC-P)

• Incubate primary antibody overnight at 4°C in humid chamber

• Use appropriate HRP-conjugated secondary antibody with compatible detection system

Controls and Validation:

• Include positive control tissues (human breast or prostate carcinoma)

• Include a negative control by omitting primary antibody

• Consider dual staining with markers of cell compartments (nuclear, cytoplasmic) to confirm appropriate localization

Signal Development and Counterstaining:

• DAB (3,3'-diaminobenzidine) substrate for chromogenic detection

• Counterstain with hematoxylin (diluted to avoid masking specific staining)

• Dehydrate through alcohol gradient before mounting

For semi-quantitative analysis, establish a scoring system based on staining intensity and percentage of positive cells in different compartments (nuclear vs. cytoplasmic).

What are the critical parameters for immunofluorescence detection of GTF2H2C?

For successful immunofluorescence detection of GTF2H2C:

Cell/Tissue Preparation:

• For cell cultures: fix with 4% paraformaldehyde (10 min, room temperature)

• For tissues: use fresh-frozen sections or FFPE with appropriate antigen retrieval

• Permeabilize with 0.2% Triton X-100 in PBS (10 min, room temperature)

Staining Protocol:

• Block with 5% normal serum and 1% BSA in PBS (1 hour, room temperature)

• Primary antibody dilutions:

  • ABIN7127037: validated for IF, use at 1:50-1:200

  • NBP308896: use at 1-2 μg/mL

• Incubate primary antibody overnight at 4°C

• Use fluorophore-conjugated secondary antibodies (Alexa Fluor series recommended)

• Counterstain nuclei with DAPI (1 μg/mL, 5 min)

• Mount with anti-fade mounting medium

Critical Controls:

• Include cells with confirmed GTF2H2C expression and knockout/knockdown controls if available

• Perform peptide competition assay to confirm antibody specificity

• Include single-stained samples for accurate compensation in multi-color experiments

Imaging Parameters:

• Start with lower magnification to identify regions of interest before moving to higher magnification

• Adjust exposure times to avoid saturation

• Collect Z-stacks for co-localization studies

• Use consistent settings across comparative samples

GTF2H2C typically shows both nuclear and cytoplasmic localization, with enrichment in nuclear foci that correspond to sites of active transcription. This distribution pattern serves as an internal validation of staining specificity .

How can I validate GTF2H2C antibody specificity for chromatin immunoprecipitation (ChIP) experiments?

Validating GTF2H2C antibodies for ChIP applications requires rigorous testing, as not all antibodies suitable for Western blot or immunostaining work effectively in ChIP:

Pre-ChIP Validation:

• Perform IP with the antibody followed by Western blot to confirm pull-down of GTF2H2C

• Test antibody in immunofluorescence to verify nuclear localization

• If available, use knockout/knockdown systems as negative controls

ChIP Protocol Optimization:

• Crosslinking: start with standard 1% formaldehyde for 10 minutes

• Sonication: optimize to achieve DNA fragments of 200-500 bp

• Immunoprecipitation: test multiple antibody concentrations (2-10 μg per reaction)

• Include IgG control from the same species as the GTF2H2C antibody

• Include positive control antibody (e.g., RNA Polymerase II) to verify protocol efficacy

ChIP-qPCR Validation:

• Design primers for known TFIIH-associated promoters

• Compare enrichment to IgG control (>10-fold enrichment suggests specificity)

• Include negative control regions (gene deserts or heterochromatic regions)

ChIP-seq Considerations:

• Analyze peak distribution patterns (GTF2H2C should show enrichment at promoters and active transcription sites)

• Perform motif analysis on called peaks (should identify transcription initiation sequences)

• Compare binding profiles with other TFIIH components to confirm co-localization

While the search results don't explicitly mention ChIP applications for the listed antibodies, monoclonal antibodies like ABIN7127037 or NBP308896 that have been validated for nuclear protein detection would be reasonable starting candidates for ChIP optimization .

What approaches should I use to investigate the interaction between GTF2H2C and other components of the TFIIH complex?

