Sample Submission Guidelines
What is Hi-C Sequencing?
DNA and chromosomes occupy the 3D space within the nucleus. While genetic information is stored linearly, gene expression, regulation, and enhancer-promoter interactions occur within intricately folded chromatin structures. This spatial organization fundamentally influences genomic function.
Hi-C technology is a powerful method used to capture the three-dimensional architecture of genomes by mapping chromatin interactions within the nucleus. The process begins with crosslinking nuclear chromatin conformations, which helps to preserve the spatial arrangement of chromatin regions near one another. Next, restriction enzyme digestion is performed to break the chromatin into smaller fragments, followed by proximity ligation, a technique that facilitates the joining of fragments that were in close spatial contact. The resulting chimeric fragments are then subjected to high-throughput sequencing, allowing for the generation of vast amounts of data that represent the chromatin interactions. Finally, bioinformatic reconstruction is used to process this data and construct a genome-wide map of spatial interactions, helping researchers identify key regulatory elements and structural mechanisms that influence genomic function. This comprehensive approach enables a deeper understanding of how the genome is organized and how its spatial configuration impacts gene regulation and cellular processes.
Houda Belaghzala, Job Dekker., et al. "Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation." Methods 123 (2017)
Applications of Hi-C Sequencing?
Unlock critical insights into genome architecture with Hi-C sequencing. At CD Genomics, our platform enables researchers to explore gene regulation, map chromatin interactions, and uncover 3D structural variations in various biological contexts.
- Gene Regulation Mechanisms
Construct genome-wide interaction maps to identify distal regulatory elements and elucidate the roles of compartments, TADs, and chromatin loops.
- Synthetic Biology
Characterize the spatial organization and functional dynamics of engineered genomic systems.
- Chromosome-Level Genome Assembly
Scaffold contigs using chromatin interaction patterns (intra-chromosomal > inter-chromosomal; distance-dependent decay).
- Haplotype Phasing
Generate phased assemblies using heterozygous SNPs and cis-linked read pairs.
- Disease & Cancer Research
Integrate 3D genomics with multi-omics (WGS/RNA-seq/ATAC-seq) to unravel disease mechanisms.
- Cellular Differentiation
Profile chromatin dynamics across developmental stages or environmental conditions.
- Plant Stress Response & Agronomic Traits
Correlate chromatin structural variations with transcriptomic/epigenetic datasets under biotic/abiotic stress.
- Microbial Adaptation
Map 3D restructuring (CID/TAD boundaries) in bacteria/fungi under selective pressure to reveal resistance mechanisms.
- Pan-3D Genomics
Define structural variations (compartments, TADs) across pan-genomes to characterize 3D functional diversity.
Hi-C Sequencing Service Options
CD Genomics offers a variety of flexible Hi-C sequencing service types to cater to different research objectives and budget requirements:
| Service Type | Best Application | Key Benefit |
|---|---|---|
| Standard Hi-C Sequencing | Genome assembly, TAD/Compartment analysis. | Comprehensive: Global view of chromatin architecture. |
| Capture Hi-C (Targeted) | Studying specific promoters or disease loci (≤6Mb). | High Resolution: Deeper coverage of loops with lower cost/noise. |
| Meta Hi-C (3C) | Complex microbial communities. | Metagenomic Scaffolding: Assign plasmids/phages to specific host genomes. |
Whole Genome Sequencing Service Workflow
At CD Genomics, we offer a seamless, end-to-end sequencing service designed to ensure consistent, high-quality results. Our standardized workflow—from sample submission to data delivery—is built to support reproducibility, streamline research, and accelerate discovery across all types of genomic studies.
How We Do It:
Crosslinking: We "freeze" the nucleus to preserve 3D chromatin structures.
Digestion & Ligation: Chromatin is digested and re-ligated, joining DNA strands that are physically close in 3D space, even if far apart in the linear sequence.
Sequencing & Mapping: The resulting chimeric libraries are sequenced to generate a genome-wide contact map.
Technical Note: Our optimized Hi-C protocols reduce background noise and ensure high-resolution detection of Topological Associating Domains (TADs) and chromatin loops.
Hi-C Sequencing Bioinformatics Analysis
CD Genomics offers comprehensive and flexible bioinformatics analysis services, ranging from basic data processing to advanced customized analyses.
Standard Analysis Includes:
Quality Control (Interaction rate, valid pairs).
Interaction Heatmap Generation (Global & Local).
A/B Compartment Identification.
TAD Calling & Boundary Analysis.
Advanced/Custom Analysis:
Differential Topology: Compare chromatin structures between conditions (e.g., Treated vs. Control).
Multi-Omics Integration: Overlay Hi-C loops with RNA-seq expression data or ATAC-seq accessibility peaks.
3D Modeling: Computational reconstruction of the physical genome structure.
Your Data Package
Raw Data: FASTQ files.
Mapped Data: BAM/VCF files.
Visualization: Interaction heatmaps, TAD plots, and Circos plots.
Report: Comprehensive PDF report with methods and citations.
