G4 CUT&Tag Service for Native DNA G-Quadruplex Mapping
Our G4 CUT&Tag service maps DNA G-quadruplexes (G4s) directly in native chromatin with high resolution and low background. Using BG4-based CUT&Tag chemistry, CD Genomics generates reliable G4 profiles from low-input samples for research use only.
Compared with G4 ChIP-seq and in vitro G4-seq, G4 CUT&Tag reduces input requirements and non-specific noise, helping you capture functional G4 sites involved in transcription, replication, DNA methylation, and genome stability.
- BG4 G4 CUT&Tag chemistry targets pA-Tn5 to native DNA G-quadruplex structures, enabling precise genome-wide G4 mapping at promoters, enhancers, telomeres, and CpG islands.
- Low-input CUT&Tag workflow delivers robust G4 profiles from as few as 1×10⁵–10⁶ cells, making G4 analysis feasible for rare cell populations, organoids, and precious research samples.
- Integrated sequencing and analysis pipeline provides QC'd data, G4 peak calls, and functional annotation, so your team can move quickly from raw reads to interpretable G-quadruplex maps.
All CD Genomics sequencing services are for research use only.
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What Is G4 CUT&Tag Sequencing
G4 CUT&Tag sequencing is a genome-wide method for mapping DNA G-quadruplex (G4) structures directly in native chromatin. It combines a G4-specific probe, such as the BG4 antibody, with the CUT&Tag workflow to generate high-resolution, low-background G4 profiles from low-input samples.
In a typical G4 CUT&Tag experiment, intact nuclei are immobilised on beads and incubated with a G4-binding antibody that recognises native G-quadruplexes on DNA. A secondary antibody then recruits a protein A–Tn5 transposase fusion, which inserts sequencing adapters next to antibody-bound G4 sites. After library preparation and high-throughput sequencing, the tagged fragments reveal the genomic distribution of DNA G-quadruplexes.
Key features at a glance
- Native chromatin context – G4 structures are profiled in permeabilised nuclei, preserving the physiological chromatin environment instead of refolding DNA in vitro.
- Low-input requirement – Optimized CUT&Tag chemistry enables genome-wide G4 mapping from relatively small numbers of cells or limited tissue.
- High signal-to-noise – In situ tagmentation at antibody-bound sites reduces nonspecific background, improving peak detection at promoters, enhancers, telomeres, and other regulatory regions.
Why Map DNA G-Quadruplexes with G4 CUT&Tag
DNA G-quadruplexes (G4s) are four-stranded structures formed by guanine-rich sequences. They are enriched at promoters, enhancers, telomeres, CpG islands, and replication origins, where they can influence transcription, DNA replication, DNA methylation, and genome stability. G4 CUT&Tag sequencing lets you map these structures genome-wide in native chromatin, so you can distinguish functional G4s from simple sequence motifs.
G4 CUT&Tag is particularly useful when you want to:
- Link G4s to gene expression by mapping G4 structures at key promoters and enhancers and comparing them with changes in mRNA levels, transcription factor binding, or histone marks.
- Characterize regulatory G4s beyond promoters by profiling G4s in enhancers and UTRs and integrating the maps with ATAC-seq or RNA-seq to identify truly active regulatory sites.
- Study replication, telomeres, and genome stability by locating G4s at replication origins and telomeres and assessing their association with fork stalling, telomere maintenance, or DNA damage.
- Explore epigenetic cross-talk by combining G4 CUT&Tag with DNA methylation profiling (e.g., WGBS) to test how methylation patterns correlate with G4 formation around transcription start sites.
- Support mechanism-of-action and target validation by tracking G4 landscape changes after helicase perturbation, oncogenic mutations, or treatment with G4-targeting compounds in cancer, neurodegeneration, infection, or developmental models.
By providing low-input, high-resolution DNA G-quadruplex maps in native chromatin, G4 CUT&Tag offers more mechanistic insight than prediction-only tools or bulk biochemical assays, while remaining practical for routine research projects.
