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Targeted Chromatin Capture (T2C) Service

Uncover high-resolution chromatin interactions at specific genomic loci with a cost-effective, hybrid 3D genomics approach.

  • High Resolution: Achieve restriction-fragment level resolution (approx. 2–6 kb).
  • Cost-Effective: Focus sequencing depth solely on regions of interest (ROI).
  • Verified QC: Strict quality control including valid interaction percentages and cis/trans ratios.
  • Custom Design: Tailored probe/primer design for your specific genomic targets.
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Targeted Chromatin Capture (T2C) visualizing specific enhancer-promoter interactions.

Service Overview

Understanding how the genome folds is critical for regulating gene expression, but traditional methods often force a trade-off between cost and resolution. Targeted Chromatin Capture (T2C) is a powerful 3D genomics technique designed to bridge this gap. It combines the principles of Chromosome Conformation Capture (3C) with hybridization-based capture to analyze specific regions of interest (ROI) at unprecedented detail.

Unlike genome-wide Hi-C, which requires massive sequencing depth to resolve fine details, T2C focuses all sequencing power on specific loci (ranging from a few hundred kilobases to several megabases). This allows researchers to achieve restriction-fragment level resolution (often 2–6 kb) without the high cost of deep whole-genome sequencing.

CD Genomics provides a comprehensive T2C service designed for researchers who need to validate enhancer-promoter loops, study structural variations, or dissect complex gene clusters. Our end-to-end solution includes probe design, library preparation, sequencing, and bioinformatic analysis, delivering data that is ready for publication.

Why Choose T2C for Your Research?

  • Unmatched Resolution: Deep sequencing of specific loci (e.g., 2kb–6kb resolution).
  • Cost-Efficiency: No need to sequence the "gene desert" background.
  • Comprehensive QC: CD Genomics unique QC metric report (valid interaction pairs, cis/trans ratio).

Comparison: T2C vs. Hi-C and Other Methods

Choosing the right 3D genomics tool depends on your research question. T2C is ideal when you have a specific hypothesis about a genomic region and need the highest possible resolution.

Feature T2C (Targeted Chromatin Capture) Hi-C Sequencing Capture Hi-C 4C-Seq
Scope Specific Loci (Regions of Interest) Genome-wide Hundreds of loci / Whole Exome One viewpoint to genome-wide
Resolution Very High (Restriction Fragment, ~2-6kb) Medium (Variable, depends on depth) High High (near viewpoint)
Sequencing Cost Low (Targeted depth only) High (Requires deep sequencing) Medium-High Low-Medium
Best For Deep analysis of specific genes, TADs, or loops. Global discovery of TADs and compartments. Screening interactions across many promoters. Discovering unknown partners of one "bait."

Applications of T2C

Our T2C service is particularly suited for "Evaluation" and "Validation" stages of research where broad discovery is no longer the goal, and specific mechanisms need to be proven.

1. Fine-Mapping GWAS Variants

Genome-Wide Association Studies (GWAS) often identify variants in non-coding regions. T2C can link these variants to their target genes (Variant-to-Gene mapping) by detecting physical loops, even if the gene is megabases away.

2. Dissecting Complex Gene Clusters

For regions with high gene density or complex regulatory landscapes (e.g., Hox clusters or globin genes), T2C provides the resolution needed to distinguish between neighboring interactions.

3. Validation of Hi-C Results

Use T2C to validate interactions detected in low-resolution Hi-C maps, confirming that a "fuzzy" contact is a bona fide regulatory loop.

4. Structural Variation Analysis

Investigate how translocations, inversions, or deletions alter the local 3D chromatin structure and affect gene expression.

T2C Service Workflow

Our T2C workflow follows strict Standard Operating Procedures (SOPs) to ensure reproducibility. We handle the complex steps of probe design and capture so you can focus on biology.