Sample Requirements
| Sample Type | Minimum Quantity |
|---|---|
| Cell Lines | ≥ 106 cells |
| Blood (EDTA) | ≥ 1 mL |
| Animal Tissue | ≥ 1 g (muscle, liver) |
| Palent Tissue | ≥ 2 g (fresh yong leaves) |
Tips:
- Snap-freeze fresh samples in liquid nitrogen and ship on dry ice.
- DNA extraction services available upon request.
- For special sample types or low-input scenarios, contact us for a customized plan.
Why Choose CD Genomics for Hi-C Sequencing?
CD Genomics offers state-of-the-art Hi-C sequencing services with industry-leading technology and comprehensive bioinformatics support. Our expert team ensures accurate results, timely delivery, and exceptional customer service, making us a trusted partner for all your genomic research needs.
- State-of-the-Art Technology:
CD Genomics uses the latest next-generation sequencing (NGS) platforms, ensuring high accuracy, high resolution, and reliable data that meets the needs of cutting-edge genomic research.
- Comprehensive Bioinformatics Support:
Our expert bioinformatics team provides thorough analysis of sequencing data, including chromatin interaction mapping, 3D genome modeling, and statistical analysis, helping you make sense of complex genomic structures.
- Customizable Service Options:
We understand that every research project is unique. That's why we offer flexible Hi-C sequencing options—ranging from standard to high-resolution and custom solutions—tailored to your specific research needs and budget.
- Expert Guidance Throughout the Process:
Our team of experienced researchers and bioinformaticians support you from start to finish. From DNA sample preparation to result interpretation, we ensure you receive the highest level of expertise every step of the way.
- Unparalleled Customer Support:
With a customer-first approach, we offer personalized service and expert advice. Our team is always available to answer questions and provide support, ensuring a smooth and seamless experience for every client.
References:
- Houda Belaghzala, Job Dekker., et al. "Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation." Methods 123 (2017): 56-65 https://doi.org/10.1016/j.ymeth.2017.04.004
- Erez Lieberman-Aiden, Nynke L. van Berkum, et al. "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome." Science 326, no. 5950 (2009): 289–293. https://doi.org/10.1126/science.1181369
- Schöpflin, Robert, et al. "Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes." Nature Communications 13.1 (2022): 6470.DOI: https://doi.org/10.1038/s41467-022-34053-7
- Xiaofei Zeng, Zili Yi., et al. "Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes." Nature Plants (2024): 39103456. https://doi.org/10.1038/s41477-024-01755-3
- Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, et al. "Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide." BMC Genomics 21 (2020): 175. https://doi.org/10.1186/s12864-020-6580-6
Demo
Figure 1: Integrated Hi-C Workflow and Quality Control Metrics
Figure 2: Global Landscape of Chromatin Compartmentalization and Topology.
Figure 3: Fine-Scale Resolution of Topological Associating Domains (TADs) and Functional Interpretation.
FAQ
1. Why is 3D Genomics Research Important
While genetic information is encoded in the linear sequence of the genome, gene expression, regulation, and interactions between genes and regulatory elements occur within the complex three-dimensional structure of chromatin. This spatial arrangement plays a pivotal role in gene expression, influenced by various regulatory elements. Therefore, studying the 3D conformation of the genome is essential for understanding the regulatory mechanisms that control gene expression.
2. Does Hi-C Require Biological Replicates? What is the Required Data Volume?
Based on current research, it is recommended to perform Hi-C with two biological replicates. The sequencing depth for each sample depends on the resolution required, typically ranging from 100x to 300x genome coverage.
3. What Do Some Key Terms in 3D Genomics Mean?
1) chromatinterritory：The spatial domain occupied by chromatin within the nucleus.
2) compartment：Regions of chromatin, classified into A (euchromatin) and B (heterochromatin) compartments in higher organisms.
3) TAD：A domain within the genome where genes interact frequently with each other, while interactions with genes from other TADs are minimal. These domains are generally insulated from one another.
4) loop：Chromatin loops formed by interactions between two genes, resulting in a circular chromatin structure, observed at high resolution.
5) cisintra-chromosome interaction ：Interactions between genes located on the same chromosome.
6) transinter-chromosome interaction：Interactions between genes located on different chromosomes.
4. How Should Low Cell Number Samples Be Submitted?
For low-cell number samples, suspend the sample in 10 µL of PBS using low-adhesion PCR tubes to minimize sample loss. Freeze the sample quickly in liquid nitrogen and ship it on dry ice.
5. What Are the Advantages and Disadvantages of Promoter Capture Hi-C Compared to Hi-C?
Advantages:1) With the same amount of data, Promoter Capture Hi-C provides deeper coverage of target regions, offering more detailed interaction data. 2) Compared to Hi-C's genome-wide interaction data, Promoter Capture Hi-C has lower background noise, higher resolution, and more distinct, abundant loop structures. Disadvantages: 1) Promoter Capture Hi-C only captures interactions involving promoters and does not provide comprehensive genome-wide interaction data.
6. What is the Experimental Workflow for Promoter Capture Hi-C?
Crosslinking-End repair (biotin labeling)-Ligation, Fragmentation and biotin capture-Next-generation library preparation-Probe hybridization and capture-Promoter Capture Hi-C library construction
