ExperimentTypeDilution Hi-C

   March 28th, 2019 at 7:30pm
Reference Publication
Lieberman-Aiden E et al. (2009) doi:10.1126/science.1181369
Lieberman-Aiden E, van Berkum NL, et al., Science (New York, N.Y.) 2009


Experiment Category 
Assay Classification 
3C via Ligation
Experimental Purpose 
DNA-DNA Pairwise Interactions
Raw Files Available 
Reads (fastq) provided by lab

Assay Description

Dilution Hi-C

Dilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique.

The protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.

Advances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol.

See Lieberman-aiden et al., 2009 for more details on dilution Hi-C.

Image source: Lieberman-aiden et al., 2009, Figure 1A