UNIT 21.14 Chromosome Conformation Capture Carbon Copy Technology
Published Online: 1 OCT 2007
Copyright © 2007 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Molecular Biology
How to Cite
Dostie, J., Zhan, Y. and Dekker, J. 2007. Chromosome Conformation Capture Carbon Copy Technology. Current Protocols in Molecular Biology. 80:21.14:21.14.1–21.14.13.
- Published Online: 1 OCT 2007
- Published Print: OCT 2007
Chromosome conformation capture (3C) is used to quantify physical DNA contacts in vivo at high resolution. 3C was first used in yeast to map the spatial chromatin organization of chromosome III, and in higher eukaryotes to demonstrate that genomic DNA elements regulate target genes by physically interacting with them. 3C has been widely adopted for small-scale analysis of functional chromatin interactions along (cis) or between (trans) chromosomes. For larger-scale applications, chromosome conformation capture carbon copy (5C) combines 3C with ligation-mediated amplification (LMA) to simultaneously quantify hundreds of thousands of physical DNA contacts by microarray or ultra-high-throughput DNA sequencing. 5C allows the mapping of extensive networks of physical interactions among large sets of genomic elements throughout the genome. Such networks can provide important biological insights, e.g., by identifying relationships between regulatory elements and their target genes. This unit describes 5C for large-scale analysis of cis- and trans-chromatin interactions in mammalian cells. Curr. Protoc. Mol. Biol. 80:21.14.1-21.14.13. © 2007 by John Wiley & Sons, Inc.
- chromatin structure;
- epigenetic regulation;
- systems/network biology;
- DNA looping;
- high throughput