Chromatin Conformation Capture Carbon Copy

5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA ligated and digested with restriction enzymes. The resulting DNA fragments are amplified using ligation-mediated PCR and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.

• Different from 4C, 5C provides a matrix of interaction frequencies for many pairs of sites (de Wit et al., 2012)
• Can be used to reconstruct the (average) 3D conformation of larger genomic regions

• Requires a priori information of the regulatory sites (Sati et al., 2016)
• Detection may not necessarily mean an interaction, resulting from random chromosomal collisions
• Cannot scale to genome-wide studies that would require a large amount of primers

Chromatin Conformation Capture Carbon Copy

5C (Dostie et al., 2007) allows concurrent determination of interactions among multiple sequences and is a high-throughput version of 3C (Sajan et al., 2012). In this method, DNA-protein complexes are crosslinked using formaldehyde. The sample is fragmented and the DNA ligated and digested with restriction enzymes. The resulting DNA fragments are amplified using ligation-mediated PCR and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.

• Different from 4C, 5C provides a matrix of interaction frequencies for many pairs of sites (de Wit et al., 2012)
• Can be used to reconstruct the (average) 3D conformation of larger genomic regions

• Requires a priori information of the regulatory sites (Sati et al., 2016)
• Detection may not necessarily mean an interaction, resulting from random chromosomal collisions
• Cannot scale to genome-wide studies that would require a large amount of primers