To investigate interactions between GTF2H2C and other TFIIH components:

Co-immunoprecipitation (Co-IP):

• Use GTF2H2C antibodies (preferably monoclonal) for pull-down experiments

• Alternatively, tag GTF2H2C with epitope tags (HA, FLAG, etc.) if antibody efficiency is limiting

• Identify interacting partners by Western blot or mass spectrometry

• Verify reciprocal interactions using antibodies against known TFIIH components (p89/XPB/ERCC3, p62, p52, p44, and p34)

Proximity Ligation Assay (PLA):

• Combine antibodies against GTF2H2C and potential interacting partners

• Verify that antibodies are from different species to enable PLA detection

• Quantify interaction signals in different cellular compartments or conditions

Bimolecular Fluorescence Complementation (BiFC):

• Create fusion constructs of GTF2H2C and other TFIIH components with split fluorescent protein fragments

• Analyze reconstituted fluorescence as evidence of protein-protein interaction

• Include appropriate negative controls (non-interacting proteins)

FRET/FLIM Analysis:

• Tag GTF2H2C and interacting partners with compatible fluorophores

• Measure energy transfer as indicator of protein proximity

• Calculate interaction distances to model complex architecture

Analytical Size Exclusion Chromatography:

• Isolate native complexes from nuclear extracts

• Use GTF2H2C antibodies to identify fractions containing the protein

• Analyze co-fractionation with other TFIIH components

Functional Interaction Analysis:

• Perform siRNA knockdown of GTF2H2C

• Assess impact on TFIIH complex formation and stability

• Measure effects on transcription and DNA repair activities

These approaches should be combined to build a comprehensive understanding of GTF2H2C's role within the TFIIH complex, focusing on both structural and functional aspects of these interactions .

How can I distinguish between GTF2H2C and other closely related GTF2H2 family members in my experiments?

Distinguishing GTF2H2C from other GTF2H2 family members requires careful antibody selection and experimental design:

Antibody Selection Strategies:

• Choose antibodies targeting unique regions that differ between family members

• The N-terminal antibody ABIN2792028 targets the sequence "HLYVVVDGSR TMEDQDLKPN RLTCTLKLLE YFVEEYFDQN PISQIGIIVT" - verify this sequence's uniqueness through alignment with other GTF2H2 family members

• For monoclonal antibodies, request epitope information from manufacturers to confirm specificity

Western Blot Discrimination:

• Use high-resolution gels (10-12% acrylamide) to separate closely related proteins

• Include positive controls for each family member if available

• Consider 2D electrophoresis to separate based on both MW and pI

• Look for slight molecular weight differences (GTF2H2C: 44 kDa)

RT-PCR/qPCR Approaches:

• Design primers spanning unique exon junctions or sequence variations

• Validate primer specificity using overexpression constructs

• Perform melt curve analysis to confirm single amplicon

• Use digital PCR for absolute quantification of each family member

Mass Spectrometry Validation:

• Identify unique peptides that distinguish between family members

• Target these unique peptides in multiple reaction monitoring (MRM) assays

• Quantify relative abundance of each family member in your sample

Genetic Manipulation:

• Use CRISPR/Cas9 to selectively knock out GTF2H2C

• Confirm specific targeting using sequencing

• Validate antibody specificity using knockout cells as negative controls

Bioinformatic Analysis:

• Compile expression data from public databases to predict relative abundance in your experimental system

• Use this information to interpret ambiguous signals

By combining multiple approaches, you can achieve reliable discrimination between GTF2H2C and other family members, which is critical for accurate functional characterization .

What are the best approaches for quantitative analysis of GTF2H2C expression levels in human tissue samples?

For quantitative analysis of GTF2H2C expression in human tissues:

Tissue Preparation Considerations:

• Fresh-frozen tissues preserve protein integrity better than FFPE samples

• For FFPE, ensure consistent fixation times (24 hours recommended)

• Collect paired normal and diseased tissues from the same patient when possible

• Verify tissue quality and cellular composition by H&E staining

Western Blot Quantification:

• Use recombinant GTF2H2C protein to create standard curves

• Include loading controls appropriate for your tissue type (β-actin may vary; consider GAPDH or α-tubulin)

• Analyze multiple biological replicates (minimum n=3 per condition)

• Use digital imaging and analysis software rather than film for linear quantification

• Normalize to total protein (Ponceau S or similar) rather than single housekeeping genes

Immunohistochemistry Quantification:

• Develop a scoring system combining intensity (0-3+) and percentage of positive cells

• Use digital pathology software for unbiased quantification

• Consider multiplexed approaches to correlate with cell type markers

• Include tissue microarrays for high-throughput comparison across multiple samples

Flow Cytometry (for fresh tissues or cultured cells):

• Use NBP308896 or ABIN7127037 antibodies validated for flow cytometry

• Include appropriate isotype controls

• Permeabilize cells for intracellular staining

• Quantify mean fluorescence intensity and percentage of positive cells

• Consider combining with cell cycle analysis to detect expression variations

RT-qPCR (for mRNA level correlation):

• Design primers specific to GTF2H2C

• Use absolute quantification with standard curves

• Select reference genes validated for your specific tissue type

• Correlate mRNA and protein levels to identify post-transcriptional regulation

For comprehensive analysis, consider combining multiple quantification methods to overcome the limitations of each individual approach. Human breast and prostate carcinoma tissues have been validated as positive controls for GTF2H2C expression studies .

