Capture Hi-C: Characterization of chromatin contacts

Hi-C (high throughput chromosome conformation capture) is a powerful tool designed to explore the genome-wide collection of chromosomal contacts within a cell population. However, the highly complex nature of Hi-C libraries often precludes the robust identification of interactions between individual restriction fragments with high resolution and statistical significance. This challenge led to the incorporation of sequence capture technology into Hi-C protocols, giving rise to a Capture Hi-C methodology. In this chapter, we review the general principles of the technique and provide a view emanating from our experience employing this approach to study the dynamics of episomal viral DNA contacts during specific stages of the viral life cycle.