G4 ChIP-Seq is a chromatin immunoprecipitation sequencing method that maps DNA G-quadruplex structures across the genome in vivo.
A G-quadruplex–specific antibody is used to pull down folded G4 DNA from crosslinked chromatin, followed by next-generation sequencing and peak calling.
This approach reveals where endogenous G4 structures actually form in native regulatory regions, not just where G-rich sequences could fold in vitro.
DNA G-quadruplexes are secondary structures formed by G-rich sequences that stack into stable four-stranded motifs.
They are enriched in promoters, enhancers, telomeres, and untranslated regions, where they can influence transcription, DNA replication, and genome stability.
By adding a structural readout on top of classic epigenetic marks, G4 ChIP-Seq helps you understand why specific loci are particularly sensitive to stress, mutation, or therapeutic intervention.
When Should You Use G4 ChIP-Seq?
You should consider a G4 ChIP-Seq service when you need to:
Map genome-wide G4 landscapes in a defined cell type, tissue, or disease model.
Test how helicases, chromatin regulators, or G4 ligands reshape G4 DNA distributions.
Link promoter G-quadruplexes to transcriptional activity, RNA-seq profiles, or ATAC-seq signals.
Compare G4 patterns between tumor and normal samples, treated and untreated cells, or developmental stages.
Compared with standard transcription factor ChIP-Seq, G4 ChIP-Seq focuses on DNA structures rather than a single protein target.
Why Map DNA G-Quadruplexes with G4 ChIP-Seq
G4 ChIP-Seq gives you a structural view of gene regulation that classical epigenetic assays cannot provide, directly showing where G4 DNA structures form in native chromatin and how they relate to transcription and genome stability.
G4 structures are enriched at promoters, enhancers, telomeres, and other regulatory elements.
Knowing exactly where these G-quadruplexes sit helps you prioritize loci that may drive transcriptional programs, replication stress, or mutation hotspots in your model.
For project planning, G4 ChIP-Seq adds a high-value structural layer to your epigenetics toolkit:
Structural chromatin mapping shows G4 DNA structures genome-wide, not just one protein target, helping you focus on G4-enriched genes and pathways that are most likely to affect your phenotype.
Sensitive readout of G4 perturbation detects how helicases, chromatin remodelers, or G4 ligands shift G4 occupancy, giving you clearer mode-of-action data for targets or compounds of interest.
Seamless integration with RNA-seq and ATAC-seq aligns G4 peaks with gene expression and chromatin accessibility, so you move from isolated observations to coherent regulatory models suitable for publication and review.
For oncology, genome stability, antiviral research, or plant breeding, this structural information reduces trial-and-error and supports more confident target selection.
Applications
Applications of G4 ChIP-Seq
G4 ChIP-Seq adds a structural layer to epigenetics studies by revealing where DNA G-quadruplexes form in native chromatin.
It is particularly useful when you need to connect sequence motifs, folded DNA structures, and gene regulation in the same model.
Transcription and Chromatin Regulation
G4 ChIP-Seq helps you understand how G-quadruplexes shape transcriptional programs:
Map promoter and enhancer G4s and relate them to RNA-seq expression levels.
Overlay G4 peaks with ATAC-seq, histone marks, and transcription factor ChIP-Seq.
Prioritise regulatory regions where G4 structures and open chromatin coincide.
Genome Stability and Cancer Research
Because G4 structures can promote replication stress and mutation hotspots, G4 ChIP-Seq is valuable in genome stability projects:
Identify G4-enriched loci at oncogenes, fragile sites, or repetitive regions.
Study how helicase mutations or replication stress conditions change G4 occupancy.
Link structural hotspots to observed mutation patterns or copy-number changes.
G4 Ligands and Mechanism-of-Action Studies
For teams developing or testing G4-targeting compounds, G4 ChIP-Seq provides a direct structural readout:
Measure how a ligand stabilises or redistributes G4 structures across the genome.
Compare treated versus control samples to highlight responsive genes and pathways.
Combine with RNA-seq to distinguish primary, structure-driven effects from downstream changes.
