Capture Hi-C Service – High-Resolution Targeted Chromatin Interaction Mapping
Unlock the 3D genome with precision. Our Capture Hi-C service integrates the power of Hi-C with custom probe design to deliver high-resolution, cost-efficient chromatin loop detection—focused only on the regions that matter most to your research.
Key Advantages:
- Targeted Insight: Zero in on specific SNPs, promoters, or regulatory elements with fully customizable probe panels.
- High-Resolution Mapping: Achieve loop detection at enzyme fragment scale (1–2 kb) for unmatched clarity.
- Data Efficiency: Capture deeper interaction details with a fraction of whole-genome Hi-C sequencing.
- Multi-Omics Integration: Combine seamlessly with ATAC-seq, CUT&Tag, or DAP-seq for richer regulatory context.
- Flexible Scope: From a few loci to genome-wide promoter coverage, tailored to your study design.
Why Choose Capture Hi-C? – Quick Benefits Snapshot
When your research demands clarity at the regulatory level, Capture Hi-C offers the precision and efficiency you need. By targeting only your regions of interest, this approach delivers richer, cleaner interaction maps while saving sequencing resources.
At-a-Glance Advantages:
- Sharper Focus: Resolve chromatin loops at 1–2 kb scale, even in complex or repetitive genomic contexts.
- Smarter Data Use: Achieve deeper coverage in key regions with significantly reduced sequencing requirements.
- Custom-Fit Design: From genome-wide promoter panels to specific SNP loci—tailored to your research question.
- Cleaner Signals: Minimized background noise compared to whole-genome Hi-C, improving loop detection confidence.
- Integration Ready: Designed to work seamlessly alongside ATAC-seq, CUT&Tag, and other epigenomic assays for comprehensive analysis.
From Hi-C to Capture Hi-C – A Focused Evolution
Hi-C has transformed our ability to map the 3D genome, revealing compartments, TADs, and chromatin loops across the entire genome. But when your focus is a small set of regions—such as disease-associated SNP loci or specific gene promoters—whole-genome Hi-C becomes an expensive and data-heavy approach. The resolution for your targets may be diluted, and achieving finer detail demands massive sequencing depth.
Capture Hi-C (cHi-C) refines the Hi-C workflow by adding a targeted capture step. Custom probes—designed to hybridize with your regions of interest—are applied to the Hi-C library, selectively enriching the fragments you care about before sequencing. This targeted enrichment offers:
- Higher Resolution in Key Regions – Down to the enzyme fragment scale (1–2 kb).
- Greater Depth per Target – Richer interaction maps without inflating total data volume.
- Lower Background – Clearer loop detection thanks to reduced non-target reads.
For studies focused on transcriptional regulation, Promoter Capture Hi-C (PCHi-C) uses probe sets targeting annotated promoter regions across the genome. This enables systematic mapping of promoter–enhancer and promoter–regulatory element interactions, making it a powerful tool for dissecting gene regulatory networks.
By transforming the "wide-angle" view of Hi-C into a "long-focus lens," Capture Hi-C gives you a cost-efficient, high-precision map of the chromatin interactions that matter most to your hypothesis—without being buried in unnecessary whole-genome data.
Technical Comparison: Traditional Hi-C vs. Capture Hi-C
| Parameter | Traditional Hi-C | Capture Hi-C |
|---|---|---|
| Sequencing volume for a 3 Gb genome | 600–1000 Gb | 10–50 Gb |
| Resolution | Binned, 5–10 kb | Enzyme fragment level (< 2 kb), no binning |
| Coverage scope | Whole genome | Custom target regions |
| Typical applications | No predefined targets, exploratory studies | High-resolution loop mapping and regulatory mechanism analysis |
Tailored Applications – Is This Your Use Case?
Every research project comes with its own focus, constraints, and unanswered questions. Capture Hi-C is designed to adapt—delivering high-value interaction data precisely where it's needed most.
If you've ever thought…
- "I'm only interested in enhancer–promoter loops for my target genes."
→ Capture Hi-C enriches your selected loci, providing high-resolution loop detection without the noise of unrelated interactions.
- "My organism's genome is huge, and I can't afford deep whole-genome Hi-C."
→ Reduce sequencing demands by focusing on specific genomic regions, freeing up budget for deeper coverage where it counts.
- "I need to connect GWAS SNPs to their potential target genes."
→ Capture Hi-C maps the physical interactions between noncoding variants and distant promoters, revealing regulatory mechanisms behind association signals.
- "I want to integrate chromatin structure with my epigenomic datasets."
→ Pair Capture Hi-C data with ATAC-seq, CUT&Tag, or ChIP-seq for multi-dimensional insights into regulatory networks.
