Chromosome Conformation Capture

Chromosomal conformational capture (3C) is a molecular biology technique used to analyze the form of chromosomes in the natural state of cells. The study of the structural properties and spatial organization of chromosomes is particularly important for understanding non-coding single nucleotide polymorphisms (SNPs), and the effects of DNA modifications and altered protein binding on gene expression. This technique is useful for studying genetics and epigenetics in model organisms and humans.

Based on the original 3C technology, many derivative technologies have been developed. All of the 3C-based technologies are based on the idea that the terminal and functionally related DNA fragments are more likely to interact. First, the 3C protocol uses cross-linking reactions to maintain the physical interaction between the DNA fragment and the associated protein. Next, chromatin is digested/sonicated and ligated. After decrosslinking and protein digestion, a library of mixed DNA is formed, and if the fragments are in three-dimensional proximity, they are likely bound together. While most technologies begin with this standard protocol, their range of output and results can vary.

Categories of Chromosomal Conformational Capture Technique
  1. 3C and chromatin immunoprecipitation (ChIP)-based 3C (ChIP-loop assay)
  2. 4C and ChIP-based 4C (Enhanced 4C)
  3. 5C and three-dimensional detection
  4. Genomic conformation capture (GCC) related techniques (Hi-C) and ChIP-based GCC (also known as 6C)


Comparison of Different 3C-based Methodologies.

Figure 1. Comparison of Different 3C-based Methodologies. (Davies J O J.; et al. 2017).

Chromosome Conformation Capture Services at Creative BioMart

Chromosome Conformation Capture

Hi-C Sequencing
Hi-C is the genome-wide extension of 3C, which refers to the capture of chromosome conformation based on high-throughput technique. It can capture the spatial interaction information between different gene loci in the whole genome, obtain three-dimensional (3D) structure information of chromatin and study the DNA elements regulating genes in the 3D space.

Chromosome Conformation Capture

CHIA-PET Sequencing
Chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing is one of the 3C technique-derived approaches, and ChIA-PET is unique compared to the Hi-C technique, which allows specific protein factors and their associated chromatin interactions to be interrogated at high resolution within the genome.

As a dedicated supplier of epigenetic research services, Creative BioMart is looking forward to work closely with your team and accelerate your epigenetics project. Our services are tailored to meet your specific needs. contact us for more information about our chromosome conformation capture service.

1. Sati S.; Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2017, 126(1): 33-44.
2. Davies J O J.; et al. How best to identify chromosomal interactions: a comparison of approaches. Nature Methods. 2017, 14(2): 125-134.

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