Computing chromosome conformation.

The "Chromosome Conformation Capture" (3C) and 3C-related technologies are used to measure physical contacts between DNA segments at high resolution in vivo. 3C studies indicate that genomes are likely organized into dynamic networks of physical contacts between genes and regulatory DNA elements. These interactions are mediated by proteins and are important for the regulation of genes. For these reasons, mapping physical connectivity networks with 3C-related approaches will be essential to fully understand how genes are regulated. The 3C-Carbon Copy (5C) technology can be used to measure chromatin contacts genome-scale within (cis) or between (trans) chromosomes. Although unquestionably powerful, this approach can be challenging to implement without proper understanding and application of publicly available bioinformatics tools. This chapter explains how 5C studies are performed and describes stepwise how to use currently available bioinformatics tools for experimental design, data analysis, and interpretation.