Figure 7.

Four model scenarios for large-scale chromatin interactions in trans. (A) “Contact first” scenario. It assumes a functional necessity for long-range movements of giant chromatin loops carrying two genes in order to achieve a “gene-kissing” event. At the “kissing” site these genes initiate the formation of a specialized expression hub with specific factors serving the particular needs for the co-regulation of these genes. (B) “Expression hub/transcription factory first” scenario. It assumes that a specialized expression hub/transcription factory already exists at a specific site in the nucleus. Genes in need for co-regulation by this unique expression hub must congress towards this site. (C) This scenario argues that numerous specialized expression hubs/transcription factories, which already exist at different nuclear sites, are responsible for co-regulated expression of a set of genes present in CTs with variable positions in different nuclei. Driven by constrained Brownian motions these genes may reach the closest hub/factory serving their special needs and stick to this hub/factory, but associate only briefly with other hubs/factories specialized for the transcription of other genes. (D) Upper: example of clockwise rotational movements of CT assemblies in a flat-shaped nucleus around an axis perpendicular to the z-axis. This rotation brings widely separated CTs located at the rim of the nucleus (left) in a position close to each other (right). At this stage the distance between the two CTs may be close enough to allow the generation of specific DNA-DNA interactions in trans by additional Brownian chromatin motions. Complex rotational movements along various axes have the potential to achieve a close neighborhood of any pair of heterologous or homologous CTs starting from random CT proximity patterns. In the lower panel this potential is exemplified by group of square dancers rotating together in a clock-wise fashion.