Functional Genomics in Non-Model Systems
G4 ChIP-Seq is also applicable to plant, fungal, and viral models:
Explore the role of G4 structures in stress responses, development, or host–pathogen interactions.
Integrate G4 profiles with existing transcriptome and chromatin data in emerging model systems.
Across these application areas, CD Genomics positions G4 ChIP-Seq as part of a broader epigenetics sequencing portfolio, enabling you to design projects that combine structural mapping with established chromatin and transcription assays in a research-use-only framework.
Technology Comparison
How Does G4 ChIP-Seq Compare to Other G4 and Epigenetics Technologies
When you plan a project around DNA G-quadruplexes, you often need to choose between several complementary methods.
The table below summarises how G4 ChIP-Seq compares with other G4 and epigenetics assays and when each is most useful.
Technology
What it measures
Key strengths
Typical use at CD Genomics
G4 ChIP-Seq
Folded G4 DNA structures in crosslinked chromatin (in vivo)
Direct structural map in native chromatin; compatible with ChIP-Seq pipelines
Prioritise functionally folded G4 sites; integrate with RNA-seq, ATAC-seq and TF/mark ChIP-Seq
G4-seq / in vitro G4 mapping
Sequence potential to form G4s in purified genomic DNA
Genome-wide catalogue of putative G4-forming sequences
Hypothesis generation; identify candidate regions before in vivo G4 ChIP-Seq validation
Specific histone marks or transcription factor binding profiles
Direct readout of chromatin state and protein–DNA interactions
Map active/repressive marks and TF binding; overlay with G4 ChIP-Seq to add a DNA structure layer
In many studies, the most informative design is to combine assays rather than choose only one.
A common pattern is to use ATAC-seq and histone or TF ChIP-Seq to define regulatory regions, then apply G4 ChIP-Seq to highlight the subset of promoters and enhancers where G-quadruplex structures add an extra regulatory dimension.
It is designed to deliver reliable DNA G-quadruplex maps that support epigenetics and gene regulation studies in a research-use-only setting.
Optimised G4 Enrichment
We use a G-quadruplex–specific antibody with tuned crosslinking, fragmentation, and washing conditions to enrich folded G4 structures from native chromatin.
This setup improves signal-to-noise and supports confident peak detection, even in complex genomes.
G4-specific pull-down from crosslinked chromatin
Reduced non-specific background and cleaner peak profiles
Recommended use of input controls and biological replicates for reproducible comparisons
Flexible Sequencing Options
G4 ChIP-Seq libraries are sequenced on Illumina platforms with configurations matched to your project.
You can balance depth and cost according to genome size and the number of conditions.
Paired-end sequencing for accurate alignment and peak boundaries
Depth options for pilot screens or deep profiling
Support for human, mouse, plant, and microbial genomes
Ready for Multi-Omics Integration
We process G4 ChIP-Seq data in formats that align with RNA-seq, ATAC-seq, and histone mark ChIP-Seq.
This makes it straightforward to overlay G4 peaks with chromatin accessibility, histone modifications, and gene expression.
Harmonised pipelines for G4 ChIP-Seq and other epigenetics assays
Direct comparison of G4 sites with transcription and chromatin states
Outputs prepared for downstream custom analysis and publication
Workflow
G4 ChIP-Seq Experimental Workflow
Our G4 ChIP-Seq workflow is standardised from sample collection to annotated G4 peaks, so you receive reproducible structural maps that are easy to interpret and reuse.
Step 1 – Sample Collection and Crosslinking
Cells or tissues are collected under your defined conditions and crosslinked to preserve DNA structures and chromatin context.
Step 2 – Chromatin Fragmentation
Crosslinked chromatin is isolated and fragmented to a suitable size range (typically 100–500 bp), with fragment profiles checked before enrichment.
Step 3 – G4 Immunoprecipitation
A G-quadruplex–specific antibody is used to pull down folded G4 structures from native chromatin, followed by stringent washes to reduce background.
Step 4 – Library Preparation and Sequencing
Enriched DNA is converted into indexed libraries and sequenced on Illumina platforms with paired-end runs tailored to your genome and depth requirements.