Popular Research Applications:
- High-resolution mapping of disease-associated loci
- Genome-wide promoter interactome profiling
- Functional validation of candidate regulatory elements
- Investigating viral integration and host interaction sites
- Studying developmental stage–specific chromatin rearrangements
With a customizable probe design strategy, Capture Hi-C can be scaled to match anything from a single locus study to genome-wide promoter coverage—making it a versatile choice for diverse research goals.
Service Workflow – Transparent & Expert
From your initial hypothesis to a set of interaction maps ready for publication, our Capture Hi-C service is built to give you confidence at every step. We combine rigorous lab procedures with specialized bioinformatics to ensure your data is both accurate and actionable.
1. Define Your Target Regions
You identify the genomic loci of interest—such as promoters, SNP regions, or regulatory elements—and share your research goals with our technical team.
2. Custom Probe Design & Synthesis
We create a tailored probe panel to enrich your chosen regions. The scale can range from a few loci to genome-wide promoter coverage, with designs optimized for specificity and efficiency.
3. Hi-C Library Preparation & Probe Hybridization
Your samples undergo the Hi-C protocol, after which the library is hybridized with your custom probes to selectively capture interaction fragments from the target regions.
4. Targeted Sequencing
The enriched library is sequenced at a depth that ensures robust coverage of your targets while minimizing unnecessary data generation.
5. Data Analysis & Reporting
Our bioinformatics pipeline processes the data—detecting loops, annotating interactions, and integrating with relevant genomic features—so you receive results that are directly relevant to your study.
By keeping you informed at each stage, we make the process as predictable as the results are precise.
Bioinformatics Analysis – Turning Reads into Discovery
High-quality sequencing data is only the beginning. Our specialized bioinformatics pipeline transforms raw reads into meaningful biological insights, giving you a clear view of the 3D regulatory landscape in your target regions.
Our Analysis Workflow Includes:
- Data Quality Control – Filtering and trimming raw reads, removing adapters, and assessing library complexity to ensure reliable downstream results.
- Read Mapping & Filtering – Aligning reads to the reference genome, removing duplicates, and retaining only valid interaction pairs.
- Loop Detection & Interaction Calling – Identifying statistically significant chromatin loops within your targeted capture regions, using algorithms optimized for Capture Hi-C data.
- Functional Annotation – Linking interaction anchors to genomic features such as promoters, enhancers, and SNPs for biological interpretation.
- Variant–Gene Mapping – For GWAS or variant studies, mapping noncoding SNPs to potential target genes via loop connections.
- Data Visualization – Generating interaction heatmaps, arc diagrams, and genome browser tracks for direct integration into publications or further analysis.
- Multi-Omics Integration (Optional) – Overlaying Capture Hi-C loops with ATAC-seq, CUT&Tag, or ChIP-seq data to create a richer regulatory network model.
Our goal is to provide you with clean, well-annotated datasets that can be directly applied to hypothesis testing, figure preparation, or downstream computational modeling.
Sample Requirements – Setting the Stage for Success
| Sample Type | Minimum Input | Key Notes |
|---|---|---|
| Fresh cultured cells (fixed by client) | ≥ 2 × 10⁶ cells | Free from contamination; avoid freeze–thaw cycles |
| Fresh animal tissue | ≥ 500 mg | Ship on dry ice; maintain chromatin integrity |
| Fresh plant tissue | ≥ 1 g | Ship on dry ice; maintain chromatin integrity |
Additional Recommendations:
- Provide reference genome information for your species.
- Include basic QC data (e.g., DNA integrity) if available to accelerate project initiation.
Deliverables – What You Will Receive
Our Capture Hi-C service provides more than raw sequencing files—it delivers a complete package of data and interpretation tools to accelerate your research.
You will receive:
- Raw Sequencing Data – FASTQ files containing all reads generated from your targeted capture regions.
- Processed Interaction Data – Mapped, filtered, and validated chromatin interaction pairs in standard formats.
- Loop Calling Results – Statistically supported interaction loops with genomic coordinates.
- Functional Annotations – Interaction anchors linked to promoters, enhancers, and other regulatory elements.
- Publication-Ready Visualizations – Heatmaps, arc plots, and genome browser tracks for easy integration into figures.
- Comprehensive Bioinformatics Report – Detailed description of methods, QC metrics, interaction statistics, and biological interpretation.
All deliverables are formatted for compatibility with common genome browsers and analysis platforms, ensuring you can directly integrate them into ongoing projects or publications.
Multi-omics results visualization of ATAC-seq, CUT&Tag, and pcHi-C
Circos plot of genome-wide cis significant interaction sites
Circular plot of cis significant interaction sites on a single chromosome
Regulatory elements in non-promoter regions interacting with promoters