  1. Consultation & Design: We define the Region of Interest (ROI) and design specific capture probes/primers based on the restriction enzyme cut sites.
  2. Crosslinking & Digestion: Cells are crosslinked to freeze 3D structures, then digested with a restriction enzyme (e.g., ApoI or HindIII).
  3. Ligation: DNA fragments that are physically close are ligated together, forming chimeric molecules.
  4. Targeted Capture: Unlike global methods, we use hybridization capture to enrich only the DNA chimeras belonging to your Region of Interest.
  5. Library Prep & Sequencing: Enriched libraries are sequenced on Illumina platforms (PE150).
  6. Bioinformatics Analysis: Data processing includes mapping, filtering, and generation of high-resolution interaction matrices.

T2C service workflow from sample preparation to data analysis.

Sample Requirements

High-quality input material is essential for successful 3D genomics. Please review the requirements below before shipping.

Sample Type Recommended Amount Preparation Method Shipping Condition
Cell Lines 5 × 106 – 107 cells Fresh crosslinked (1–2% Formaldehyde) OR Flash frozen pellets Dry Ice
Animal Tissue 50 – 100 mg Flash frozen in liquid nitrogen immediately after resection Dry Ice
Blood ≥ 2 mL whole blood EDTA anticoagulation tube (fresh or frozen) Dry Ice
Plant Tissue 0.5 – 1 g (young leaves) Flash frozen in liquid nitrogen Dry Ice

Note: Specific input requirements may vary based on the genome size and the number of regions targeted. Please contact our technical team for a custom consultation.

Case Study: Dissecting the Hbb Locus

Note: This case study illustrates the capability of the T2C methodology as described in peer-reviewed literature.

The mouse Beta-globin (Hbb) locus is a classic model for studying long-range gene regulation. Researchers needed to understand how the Locus Control Region (LCR) interacts with specific globin genes during differentiation, but existing methods lacked the resolution or were too costly.

The study employed Targeted Chromatin Capture (T2C) to analyze the chromatin conformation of the Hbb locus. By designing probes specifically for this region, the team could sequence the local interactions at very high depth.

The T2C data generated high-resolution interaction maps that clearly identified specific contacts between the LCR and the active globin genes. The resolution was sufficient to distinguish individual restriction fragments, revealing a precise folding structure that was consistent with 4C-seq data but provided a more comprehensive "many-to-many" view of the region.

High-resolution interaction map of the Hbb locus generated by T2C

T2C successfully resolved the fine 3D structure of the Hbb locus, demonstrating its utility as a cost-effective, high-resolution tool for studying specific gene regulatory networks.

Source: Targeted Chromatin Capture (T2C): a novel method for high resolution genomic analysis. Nature Methods.

Data Analysis & Deliverables

CD Genomics provides "Analysis-Ready" deliverables. We don't just give you raw reads; we provide the biological insights.

Raw Data & QC
FASTQ files (Clean data) and a comprehensive QC Report including Valid Interaction Pairs %, Cis/Trans interaction ratio, and On-target rate.

Visualization
High-resolution Interaction Heatmaps (2D) and Virtual 4C plots (Viewpoint analysis).

Interaction List
Significant loops and contact domains provided in BED/TXT format for easy integration with genome browsers.

Comparison Visualization
Comparison of resolution between standard Hi-C and Targeted Chromatin Capture (T2C)

Ready to visualize your specific genomic region? Contact us to discuss your project.

Frequently Asked Questions

References

  1. Kolovos, P., et al. (2014). Targeted Chromatin Capture (T2C): a novel method for high resolution genomic analysis. Nature Methods, 11(8), 843–848.
  2. Sati, S., & Cavalli, G. (2017). Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma, 126(1), 33–44.
  3. Despang, R., et al. (2019). Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nature Genetics, 51, 1263–1271.

For Research Use Only. Not for use in diagnostic procedures. CD Genomics does not provide clinical diagnosis or treatment recommendations. All comparisons are based on general technical specifications and may vary by specific experimental design.

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High-confidence 3D genomics services for chromatin interaction analysis and regulatory insight.

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