Step 5 – Bioinformatics and Reporting
Reads are cleaned, aligned, and processed through a dedicated G4 ChIP-Seq pipeline to deliver peak calls, genomic annotation, and summary plots ready for integration with RNA-seq, ATAC-seq, or other epigenetics datasets.
Bioinformatics
G4 ChIP-Seq Data Analysis
Our G4 ChIP-Seq data analysis pipeline is designed to turn raw reads into interpretable maps of DNA G-quadruplex structures.
You receive processed data that are ready for comparison, integration, and figure preparation.
For each project, we typically perform:
Raw data quality control and adapter/low-quality trimming
Read alignment to the reference genome with mapping statistics
Peak calling to identify G4-enriched regions per sample or group
Annotation of G4 peaks to promoters, genes, UTRs, and intergenic regions
Genome-wide distribution plots by genomic feature, chromosome, and peak length
Signal profiles and heatmaps around transcription start sites or other landmarks
For comparative studies, the analysis can be extended to:
Differential G4 peak analysis between conditions, treatments, or cell types
Functional enrichment of genes linked to changing G4 regions
Clustering or dimensionality reduction to group samples by G4 profiles
This structure gives you a consistent view of G4 occupancy and dynamics that can be aligned with RNA-seq, ATAC-seq, or other epigenetics datasets.
Deliverables
Deliverables and Demo Results
We provide a clear package of files and visual outputs so you can move directly into interpretation and reporting:
Clean FASTQ files, aligned BAM files, and peak BED files
Annotated G4 peak tables with genomic coordinates and summary statistics
Key visualisations, such as G4 peak tracks, heatmaps, and distribution plots, in publication-ready formats
A concise analysis report describing main methods, parameters, and notable observation
GO and pathway analysis of genes associated with differentially enriched regions.
Chromosomal distribution of enriched G4 ChIP-Seq fragments
Sequence logos showing enriched DNA motifs identified from G4 ChIP-Seq peaks
Heatmaps and average profiles
Sample
Sample Types and Requirements for G4 ChIP-Seq
Our G4 ChIP-Seq service supports multiple organisms and sample formats.
The table below summarises typical sample types and recommended input amounts to help you plan your experiment.
Sample type
Typical examples
Recommended input (per sample)
Notes
Mammalian cells
Cell lines, primary cells
~1 × 10⁷–10⁸ cells, good viability before fixation
For projects providing immunoprecipitated DNA only
Actual G4 ChIP-Seq sample requirements may vary with organism, genome size and study design.
If you expect very low input or heavily processed samples, we recommend discussing feasibility with CD Genomics before collection.
Collection, Fixation and Shipping
To preserve G4 structures and chromatin context:
Fix cells or tissues, usually with formaldehyde, following our G4 ChIP-Seq sample preparation guidelines.
Avoid strong denaturants such as TRIzol before crosslinking.
Store fixed material at −80 °C whenever possible.
For shipping:
Send cells and tissues on dry ice.
Ship DNA samples on cold packs or dry ice, depending on transit time.
Case
Case Study
Our Advantage
Why Choose CD Genomics for G4 ChIP-Seq
CD Genomics combines an optimized G4 ChIP-Seq wet-lab workflow with a mature analysis pipeline, so your structural epigenetics data are immediately useful for project planning and decision-making.
Study design support – We help you match samples, replicates, sequencing depth and controls to your biological question and budget, reducing the risk of underpowered studies and re-runs.
Optimised G4 ChIP-Seq workflow – A G-quadruplex–specific antibody, tuned crosslinking and controlled enrichment deliver clean, high-confidence G4 peak profiles, even in complex, or repetitive genomes.
Integrated data and reporting – You receive raw and processed files, annotated G4 peak tables and core visualisations in standard formats aligned with RNA-seq, ATAC-seq, and other epigenetics assays, all under a research-use-only project framework.
GO and pathway analysis of genes associated with differentially enriched regions.
Chromosomal distribution of enriched G4 ChIP-Seq fragments
Sequence logos showing enriched DNA motifs identified from G4 ChIP-Seq peaks
Heatmaps and average profiles