Chromosome conformation capture carbon copy technology

UMMS Affiliation

Program in Gene Function and Expression

Publication Date


Document Type

Book Chapter


Chromosomes; Chromosomes, Artificial, Bacterial; DNA Primers; Molecular Biology; *Nucleic Acid Conformation; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Sequence Analysis, DNA; Templates, Genetic


Genetics and Genomics


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.

DOI of Published Version



Curr Protoc Mol Biol. 2007 Oct;Chapter 21:Unit 21.14. Link to article on publisher's site

Journal/Book/Conference Title

Current protocols in molecular biology

Related Resources

Link to Article in PubMed

PubMed ID