The role of loops on the order of eukaryotes and prokaryotes

The study of the three-dimensional organization of chromatin has recently gained much focus in the context of novel techniques for detecting genome-wide contacts using next-generation sequencing. These chromosome conformation capture-based methods give a deep topological insight into the architecture of the genome inside the nucleus. Several recent studies observe a compartmentalization of chromatin interactions into spatially confined domains. This structural feature of interphase chromosomes is not only supported by conventional studies assessing the interaction data of millions of cells, but also by analysis on the level of a single cell. We first present and examine the different models that have been proposed to elucidate these topological domains in eukaryotes. Then we show that a model which relies on the dynamic formation of loops within domains can account for the experimentally observed contact maps. Interestingly, the topological domain structure is not only found in mammalian genomes, but also in bacterial chromosomes.