Chromosome conformation capture

Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures.

The chief difference between 3C-based methods is their scope. For example, in 3C, the interactions between two specific fragments are quantified. In contrast, Hi-C quantifies interactions between all possible pairs of fragments simultaneously.

Historically, microscopy was the primary method of investigating nuclear organization.

In 1993, the Nuclear Ligation Assay was published, a method that could determine circularization frequencies of DNA in solution. This assay was used to show that estrogen induces an interaction between the prolactin gene promoter and a nearby enhancer.

Subsequently, some of the main ideas of the Nuclear Ligation Assay were further developed into the 3C assay, published in 2002 by Job Dekker and colleagues in the Kleckner lab at Harvard University.

All 3C methods start with a similar set of steps, performed on a sample of cells. First, the cell genomes are cross-linked, which introduces bonds that "freeze" interactions between genomic loci. The genome is then cut into fragments. Next, random ligation is performed. This quantifies the proximity of fragments, because fragments are more likely to be ligated to nearby fragments.

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