NG Capture-C

Next-Generation Capture-C

NG Capture-C is a refinement of 3C-Seq (Duan et al., 2012) and Hi-C (Lieberman-Aiden et al., 2009). It represents a family of methods used to analyze chromatin interactions. NG Capture-C adds multiple pull-down steps of the biotinylated fragments with magnetic beads to the 3C method.

The protocol uses formaldehyde fixation followed by restriction enzyme digestion and ligation to form ~10 kb concatamers. The DNA is extracted and sonicated. Indexing adapters are added, and the samples are pooled, purified by pull-down, and PCR-amplified. The pull-down and PCR steps can be repeated to yield up to a million-fold enrichment (Davies et al., 2016)

Advantages:

• High sensitivity to detect cis and trans interactions
• Low sample input requirements
• Sonicated capture fragments reduces cost compared to capture-C
• Sonicated capture fragments act as UMIs to reduce PCR bias

Disadvantages:

• None reported

Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Sati S. and Cavalli G. Chromosome conformation capture technologies and their impact in understanding genome function. Chromosoma. 2016;



References:

Davies J. O., Telenius J. M., McGowan S. J., et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods. 2016;13:74-80

Hay D., Hughes J. R., Babbs C., Davies J. O., Graham B. J., et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48:895-903

Edit: NG Capture-C

You must be logged in to edit this entry.

History: NG Capture-C

Revision by sbrumpton on 2017-06-21 09:37:31 - Show/Hide