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HiCAR Sequencing Service: Simultaneous Chromatin Accessibility & 3D Genome Profiling

Uncover the regulatory logic of the genome with our HiCAR Sequencing Service. By combining Tn5-mediated chromatin accessibility profiling with in situ proximity ligation, HiCAR delivers simultaneous ATAC-seq and Hi-C data from a single low-input sample. Ideally suited for assigning distal enhancers to target genes (V2G) and validating regulatory networks. RUO.

  • Dual-Omics: Simultaneous detection of open chromatin (ATAC) and 3D loops (Hi-C).
  • Regulatory Focus: Enriched for enhancer-promoter interactions driven by Tn5 bias.
  • Low Input: Robust profiling from as few as 50,000 cells.
  • Integrated Analysis: Joint calling of peaks and loops for direct variant-to-gene (V2G) assignment.
Discuss Your Multi-Omics Project

3D diagram of HiCAR mechanism showing Tn5 tagmentation and ligation.

Overview: One Experiment, Two Layers of Chromatin Data

In the quest to understand gene regulation, researchers have traditionally faced a difficult choice: study the "open" regulatory regions using ATAC-seq or map the 3D chromatin loops using Hi-C. Doing both requires separate experiments, double the sample input, and complex bioinformatics to statistically "guess" how the two datasets relate.

Our HiCAR Sequencing Service (High-throughput Chromatin Accessibility and high-resolution contact sequencing) eliminates this dilemma. By utilizing a specially optimized Tn5 transposase chemistry, HiCAR performs two critical tasks in a single tube: it identifies accessible chromatin regions (like promoters and enhancers) and simultaneously captures the physical DNA loops that connect them. This "co-assay" approach provides a direct, experimental link between regulatory elements and their target genes.

Service Snapshot

  • Method: Tn5-mediated proximity ligation.
  • Output: Paired-end reads containing both ATAC and Hi-C information.
  • Resolution: High-resolution enhancer-promoter loops.
  • Input: ~50,000 to 100,000 cells.

Why Choose HiCAR?

True Multi-Omics Integration

HiCAR captures accessibility and interaction on the same DNA molecules. This physical linkage dramatically reduces false positives when assigning distal enhancers to target genes, providing high-confidence candidates for downstream validation.

High-Resolution Regulatory Loops

HiCAR uses Tn5 transposase, which naturally prefers open, active chromatin. This biases the sequencing library toward the most biologically relevant regions—promoters and enhancers—allowing you to detect fine-scale regulatory loops with significantly less sequencing effort.

Efficiency for Rare Samples

HiCAR's streamlined, in situ workflow is optimized for low inputs, requiring only ~50,000 cells to generate high-quality, dual-omics maps. This efficiency opens the door to regulatory profiling in systems that were previously inaccessible.

Technical Comparison: HiCAR vs. Hi-C vs. ATAC-seq

Feature HiCAR (Our Service) Standard Hi-C ATAC-seq
Data Output 3D Structure + Accessibility 3D Structure Only Accessibility Only
Enzyme Tn5 Transposase Restriction Enzyme Tn5 Transposase
Targeting Active Regulatory Elements Whole Genome (Uniform) Open Chromatin
Input Requirement Low (~50k cells) Moderate to High Low
Best For V2G Assignment, Rare Cells TADs, Compartments Peak Calling

Our HiCAR Workflow: Tn5-Mediated Proximity Ligation

The HiCAR workflow is an elegant modification of the standard Hi-C protocol, replacing restriction digestion with transposase-mediated engineering.

  1. Crosslinking & Permeabilization: Cells are treated with formaldehyde to freeze 3D structures and permeabilized.
  2. Tn5 Tagmentation: Tn5 transposase specifically targets and cuts "open" chromatin regions, attaching adapters.
  3. Proximity Ligation: DNA ends are ligated together while held in their 3D conformation, capturing interactions.
  4. Reverse Crosslinking & Purification: Protein crosslinks are reversed and DNA is purified.
  5. Library Amplification: The library is amplified and ready for sequencing, minimizing sample loss.

Step-by-step workflow diagram of the HiCAR sequencing service.

Sample Requirements

Sample Type Recommended Input Minimum Input* Storage/Transport
Cell Lines 100,000 cells 50,000 cells Flash Frozen Pellet
Primary Cells 100,000 cells 50,000 cells Fresh or Cryopreserved
Tissue 10-20 mg ~5 mg Flash Frozen (Liquid Nitrogen)
FACS Sorted Cells 100,000 cells 50,000 cells Pellet immediately & freeze

*Note: Success with minimum input depends on sample viability. Please consult our technical team for projects involving <50,000 cells.

Demo Results: Co-Visualizing Open Chromatin and HiCAR Loops

The power of HiCAR lies in the integrated visualization. We provide comprehensive data packages that allow you to see the multi-dimensional regulation of your genes of interest.

  • Top Track (Accessibility): ATAC-like peaks showing open chromatin regions (promoters/enhancers).
  • Bottom Track (Interactions): HiCAR chromatin contact arcs (loops) anchored specifically at the peaks in the top track.
  • Interpretation: Immediately see which distal enhancer peak is physically looping to which gene promoter.

Composite genome track showing accessibility peaks at promoters/enhancers and HiCAR contact arcs.Integrated Tracks

Case Study: High-Sensitivity Mapping of Regulatory Loops

Understanding how genetic variants in non-coding regions affect disease risk is a major challenge. Standard Hi-C often lacks the resolution to link these variants to their target genes, while ATAC-seq identifies the variants but not their targets. A 2022 study published in Molecular Cell sought to resolve this using HiCAR.

The researchers applied HiCAR to K562 human leukemia cells and primary human muscle stem cells. They aimed to validate the method's ability to capture both open chromatin features and high-resolution chromatin loops from low-input material.

The HiCAR data (Figure 3A) demonstrated a striking concordance with separate high-depth Hi-C and ATAC-seq datasets. Crucially, HiCAR successfully identified high-resolution enhancer-promoter loops that were specifically anchored at open chromatin regions. These "anchored" loops provided a much cleaner regulatory map than standard Hi-C, which often contains structural noise.

Data showing HiCAR performance compared to in situ Hi-C and HiChIP.

This study established HiCAR as a robust, sensitive, and efficient method for analyzing open-chromatin-associated genome organization. It confirmed that HiCAR can serve as a powerful "all-in-one" tool for dissecting the 3D regulatory genome. (Source: HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization, Molecular Cell, 2022.)

Frequently Asked Questions

References

  1. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Molecular Cell. 2022.
  2. Trac-looping measures genome structure and chromatin accessibility. Nature Methods. 2018.
  3. OCEAN-C: mapping hubs of open chromatin interactions across the genome. Genome Biology. 2018.
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High-confidence 3D genomics services for chromatin interaction analysis and regulatory insight.

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