Figure 1.

Models to account for gene expression neighborhoods. Several models (or combinations of models) could account for the observed phenomenon of gene expression neighborhoods. (a) Incidental regulation. A transcription factor (green oval) binds at a target gene (green arrow) and incidentally up-regulates neighboring genes. In this model, the level of expression of neighboring genes is determined by proximity to the target gene and is expected to decrease with distance from the target gene (the green line at the top of each panel indicates the gene expression profile across the neighborhood). (b) A structural domain model. A discrete 'open' chromatin domain is created as a result of activation of a target gene within the domain. Flanking boundary or insulator elements (yellow ovals) define the neighborhood and the limits of the open chromatin domain. (Note the 'square wave' expression profile.) (c) Expression neighborhoods in three-dimensional space. In this model, activation of a target gene results in its recruitment to a specific nuclear location. This would necessarily involve the co-recruitment of neighboring genes. The particular subnuclear location exposes the neighborhood to increased concentrations of components of the transcriptional machinery (the image shows two segments of chromatin with two neighborhoods in the vicinity of a (green) nuclear body).