Choosing the Right G4 Mapping Method
Once you decide to study DNA G-quadruplexes, the key question is which mapping strategy best matches your sample type and research goal. The overview below compares G4 CUT&Tag sequencing with other commonly used G4 profiling approaches.
| Attribute | G4 CUT&Tag | G4 ChIP-seq | In vitro G4-seq | G4 prediction tools |
|---|---|---|---|---|
| Sample input | Low–moderate cell numbers; limited tissue | High cell numbers; bulk tissue | Genomic DNA | No biological material |
| Context | Native chromatin in permeabilised nuclei | Crosslinked chromatin | DNA refolded in solution | In silico sequence analysis |
| Resolution & background | High resolution; low background | Moderate–high background; sonication noise | High motif resolution; no chromatin info | Motif-level only; no occupancy |
| Main strength | Native, condition-dependent G4 maps from low input | Established workflow in equipped labs | Detects potential G4-forming sequences | Rapid genome-wide G4 motif screening |
| Typical use case | Functional G4 profiling in limited or precious samples | Projects with abundant material and existing ChIP-seq infrastructure | Survey of G4 sequence propensity across the genome | Hypothesis generation and initial target selection |
For projects that focus on native, condition-dependent G4 structures and have limited material, we generally recommend G4 CUT&Tag as the primary experimental approach. When needed, we can complement CUT&Tag data with in vitro G4-seq or computational prediction to explore sequence propensity and validate candidate regions in more detail.
Integrating G4 CUT&Tag with Other Omics
G4 CUT&Tag becomes most powerful when it is analysed alongside other genomic and epigenomic layers. CD Genomics can coordinate G4 CUT&Tag sequencing with complementary assays and deliver harmonised outputs for integrated analysis.
Typical multi-omics combinations
- G4 CUT&Tag + ATAC-seq
Relate DNA G-quadruplexes to chromatin accessibility to see which G4 sites sit in open, regulatory regions.
- G4 CUT&Tag + ChIP-seq / CUT&Tag
Overlay G4 maps with histone marks (e.g., H3K4me3, H3K27ac) or transcription factor binding (e.g., CTCF) to dissect regulatory mechanisms.
- G4 CUT&Tag + DNA methylation (WGBS/RRBS)
Examine how DNA methylation patterns correlate with G4 formation around promoters and other regulatory elements.
- G4 CUT&Tag + RNA-seq
Connect changes in G4 landscapes to gene expression profiles in the same samples or matched conditions.
Benefits of a coordinated design
- Consistent sample handling and batch management across assays
- Matched file formats and genome builds for straightforward integration
- A single technical contact for planning, execution, and data delivery across the full multi-omics project
Why Partner with CD Genomics for G4 CUT&Tag Sequencing
Selecting G4 CUT&Tag as a method is only the first step; execution quality and analysis depth determine how much insight you actually gain. CD Genomics combines optimized wet-lab workflows with dedicated bioinformatics to deliver consistent, publication-ready G4 CUT&Tag data.
Assay setup tailored to your system – We tune antibody conditions, nuclei preparation, and library parameters to your cell type, species, and sample quality, reducing trial-and-error and lowering the risk of failed libraries.
Consistent, review-ready data quality – Each project includes internal controls and standard QC metrics such as alignment rates, enrichment scores, and replicate concordance, so you can directly use the outputs in manuscripts and internal reports.
Built-in G4 CUT&Tag bioinformatics expertise – Our dedicated pipelines cover core G4 peak calling through to functional annotation and optional integration with other epigenomic or transcriptomic datasets, shortening the path from raw reads to biological conclusions.
Support for coordinated multi-omics designs – We can plan G4 CUT&Tag alongside ATAC-seq, ChIP-seq/CUT&Tag, WGBS/RRBS, RNA-seq, or Hi-C and deliver harmonized outputs, making it easier to compare G4 patterns with chromatin accessibility, histone marks, DNA methylation, or 3D genome structure.