How should I interpret contradictory results between different GTF2H2C antibodies?

When facing contradictory results between different GTF2H2C antibodies:

Systematic Validation Approach:

• Compare the exact epitopes targeted by each antibody (N-terminal vs. C-terminal vs. full-length)

• Consider epitope accessibility in different experimental conditions

• Verify antibody specificity using:

  • Western blot with recombinant GTF2H2C protein

  • GTF2H2C overexpression systems

  • siRNA/shRNA knockdown or CRISPR knockout controls

  • Peptide competition assays

Common Causes of Discrepancies:

• Post-translational modifications masking specific epitopes

• Alternative splicing variants recognized differently by antibodies

• Cross-reactivity with other GTF2H2 family members

• Fixation/denaturation affecting epitope conformation differently

• Batch-to-batch variation (especially for polyclonal antibodies)

Resolution Strategies:

• Perform side-by-side comparison using standardized protocols

• Use orthogonal detection methods (e.g., mass spectrometry)

• Prioritize results from antibodies with most extensive validation

• Consider the biological context of your experiment

• Consult literature for similar discrepancies and their resolution

Documentation and Reporting:

• Thoroughly document all antibody information (catalog number, lot, dilution)

• Report discrepancies transparently in publications

• Include all validation experiments in supplementary materials

• Specify which antibody was used for each specific result

Understanding the biological basis of contradictory results can often lead to new insights about protein regulation, modification, or interaction that might otherwise be overlooked .

What are the most common technical challenges when working with GTF2H2C antibodies and how can they be overcome?

Common technical challenges with GTF2H2C antibodies and their solutions:

Challenge 1: Weak or Absent Signal

• Potential causes: Low protein expression, inefficient extraction, epitope masking

• Solutions:

  • Enrich nuclear fraction for better protein yield

  • Try multiple antigen retrieval methods for IHC/IF

  • Increase antibody concentration incrementally

  • Extended primary antibody incubation (overnight at 4°C)

  • Use signal amplification systems (TSA, polymeric detection)

  • Try different antibodies targeting different epitopes

Challenge 2: High Background

• Potential causes: Non-specific binding, excessive antibody concentration, inadequate blocking

• Solutions:

  • Optimize blocking (test BSA vs. normal serum vs. commercial blockers)

  • Increase washing duration and number of washes

  • Titrate antibody to find optimal concentration

  • Pre-adsorb polyclonal antibodies with tissue powder

  • Use monoclonal antibodies for higher specificity

Challenge 3: Multiple Bands in Western Blot

• Potential causes: Degradation, isoforms, cross-reactivity, post-translational modifications

• Solutions:

  • Use fresh samples with protease inhibitors

  • Verify band pattern with different antibodies

  • Perform peptide competition assays

  • Use additional purification steps before Western blot

  • Compare with predicted molecular weight (44 kDa)

Challenge 4: Variable Results Across Experiments

• Potential causes: Antibody instability, protocol inconsistencies, sample variability

• Solutions:

  • Aliquot antibodies to avoid freeze-thaw cycles

  • Standardize protocols with detailed SOPs

  • Include positive controls in every experiment

  • Use automated systems where possible

  • Consider lot-to-lot testing when reordering antibodies

Challenge 5: Species Cross-Reactivity Issues

• Potential causes: Epitope sequence variations across species

• Solutions:

  • Select antibodies with confirmed reactivity for your species

  • Verify epitope conservation through sequence alignment

  • Validate with species-specific positive controls

  • Consider developing custom antibodies for novel model organisms

Documenting optimization steps systematically will save time in future experiments and provide valuable troubleshooting information for publications .

How can I accurately assess GTF2H2C localization and expression changes during DNA damage response?

To accurately assess GTF2H2C dynamics during DNA damage response:

Experimental Design:

• Establish appropriate DNA damage models:

  • UV irradiation (10-50 J/m²) for nucleotide excision repair activation

  • Ionizing radiation (2-10 Gy) for double-strand break induction

  • Chemical agents (cisplatin, hydrogen peroxide, etc.)

