Chromosome Conformation Capture - Advantages and Disadvantages

Advantages and Disadvantages

A significant confounding factor in the 3C technology is the frequent random collisions of chromosomal regions to one another, which means that the detection of a product does not always mean a specific interaction has occurred between two regions. Therefore, a specific interaction between two regions is only confirmed when the interaction occurs at a higher frequency than with neighboring DNA.

The ChIP-loop may be useful in identifying long-range cis-interactions and trans interaction mediated through proteins since frequent DNA collisions will not occur.

The 5C technique overcomes the junctional problems at the intramolecular ligation step and is useful for constructing complex interactions of specific loci of interest. This approach is unsuitable for conducting genome-wide complex interactions since that will require millions of 5C primers to be used.

In contrast to 3C and 5C, the 4C technique does not require the prior knowledge of both interacting chromosomal regions. Results obtained using 4C are highly reproducible with most of the interactions that are detected between regions proximal to one another. On a single microarray, approximately a million interactions can be analyzed.

A common problem in all of these techniques is the requirement of a great number of cells, especially in the high-throughput methodologies. A single mammalian cell only provides two copies of any given restriction fragment, which can be ligated to only one other partner in 3C. Therefore any kind of quantitative analysis requires a large number of cells due to the need to determine the specification of an interaction between two regions. Experiments using the 4C technique routinely process ten million cells for analysis on a single microarray.