Chromatin Conformation Capture Sequencing

3C-Seq (Duan et al., 2012), Capture-C, and Hi-C (Lieberman-Aiden et al., 2009) comprise a family of methods for analyzing chromatin interactions. Capture-C adds an additional pull-down of the biotinylated fragments with magnetic beads to the 3C method. A new refinement of the Capture-C method (NG Capture-C) is available (Davies et al., 2016). The Hi-C approach extends 3C-Seq to map chromatin contacts genome-wide, and it has also been applied to studying in situ chromatin interactions(Sati et al., 2016) (Rao et al., 2014).

In this method, DNA-protein complexes are crosslinked with formaldehyde. The sample is fragmented, and the DNA is extracted, ligated, and digested with restriction enzymes. The resulting DNA fragments are PCR-amplified and sequenced. Deep sequencing provides base-pair resolution of the ligated fragments.


  • Allows detection of long-range DNA interactions
  • High-throughput method


  • Detection may result from random chromosomal collisions
  • Less than 1% of DNA fragments actually yield ligation products (Bourgo et al., 2016)
  • Due to multiple steps, the method requires large amounts of starting material


Illumina Library prep and Array Kit Selector


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