What is Hi-C Sequencing?

Hi-C Sequencing is a chromosome conformation capture (3C)-based technology that reveals the three-dimensional (3D) organization of the genome by identifying physical interactions between chromatin regions. Since genome function depends not only on DNA sequence but also on chromatin architecture, Hi-C provides valuable insights into gene regulation, chromosome organization, and genome structure.

The workflow involves chromatin crosslinking, restriction enzyme digestion, proximity ligation, library preparation, high-throughput sequencing, and bioinformatics analysis to generate genome-wide chromatin interaction maps. These data help identify chromatin loops, topologically associating domains (TADs), genomic compartments, and other structural features that influence genome function.

Applications of Hi-C Sequencing

Hi-C Sequencing supports a broad range of research applications, including:

• • Chromosome-Level Genome Assembly and scaffold construction

• • 3D Genome Organization and chromatin interaction analysis
• • Gene Regulation through enhancer-promoter interaction mapping
• • Haplotype Phasing and structural variation analysis
• • Cancer and Disease Research using integrated multi-omics approaches
• • Developmental Biology and cellular differentiation studies
• • Plant Genomics for stress response and trait discovery
• • Microbial Genome Organization and host-microbe interaction studies
• • Synthetic Biology and engineered genome analysis
• • Comparative and Pan-Genome Research

Hi-C Sequencing Service Options

Hi-C Sequencing Workflow

Our end-to-end workflow is designed to generate accurate and reproducible chromatin interaction data.

• Sample preparation and chromatin crosslinking

• Restriction enzyme digestion

• Proximity ligation of interacting DNA fragments

• Hi-C library preparation

• High-throughput sequencing

• Chromatin interaction mapping

• Bioinformatics analysis and visualization

• Final report and data delivery

Bioinformatics Analysis

Our comprehensive analysis pipeline includes:

• Standard Analysis

• - Raw data quality assessment
• - Chromatin interaction heatmaps
• - A/B compartment identification
• - TAD detection and boundary analysis
• - Chromosome interaction statistics

• Advanced Analysis

• - Differential chromatin interaction analysis
• - Multi-omics integration with RNA-seq, ATAC-seq, and WGS
• - 3D genome reconstruction
• - Customized downstream analysis based on research objectives

Deliverables

Each project includes:

• • Raw sequencing data (FASTQ)
• • Processed alignment files (BAM)
• • Chromatin interaction matrices
• • Heatmaps, Circos plots, and TAD visualizations
• • Comprehensive bioinformatics report
• • Quality control metrics
• • Project documentation and data interpretation support

Sample Requirements

Sample Guidelines

• • Fresh samples are recommended for optimal results.
• • Snap-freeze tissues in liquid nitrogen and ship on dry ice.
• • DNA extraction services are available upon request.
• • Please contact us for low-input or specialized sample types.

Why Choose N2Jenomics Lab Pvt. Ltd.?

• • Advanced Hi-C sequencing using industry-leading NGS platforms
• • High-quality chromosome-scale genome assembly solutions
• • Comprehensive bioinformatics and 3D genome analysis
• • Flexible workflows tailored to diverse research applications
• • Experienced genomics and bioinformatics specialists
• • End-to-end project support from sample processing to final data interpretation

1. Why is 3D genome analysis important?

Although DNA is organized as a linear sequence, gene regulation is controlled by the three-dimensional arrangement of chromatin within the nucleus. Hi-C sequencing helps uncover these spatial interactions, providing valuable insights into gene expression, genome organization, and regulatory mechanisms.

2. Are biological replicates recommended for Hi-C sequencing?

Yes. Two biological replicates are generally recommended to improve data reliability and reproducibility. The required sequencing depth depends on the genome size and the desired resolution of chromatin interaction analysis.

3. What are the key concepts in Hi-C and 3D genomics?

• • Chromosome Territory: The distinct spatial region occupied by each chromosome within the nucleus.

• • A/B Compartments: Large chromatin domains representing active (A) and inactive (B) genomic regions.
• • Topologically Associating Domains (TADs): Genomic regions with frequent internal interactions that help regulate gene activity.
• • Chromatin Loops: Physical interactions between distant genomic elements, such as enhancers and promoters.
• • Cis Interactions: Chromatin interactions occurring within the same chromosome.
• • Trans Interactions: Chromatin interactions occurring between different chromosomes.

4. How should low-input samples be prepared?

Low-cell-number samples should be suspended in a small volume of PBS, frozen immediately in liquid nitrogen, and transported on dry ice to preserve chromatin integrity. Please contact our team for specific recommendations based on your sample type.

5. How does Capture Hi-C differ from standard Hi-C?

Standard Hi-C provides a genome-wide view of chromatin interactions, whereas Capture Hi-C enriches selected genomic regions, such as promoters or disease-associated loci. This targeted approach offers higher resolution and sequencing efficiency for regions of interest while reducing background noise.

6. What is the workflow for Capture Hi-C?

Capture Hi-C involves chromatin crosslinking, DNA digestion and ligation, library preparation, target enrichment using capture probes, high-throughput sequencing, and bioinformatics analysis to identify high-resolution chromatin interactions within selected genomic regions.