Flexible project scopes from pilot to cohorts – Whether you are running a small feasibility study or a larger cohort, you work with a single technical contact who coordinates design, timelines, and deliverables across the entire project.
Together, these capabilities make CD Genomics a reliable partner for G4 CUT&Tag sequencing in discovery biology, target validation, and preclinical research.
G4 CUT&Tag Workflow at CD Genomics
Our G4 CUT&Tag workflow efficiently takes you from samples to interpretable G-quadruplex maps.
- Study design & sample review
We align on species, sample types, comparison groups, and input amounts, then recommend appropriate controls, replicates, and sequencing depth for your G4 CUT&Tag project.
- Nuclei preparation & bead binding
Cells or tissues are gently processed to isolate intact nuclei, which are immobilised on ConA-coated magnetic beads to support antibody binding and in situ tagmentation.
- G4 antibody binding in native chromatin
Bead-bound nuclei are incubated with a G4-specific antibody (BG4 or similar), followed by a secondary antibody to amplify signal and provide docking sites for the protein A–Tn5 (pA-Tn5) fusion.
- pA-Tn5 tagmentation at G4 sites
pA-Tn5 is recruited to antibody-bound G4 structures and activated with magnesium, cutting DNA near G4 sites and inserting adapters directly in native chromatin.
- Library preparation, sequencing & data handover
Adapter-tagged fragments are purified, amplified, QC'd, and sequenced on an Illumina platform. Cleaned reads and initial G4 peak calls are delivered and passed into the full bioinformatics pipeline described in the next section.
Sample Requirements and Shipping Guidelines
To obtain high-quality G4 CUT&Tag sequencing data, we recommend planning samples with the following basic requirements in mind. All CD Genomics services are for research use only and not intended for diagnostic or therapeutic applications.
Supported sample types
- Cultured cells: adherent or suspension cell lines, primary cells, organoids
- Fresh or frozen tissues: animal or human research tissue, small research biopsies
- Other models (yeast, bacteria, plant tissues, specialised samples): on consultation
Recommended input (guideline values)
- Cultured cells: ~1 × 10⁵ – 1 × 10⁶ viable cells per sample (viability ideally ≥ 85–90%)
- Tissues: ~20–50 mg per sample, depending on tissue type and cellularity
If your material is significantly below these ranges, share your estimated input; we will assess feasibility and adjust expectations before starting.
Collection and storage
- Avoid Trizol or other strong lysis/extraction reagents for G4 CUT&Tag samples.
- Cells: harvest gently, freeze in appropriate freezing medium, store in liquid nitrogen or at −80 °C.
- Tissues: snap-freeze as soon as possible and store at −80 °C in clearly labelled tubes.
Shipping
- Ship samples on dry ice in insulated containers.
- Avoid repeated freeze–thaw cycles; plan a single shipment with sufficient dry ice.
- Include a simple sample list (IDs, type, treatment, estimated input) matching your digital submission.
Sequencing Strategy and Recommended Depth
Our G4 CUT&Tag sequencing service is optimized to balance resolution, cost, and downstream analysis requirements for genome-wide DNA G-quadruplex mapping.