• Include appropriate time course (immediate, 1h, 6h, 24h post-damage)

• Use synchronized cell populations to control for cell cycle variations

Localization Analysis:

• Perform immunofluorescence with validated antibodies (ABIN7127037 or NBP308896)

• Co-stain with DNA damage markers (γH2AX, 53BP1, BRCA1)

• Use confocal microscopy for high-resolution co-localization analysis

• Quantify nuclear foci formation using automated image analysis

• Consider live-cell imaging with fluorescently-tagged GTF2H2C to track dynamic changes

Expression Quantification:

• Fractionate cells into cytoplasmic, nucleoplasmic, and chromatin-bound fractions

• Analyze GTF2H2C distribution across fractions by Western blot

• Normalize to appropriate loading controls for each fraction

• Consider phospho-specific antibodies if available (phosphorylation often regulates damage response proteins)

Functional Assessment:

• Combine with chromatin immunoprecipitation to map GTF2H2C recruitment to damage sites

• Perform proximity ligation assays to detect interactions with other repair factors

• Use CRISPR/siRNA to modulate GTF2H2C levels and assess impact on repair efficiency

• Measure transcription recovery after damage as functional readout of TFIIH activity

Data Integration:

• Correlate GTF2H2C dynamics with cell survival and DNA repair kinetics

• Compare responses across different damage types and cell lines

• Integrate with transcriptional profiling to assess global impact

This multifaceted approach provides a comprehensive view of GTF2H2C's role in the DNA damage response, capturing both spatial redistribution and functional interactions that might be missed by single-method approaches .

What are the considerations for developing phospho-specific antibodies against GTF2H2C?

Developing phospho-specific antibodies against GTF2H2C requires careful planning:

Target Phosphorylation Site Selection:

• Conduct bioinformatic analysis to identify conserved phosphorylation sites

• Prioritize sites with known regulatory functions or those in functional domains

• Consider sites identified in phosphoproteomic studies

• Focus on sites regulated during DNA damage response or cell cycle

Peptide Design Principles:

• Center the phosphorylated residue in the immunizing peptide

• Include 7-20 amino acids surrounding the phosphorylation site

• Ensure peptide uniqueness relative to other GTF2H2 family members

• Consider peptide solubility and secondary structure

Production Strategy:

• Generate paired antibodies: phospho-specific and total protein

• Use the same host species for both antibodies to facilitate detection strategies

• Consider monoclonal development for long-term reproducibility

• For polyclonal approaches, purify using both positive and negative affinity columns

Validation Requirements:

• Test specificity against phosphorylated and non-phosphorylated peptides

• Verify using phosphatase treatment of lysates

• Validate using phosphomimetic (S/T to D/E) and phospho-dead (S/T to A) mutants

• Confirm using cells treated with kinase inhibitors or activators

Application Optimization:

• For Western blot: include phosphatase inhibitors in lysis buffers

• For IHC/IF: test multiple fixation methods as some may better preserve phospho-epitopes

• For IP: optimize buffer conditions to maintain phosphorylation status

• For all applications: minimize sample processing time to reduce phosphatase activity

While the search results don't mention existing phospho-specific antibodies for GTF2H2C, this approach would be valuable for researchers investigating regulatory mechanisms of this protein in transcription and DNA repair pathways.

How can I apply single-cell analysis techniques to study GTF2H2C expression heterogeneity in tumor samples?

Applying single-cell techniques to study GTF2H2C heterogeneity in tumors:

Single-Cell Protein Analysis:

• Flow Cytometry/Mass Cytometry (CyTOF):

  • Use GTF2H2C antibodies validated for flow cytometry (NBP308896)

  • Combine with markers for cell cycle, stemness, and lineage

  • Include phospho-specific markers if available

  • Analyze data using dimensionality reduction (tSNE, UMAP)

• Single-Cell Western Blot:

  • Separate individual cells using microfluidic devices

  • Detect GTF2H2C using validated antibodies for Western blot

  • Quantify expression at single-cell resolution

  • Correlate with other proteins of interest

Single-Cell Genomic/Transcriptomic Analysis:

• Single-Cell RNA-Seq:

  • Isolate single cells from tumor samples

  • Generate libraries for GTF2H2C and related genes

  • Analyze expression patterns and correlations

  • Identify cell subpopulations with distinct expression profiles

• Spatial Transcriptomics:

  • Maintain spatial information while analyzing expression

  • Map GTF2H2C expression to specific tumor regions

  • Correlate with histopathological features

Integrated Multi-Omic Approaches:

• CITE-Seq:

  • Combine antibody detection with transcriptome analysis

  • Correlate protein and mRNA levels at single-cell resolution

  • Identify post-transcriptional regulation mechanisms

• Single-Cell Multimodal Omics:

  • Integrate genomic, transcriptomic, and proteomic data

  • Create comprehensive cellular profiles

  • Map GTF2H2C variations to cellular phenotypes and functions

Data Analysis and Interpretation:

• Apply clustering algorithms to identify cell subpopulations

• Construct pseudo-time trajectories to infer developmental relationships

• Correlate GTF2H2C expression with cancer stem cell markers

• Associate expression patterns with clinical outcomes

• Develop predictive models based on expression heterogeneity

These approaches enable characterization of intratumoral heterogeneity in GTF2H2C expression, potentially revealing subpopulations with distinct DNA repair capacities or transcriptional regulation that could inform personalized therapeutic strategies .

