Genome sequencing allows us to unveil the complete DNA sequence of an organism. However, to understand all genomic processes carried out in the cell nucleus it is necessary to determine its three-dimensional architecture. Advances in genomic technologies have boosted the development of new analytical methods, such as Chromosome Conformation Capture (3C), a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genes or genetic markers of interest on certain sequences that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome.