Examining changes in the chromosomal interaction network in replicative senescent, rapamycin treatment, and p65 inhibition

Analysis of HiC genome wide chromosomal interaction data in the context of replicative senescence, rapamycin treatment, the withdrawal of rapamycin, and with p65 inhibition in rapamycin withdrawal. This was done in order to determine what changes in chromosomal architecture occur during replicative senescence, and what impact rapamycin treatment or withdrawal or p65 inhibition has upon these changes. Overall design: BJ fibroblasts were grown in the presence or absence of rapamycin, and harvested at PD31 or PD66 (when the non-rapamycin treated BJ fibroblasts were senescent). A set of BJ fibroblasts treated with rapamycin were also grown to high passage (PD75+) growth arrest (HPGA), and were then either maintained in rapamycin, or withdrawn from rapamycin in the presence or absence of p65 inhibitor. in situ HiC was then performed upon each sample, and all possible pairwise combinations of samples were compared to determine whether significant changes in A/B domains were observed between conditions.