Capture-C is the newest, and in many ways most advanced 3C technology to be developed (Hughes et al., 2014). The technology gap Capture-C attempts to fill is the lack of a 3C technique that is both high resolution and high throughput. It combines 3C and next-gen sequencing with oligonucleotide capture technology (OCT).
OCT (specifically Agilent’s SureSelect used here) allows for hundreds of regions of interest to be isolated from a sample using specially designed RNA in solution. In Capture-C, a standard 3C experiment is performed; however the 3C ligated fragments are sonicated at the end. This allows the OCT protocol to enrich for the selected regions of interest. These enriched fragments are then sequenced. By performing an OCT, the cost and scale of the sequencing is greatly reduced, allowing many more samples to be processed.
The only downside of Capture-C is that it is not truly genome-wide; many but not all regions can be studied. Hughes et al. examined about 450 promoters and showed that cis DNA interactions with promoter are most likely within a 600 kb region surrounding it.
Capture-C Additional Reading
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189.
This paper introduces the principles of solution-based oligonucleotide capture. For further information on the specific assay used by Hughes et al., see this Agilent document.
- Hughes, J.R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., and Higgs, D.R. (2014). Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205-212.