Chromatin Interaction Study (Hi-C)

Next-generation Sequencing

Service Overview

Research on gene expression regulation has long been limited to genes and their regulatory elements that are linearly adjacent to them. However, accumulative evidence has shown spatially arranged chromatin interaction also plays a vital role in gene expression regulation. The 3D folding of chromosomes brings distant regulatory elements into close spatial proximity, by which regulation of genes can be achieved. 3D-structure and interactions of chromatin is one of the most crucial features in epigenetics.

Hi-C is a novel technology combining chromosome conformation capture and high-throughput sequencing. DNA fragments of long linear distance while close in spatial structures are fixed and enriched for Pair-end sequencing. This technology empowers us to reveal the interactions between chromosome compartments and 3D structure of genome, which provides vital clues for novel intergenetic regulatory mechanisms.

Experimental Workflow

3D structure of chromatin is dynamic overtime and in different cell type. The changes in 3D structures are closely related to gene expression regulation, such as A/B compartments switching, changes in TAD boundaries, disappearance and formation of loop, etc.


Joint Study with Omics

Service Advantages

Massive experience in Hi-C technology, achieving assembly of approx. 300 species and construction of approx. 1,000 Hi-C library.
Customized Restrict Enzyme design based on species, achieving over 93% valid interaction pairs in Hi-C library and average ratio of 68%.
We owns several experimental patents and bioinformatic software copyrights empowering us to provide the best Hi-C service.
Visual bioinformatic analysis system with various tools for plotting figures of your preference.

Results Demo

A/B compartments and switching analysis

TAD and differential TAD analysis
Whole genome distribution of TAD
Hierarchical clustering heatmap on DI value of differential TAD boundary
Hierarchical clustering heatmap on differential TAD boundary related DEGs
Chromatin loop and differential loop analysis
Hi-C contact heatmap with chromatin loops
Whole genome distribution of loops


1What's the recommended data volume for Hi-C interaction analysis?
If Loop analysis (enhancer-promoter interactions) is of your interest, 150X of data is recommended to achieve resolution below 10 kb. If your research mainly focus on compartment and TAD, 50X data is adequate for down stream analysis. If higher resolution, such as 5 kb, is required, we would recommend 300X data.
2Are biological replicates required for Hi-C interaction analysis?
3D-structure of chromatin is dynamic and highly related to gene expression regulation, so we strongly recommend to have at least 2 biological replicates. For tissue culture samples, we would recommend to design 3 biological replicates with each of them sequenced for 50X. The data can be combined for further analysis. However, it is not recommended for clinical samples.
3 Is it necessary to combine other omics studies with Hi-C interaction analysis?
We strongly recommend to combine the Hi-C interaction outcomes with RNA-seq. Other omics analysis such as DNA methylation sequencing, CHIP-seq, ATAC-Seq and whole genome resequencing can all be connected to reveal the biological meaning of the changes in chromatin structures. We can also provide joint analysis of Hi-C data with your existing comics data.