The genes flanking the interacting chromatin regions are up-regulated in Tera-2 cells depleted for EZH2 and in the ATRA differentiated cells. The loss of pairing between 6C partners induced by EZH2 knockdown, or by ATRA-induced cellular differentiation of the Tera-2 cells toward a neuronal lineage, is concomitant with the up-regulation of flanking genes residing in the interacting chromatin regions. Total RNA was prepared from NTC and EZH2 siRNA-treated Tera-2 cells 72 h post-transfection using RNeasy Kit (QIAGEN), followed by cDNA synthesis and real-time RT-PCR for a total of 19 genes flanking the interacting chromatin region in each 6C partner for the five clones that we studied. The relative mRNA levels of the chosen genes in NTC vs. EZH2 siRNA-treated Tera-2 cells are shown for clone 1 (A), clone 2 (B), clone 3 (C), clone 4 (D), and clone 5 (E). PCR of GAPDH mRNA was used to normalize values across different samples.