3D fluorescent in situ hybridization and nuclear architecture

Fluorescent in situ hybridization on three-dimensionally preserved nuclei (3D-FISH) is an efficient method of analyzing higher-order arrangements of chromatin, which constitutes the highest level of epigenetic gene regulation. 3D-FISH analyses have disclosed a high variability with regard to the side-by-side arrangements of chromosome territories. In contrast, a distinct radial positioning of chromatin correlating to local gene density has been shown for a large number of cell types and has been maintained over a long period during evolution. The issue of a spatial association of cotranscriptionally expressed genes, such as the formation of "expression hubs", is currently a matter of controversial discussion.