Figure 2.

Alternative explanations for interchromosomal gene associations seen by 3C analysis. (A) A direct molecular interaction of two gene loci occurs such that the formaldehyde cross-links form (gray) via their chromatin proteins. (B) Two DNA segments that localize to a common nuclear structure will infrequently be near enough to one another to be cross-linked via their chromatin proteins (left) or to be indirectly connected via mutual cross-links to the larger aggregation of splicing factors or other protein accumulations (right). The latter may involve multiple cross-links, but subsequent ligation and PCR amplification would occur in the absence of a direct in vivo molecular interaction.