Hi-C

The genomic DNA of eukaryotic organisms is not linear within the cell nucleus; instead, it is highly folded and condensed into chromatin through a 3D structure, possessing specific advanced spatial structures and conformations. With the acquisition and integration of multi-omics data, the existing linear genome-based models, such as physical proximity or genetic linkage, etc., are insufficient to explain the intricate regulatory mechanisms within cells. In 2009, Lieberman-Aiden et al. first reported the high-throughput chromosome conformation capture (Hi-C) technology in the Science. This pioneering approach focused on studying the entire cell nucleus by utilizing in situ cross-linking, restriction enzyme cleavage, proximity ligation of DNA ends, and enrichment, along with high-throughput sequencing and bioinformatic analysis. Hi-C technology allowed for the exploration of DNA sequence interactions at any position in the space across the entire genome.

Currently, Hi-C technology has been widely applied, enabling researchers to explore the intrinsic connections between 3D spatial structures of genome and gene expression regulation. Studies have shown that the hierarchical structural units of the mammalian genome, including chromosome territories (CT), chromatin compartments A/B, topologically associated domains (TADs), and chromatin loops from large to small have played crucial roles in gene transcription and expression regulation.

Among these, CTs are ubiquitous spatial structures of genome, with different chromosomes occupying distinct territories within the cell nucleus. Compartments A/B are larger structural units determined by genomic epigenetic modifications and closely associated with chromatin activity.

Generally, Compartment A represents an open chromatin compartment, usually located on autosome regions with relatively higher gene expression compared with Compartment B. In contrast, Compartment B is a closed chromatin compartment, typically located on heterochromatin regions with lower gene density and relatively lower gene expression compared with Compartment A. TADs are stable spatial structure units within the cell nucleus that regulate gene expression on a local scale, while chromatin loops represent the finest structural and functional units that directly regulate gene expression, often formed through interactions between promoters and distal enhancers. Therefore, Hi-C technology is not only useful for assisting genome assembly, but also for the study of gene expression regulation.

1. Cell Count ≥ (3,000/GS) 3.0 x 10*7 cells

(Cells should be in good condition without contamination. It is recommended to perform mycoplasma detection before sample submission. GS refers to the Genome Size in megabases, Mb).

2. Animal Tissue ≥ 3g (fresh tissue).

Precautions

1. The actual sample volume should meet the requirements for library building three times, and also be sent in 3 tubes;

2. It is required to provide customers with a formaldehyde cross-linking protocol. After completing the cross-linking, they should send the samples after the fixed cross-linking of formaldehyde;

3. If fixed conditions are not available, it is required to provide live cells and the corresponding culture medium for transportation at room temperature. For tissue samples, it is recommended to cut the tissue into pieces in the size of mung beans, and keep the tissue fresh without degradation, connective tissue or residual blood. Place the fresh tissue in 1.5ml EP tubes, freeze them with liquid nitrogen, and transport them with dry ice.