When is DNase Hi-C recommended over restriction enzyme methods?

DNase Hi-C is recommended when you need uniform coverage across the genome, particularly in regions that lack restriction sites (restriction deserts). It is also excellent for organisms with extreme GC content where standard enzymes might cut too frequently or too rarely.

What are the advantages of Hi-C 2.0?

Hi-C 2.0 is an optimized workflow designed for speed and sensitivity. It reduces the hands-on time and the required input material (cell number), making it ideal for projects with precious samples or large sample numbers that need higher throughput.

Do you offer bioinformatic analysis for these services?

Yes. All our Hi-C services come with optional comprehensive bioinformatics packages. We can provide interaction matrices (contact maps), call TADs and loops, assign A/B compartments, and perform differential topology analysis between samples.

Which method is best for clinical samples?

For clinical samples, which are often limited in quantity, Hi-C 2.0 or In situ Hi-C are preferred due to their robustness. If specific regulatory proteins are of interest (e.g., mapping enhancer loops in a specific tumor type), HiChIP might be more cost-effective.

Comprehensive Hi-C & 3D Genomics Services

Q: What is the main difference between Dilution Hi-C and In situ Hi-C?

The key difference is the ligation environment. In Dilution Hi-C, nuclei are lysed and chromatin is solubilized before ligation, which can allow random DNA ends to join (noise). In In situ Hi-C, ligation happens inside the intact nucleus, which naturally constrains DNA ends, resulting in a much cleaner library with a higher signal-to-noise ratio.

Explore the full spectrum of chromosome conformation capture technologies with our Comprehensive Hi-C & 3D Genomics Services. As a centralized hub for 3D genome mapping, we offer every generation of Hi-C chemistry—from the foundational Dilution and In situ Hi-C protocols to advanced DNase Hi-C and Micro-C variants. Whether you need global architecture mapping or fine-scale regulatory loop detection, access the right resolution for your research here. RUO.

Foundational Methods: Access standard In situ Hi-C, Dilution Hi-C, and Hi-C 2.0.
Sequence-Independent: DNase Hi-C for uniform coverage without restriction bias.
Specialized Resolution: Direct access to Micro-C, Pore-C, and protein-centric services.
Scalable Solutions: Workflows optimized for inputs ranging from cell lines to clinical tissues.

Browse Hi-C Technologies

Diagram of the Hi-C technology family tree showing In situ, Micro-C, Pore-C, and DNase methods.

Overview: A Complete Toolkit for 3D Genome Mapping

The 3D organization of the genome is not just structural; it is regulatory. To fully understand gene expression, replication, and disease mechanisms, researchers must look beyond the linear sequence to the folded architecture of chromatin. However, no single method fits every biological question. A study on global A/B compartments requires a different approach than one mapping fine-scale enhancer-promoter loops.

Our Hi-C Core serves as a centralized hub for Comprehensive Hi-C & 3D Genomics Services. We offer the complete evolution of chromosome conformation capture technologies—from the foundational Dilution Hi-C and industry-standard In situ Hi-C to advanced, sequence-independent DNase Hi-C. Whether you are validating legacy data, conducting large-scale clinical cohorts with Hi-C 2.0, or seeking nucleosome-level resolution, our portfolio ensures you have access to the exact chemistry required for your research goals.

Why Partner with Our Hi-C Core?

Technology Agnostic: We recommend the method that fits your resolution needs.
Legacy & Innovation: Support for classical protocols and cutting-edge variants.
Scalable Workflows: Optimized pipelines for low-input samples and large cohorts.

The "Core" Hi-C Portfolio (Foundational Methods)

This section details our foundational genome-wide mapping services. These methods provide "All-vs-All" interaction maps, essential for defining Topologically Associating Domains (TADs), A/B compartments, and chromatin loops.

In situ Hi-C (The Gold Standard)

High Signal-to-Noise Ratio for Robust Topology
In situ Hi-C is the modern standard for 3D genomics. Unlike earlier methods, the critical proximity ligation step is performed within intact nuclei. This physical containment prevents random intermolecular ligation (noise) between DNA fragments that are not actually close in 3D space.

Best For: Standard mapping of TADs, compartments, and loops; benchmarking against public datasets (e.g., ENCODE, 4DN).
Mechanism: Crosslinking → Digestion (Restriction Enzyme) → Biotin Fill-in → Ligation (in Nucleus) → Sequencing.

Dilution Hi-C (Classic)

The Original Protocol for Legacy Comparisons
Also known as "Solubilization Hi-C," this is the original method described in 2009. Chromatin is solubilized (diluted) prior to ligation to favor intramolecular interactions. While it has a lower signal-to-noise ratio than In situ Hi-C, it remains essential for projects that need to be strictly comparable with historical datasets generated before 2014.

Best For: Replication of legacy studies; specific comparative analyses where the original protocol is a variable.

Hi-C 2.0 (High-Efficiency)

Optimized Chemistry for Speed and Low Input
Hi-C 2.0 represents a streamlined evolution of the In situ protocol. By optimizing the lysis, digestion, and ligation buffer systems, we significantly reduce the time-to-data and the required starting material.

Best For: Clinical samples with limited material; high-throughput screening projects; large-scale population studies.

DNase Hi-C (Sequence-Independent)

Uniform Coverage Without Restriction Bias
Traditional Hi-C relies on restriction enzymes (like HindIII or DpnII) to cut DNA. This leaves "blind spots" in the genome where restriction sites are sparse. DNase Hi-C uses the enzyme DNase I for random fragmentation. This results in uniform genome coverage and higher effective resolution.

Best For: Organisms with GC-rich or AT-rich genomes; SNP-based phasing; fine-mapping loops without sequence bias.

Advanced & Specialized Hi-C Modules

For research requiring resolution beyond standard Hi-C, or for specialized multi-omics applications, explore our advanced service modules.

Standard Hi-C Sequencing

Our flagship service utilizing the In situ workflow for reliable, genome-wide chromatin interaction maps. The go-to choice for characterizing global genome architecture.

Micro-C

Resolution: Nucleosome Level. Replaces restriction enzymes with MNase to digest chromatin down to single nucleosomes. Achieves the highest possible resolution for enhancer-promoter loops.

Pore-C

Multi-Way Interactions. Combines Hi-C with Nanopore long-read sequencing to detect high-order chromatin clusters (3+ loci interacting simultaneously) on single DNA molecules.

HiChIP / ChIA-PET

Protein-Centric Mapping. Enriches for interactions involving a specific protein (e.g., CTCF, Pol II, H3K27ac), significantly reducing sequencing costs for regulatory analysis.

Method Selection Guide

Choosing the right chromosome conformation capture technology is critical for project success. Use this guide to match your biological question with the optimal method.

Research Goal	Recommended Method	Key Advantage
Global Architecture (TADs/Compartments)	In situ Hi-C	Industry standard; robust and comparable.
Enhancer-Promoter Loops (<5kb)	Micro-C	Highest resolution; breaks the restriction barrier.
High-Order Clusters (Enhancer Hubs)	Pore-C	Direct detection of multi-way contacts.
Protein-Specific Loops (e.g., CTCF)	HiChIP	Cost-effective; enriched signal.
Unbiased Coverage (No Restriction Sites)	DNase Hi-C	Uniform coverage; no sequence bias.
Low Input / Clinical Cohorts	Hi-C 2.0	Optimized efficiency for limited material.
Replicating 2010-era Studies	Dilution Hi-C	Methodological consistency with legacy data.

Flowchart for selecting the appropriate Hi-C method based on research goals.

Frequently Asked Questions

Q: What is the main difference between Dilution Hi-C and In situ Hi-C?