FIGURE 1.

Positive and negative controls for chromosome conformation capture. All possible restriction fragments after BglII digestions were present in equimolar amounts. A, two regions of calreticulin gene, CalR2.8 and CalR4.4, were cross-linked and represented a positive control. On the other hand, Cox6a1 and CalR were two functionally unrelated genes, and they did not interact in our 3C reactions. Likewise, a mitochondrial enzyme citrate synthase also failed to interact with COX4i1, COX6a1, and COX8a in our 3C reactions. B, CalR2.8 and CalR4.4, COX4i1, and COX8a as well as Tfam did not interact in the absence of a cross-linking agent (formaldehyde) or T4 ligase. Primers far beyond the BglII sites for COX4i1 and COX8a did not yield any interaction between COX subunits. Experiments were performed in triplicates.