Platform and read configuration
- Illumina short-read platforms (e.g., NovaSeq or equivalent)
- Typical configuration: paired-end 2 × 50 bp or 2 × 75 bp, suitable for CUT&Tag fragment sizes and peak calling
- Other read lengths can be arranged for specific study needs
Recommended sequencing depth
As a general guide for bulk G4 CUT&Tag:
- Standard G4 profiling:
~20–30 million uniquely mapped reads per sample for robust peak calling across the genome
- Higher-resolution or complex genomes:
Deeper coverage can be requested if you need finer peak definition or plan extensive integrative analyses
We will tailor depth recommendations based on:
- Genome size and species
- Number of conditions and replicates
- Whether you plan to integrate G4 CUT&Tag with ATAC-seq, ChIP-seq, WGBS, RNA-seq, or Hi-C
Controls and replicates
To support reliable interpretation, we generally recommend:
- At least 2 biological replicates per condition
- An appropriate negative control (e.g., IgG or no-primary-antibody CUT&Tag)
- Optional additional controls if you are testing G4-targeting ligands, helicase perturbations, or other interventions
Our team will help you choose a sequencing plan that matches your experimental question, ensuring that G4 CUT&Tag data are generated at a depth that supports confident DNA G-quadruplex peak detection and downstream analysis.
G4 CUT&Tag Data Analysis
Our G4 CUT&Tag data analysis pipeline is built to turn raw sequencing reads into reliable, interpretable DNA G-quadruplex maps, without the need for in-house bioinformatics scripting.
1. Primary processing
- Demultiplexing and adapter trimming
- Read quality filtering and alignment to the reference genome
- Mapping statistics to summarise alignment rates and coverage
2. G4 peak calling and quality control
- Peak calling optimized for G4 CUT&Tag signal profiles
- Global QC metrics, including enrichment scores and background assessment
- Replicate concordance checks to highlight robust, reproducible G4 peaks
3. Functional and genomic annotation
- Annotation of G4 peaks relative to promoters, enhancers, UTRs, exons, introns, and intergenic regions
- Linking G4 sites to nearby genes and transcription start sites
- Optional GO / pathway-style enrichment for genes associated with G4-enriched regions
4. Integrative analysis (optional)
On request, we can integrate G4 CUT&Tag data with:
- Chromatin accessibility (ATAC-seq)
- Histone marks or transcription factor binding (ChIP-seq / CUT&Tag)
- DNA methylation profiles (e.g., WGBS)
- Gene expression data (RNA-seq)
This places DNA G-quadruplex structures in the broader context of gene regulation and chromatin state, supporting clearer mechanistic conclusions.
G4 CUT&Tag Deliverables and Demo Results
We provide a concise, analysis-ready output package so your team can directly use the data in downstream work.
Data files
- Raw FASTQ files for all G4 CUT&Tag libraries and controls
- Aligned BAM files + index files mapped to the agreed reference genome
Peak and annotation outputs
- G4 peak files (e.g., BED format) for each sample or condition
- Annotation tables linking peaks to genomic features and nearest genes/TSS
Visuals and report
- Genome browser tracks and key plots (e.g., peak distribution, TSS enrichment, sample correlations)
- A brief QC and summary report describing methods, main quality metrics, and example G4 maps
GO enrichment bubble plot
Chromosome-level distribution
Heatmaps and average profiles
PCA plot
Case Study
FAQs: G4 CUT&Tag Sequencing Service
References
- Lyu, J., Shao, R., Yung, P.Y.K. et al. Genome-wide mapping of G-quadruplex structures with CUT&Tag. Nucleic Acids Research 50, e13 (2022).
- Kaya-Okur, H.S., Wu, S.J., Codomo, C.A. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nature Communications 10, 1930 (2019).
- Chambers, V.S., Marsico, G., Boutell, J.M. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nature Biotechnology 33, 877–881 (2015).
- Johnson, S.A., Paul, T., Sanford, S.L. et al. BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions. Nucleic Acids Research 52, 1763–1778 (2024).
- Varshney, D., Spiegel, J., Zyner, K.G. et al. The regulation and functions of DNA and RNA G-quadruplexes. Nature Reviews Molecular Cell Biology 21, 459–474 (2020).
- Georgakopoulos-Soares, I., Chan, C.S.Y., Ahituv, N. et al. High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biology 23, 159 (2022).
- Qian, S.H., Shi, M.W., Xiong, Y.L. et al. EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database. Nucleic Acids Research 52, D72–D80 (2024).