Application of Chromosome Conformation Capture (3C) to the Study of Human Genetic Disease


Chromosome conformation capture (3C) is a powerful technique that allows for the generation of 3‐dimensional transcriptome organisational maps. 3C facilitates the identification and quantitative measurement of distant chromosomal regulatory elements with proximal gene promoter regions. This is achieved by fixing protein onto deoxyribonucleic acid (DNA) followed by restriction enzyme digestion or sonication to shear the DNA prior to re‐ligation of the fixed DNA region. PCR amplification of a chromosomal region of interest can then be performed and quantified. Next generation sequencing platforms on prepared 3C chromatin can provide information on whole genome regulatory networks. The technology and its modified derivatives provide high levels of resolution and throughput for determining nuclear organisation and allows for the identification of novel noncoding DNA regions that are associated with controlling gene expression. 3C is providing important insights into underlying mechanisms that may be responsible for various human diseases including cancer, muscular dystrophies, neurological and metabolic disorders.

Key Concepts:

  • Chromosome conformation capture (3C) is a key strategy used to determine distant chromosomal regulatory regions involved with controlling gene expression.

  • Single nucleotide polymorphic (SNP) DNA variations in noncoding region DNA can now be interrogated to determine a functional role in altering gene expression.

  • The 3‐dimensional chromosome looping architecture can be dissected to determine multiple chromosomal regions involved with regulating gene expression through transcription factory interaction.

  • Mutations in distant chromosomal regulatory regions may lead to uncontrolled repression of oncogenes allowing for increases in tumour growth and development.

  • Identifying noncoding chromosomal regions associated with nuclear adaptive mechanisms in response to DNA mutation may allow us to determine critical regions involved with maintaining cellular homoeostasis.

  • High‐throughput sequencing strategies are allowing for unparalleled identification of DNA variation in the human genome.

Keywords: chromosome conformation capture; gene regulation; SNP; cancer; human disease; mutation; malfunction; enhancers; repressors

Figure 1.

Chromosome conformation capture. (a) Linear chromosomal DNA containing protein‐binding regions of interest. (b) Looping of chromosome allows interaction of upstream and proximal promoter region proteins. Cross‐linking with formaldehyde fixes proteins in position. (c) Restriction enzyme digestion of cross‐linked DNA produces cohesive overlapping ends. (d) Ligation of protein cross‐linked DNA. (e) Reversal of cross‐linking to remove DNA bound proteins. (f) PCR to determine cross‐linking of upstream region with the proximal promoter region.

Figure 2.

The ratio of noncoding DNA to total genomic DNA (ncDNA/tgDNA) increases with species complexity. Figure is simplified from Taft et al. .



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Horan, Martin P, and Ballard, J William O(Sep 2012) Application of Chromosome Conformation Capture (3C) to the Study of Human Genetic Disease. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0024383]