What methodological approaches should I use to investigate GTF2H2C's role in transcription-coupled DNA repair?

To investigate GTF2H2C's role in transcription-coupled DNA repair (TCR):

Genetic Manipulation:

• CRISPR/Cas9 knockout or knockdown of GTF2H2C

• Complementation with wild-type vs. mutant GTF2H2C

• Domain-specific mutations to dissect functional regions

• Inducible systems to control expression timing

DNA Damage and Repair Assays:

• Host Cell Reactivation Assay:

  • Transfect damaged reporter plasmids

  • Measure transcriptional recovery in GTF2H2C-manipulated cells

  • Compare gene-specific vs. global transcription recovery

• Strand-Specific Repair Assays:

  • Induce DNA damage with UV or chemotherapeutics

  • Measure repair rates in transcribed vs. non-transcribed strands

  • Quantify lesion removal kinetics using ligation-mediated PCR

• Immunofluorescence-Based Approaches:

  • Visualize damage-induced GTF2H2C recruitment using validated antibodies

  • Track co-localization with RNA Polymerase II and repair factors

  • Measure clearance of DNA damage markers (CPDs, 6-4PPs)

Protein-DNA Interaction Analysis:

• Chromatin Immunoprecipitation (ChIP):

  • Use GTF2H2C antibodies to pull down associated DNA

  • Analyze recruitment to damaged genes

  • Perform sequential ChIP to detect complexes containing GTF2H2C and other repair factors

• DNA-Protein Crosslinking:

  • Trap GTF2H2C at sites of damage using photoactivatable nucleotides

  • Map precise binding positions relative to damage sites

  • Determine binding dynamics during repair progression

Transcription Analysis:

• Nascent RNA Sequencing:

  • Measure impact of GTF2H2C depletion on transcription recovery after damage

  • Analyze gene-specific effects and strand bias

  • Identify transcriptional signatures associated with defective TCR

• Single-Molecule Imaging:

  • Track RNA Polymerase II elongation rates in living cells

  • Measure transcriptional arrest and restart at damage sites

  • Analyze how GTF2H2C affects these dynamics

Structural and Biochemical Approaches:

• In vitro reconstitution of TCR with purified components

• Analysis of GTF2H2C interactions with TFIIH components during TCR

• Investigation of post-translational modifications regulating GTF2H2C function in TCR

These methodological approaches provide complementary insights into GTF2H2C's specific contributions to TCR, distinguishing its roles in transcription initiation from its functions in DNA repair .

How can I integrate omics approaches to comprehensively characterize GTF2H2C function in both normal and disease states?

Integrating omics approaches to characterize GTF2H2C function requires a multi-layered strategy:

Multi-Omics Integration Framework:

• Genomics:

  • Identify genetic variants and copy number alterations affecting GTF2H2C

  • Analyze chromatin accessibility at the GTF2H2C locus using ATAC-seq

  • Map enhancer-promoter interactions using Hi-C or ChIA-PET

• Transcriptomics:

  • Profile GTF2H2C expression across tissues and disease states

  • Analyze alternative splicing patterns using RNA-seq

  • Identify co-expressed gene networks through weighted correlation analysis

• Proteomics:

  • Map GTF2H2C protein interactions using IP-MS

  • Characterize post-translational modifications through phosphoproteomics

  • Quantify protein abundance changes using TMT or SILAC labeling

• Functional Genomics:

  • Perform CRISPR screens to identify synthetic lethal interactions

  • Map GTF2H2C binding sites genome-wide using ChIP-seq

  • Analyze transcriptional responses to GTF2H2C modulation

Data Integration Strategies:

• Network-based approaches to connect GTF2H2C to disease pathways

• Machine learning models to predict functional impacts of GTF2H2C variants

• Systems biology modeling of transcription and repair processes

Validation Methodologies:

• Select key findings for targeted validation using antibody-based approaches

• Develop reporter systems to monitor GTF2H2C-dependent processes

• Create cell and animal models with defined GTF2H2C alterations

Translational Applications:

• Correlate GTF2H2C expression or mutation status with clinical outcomes

• Identify biomarkers for DNA repair deficiency

• Develop therapeutic strategies targeting GTF2H2C-dependent pathways