Fig. 4: HiC, ChIP-seq, and RNA-seq aligned datasets.

The top panel “HiC analysis” aligns differences in chromatin looping between control and 2.5 µM olaparib treated LCLs to the EBV genome. Blue arcs represent chromatin loops that are more frequent in the control genome, red arcs represent chromatin loops that are more frequently observed in the olaparib treated genome, and black arcs are loops that are unchanged between control and treatment. All arcs represent DNA-DNA interactions that occur at a statical significance of p < 0.05 from averaged biological duplicates. The middle panel “RNA-seq” displays RNA reads, forward and reverse, aligned to the EBV genome. Blue peaks pointing upward represent reads that occur more frequently in control LCLs while Red peaks pointing downwards represent reads occurring more frequently in olaparib treated LCLs. Genes with 2-fold change and q < 0.01 after correction for multiple testing (FDR) were considered as significantly differentially expressed. Bottom panel “ChIP-seq” aligns CTCF and cohesin (RAD21) tracks to the EBV genome, with and without PARP inhibition (2.5uM olaparib treatment for 72 h). The blue peaks pointing upwards represent regions of chromatin where CTCF or RAD21 binds more frequently in control samples while the red peaks pointing downwards represent regions where CTCFor RAD21 binds more frequently after PARP inhibition, respectively. Green stars represent peaks that were determined to be statistically significant binding sties via peak-calling. MACS2 software packages were used to call reads enrichment in pull-down samples compared to input samples as peaks. Analysis of peak distribution under differentiated conditions were performed with the bedtools software package for genome arithmetic. Data were visualized with deepTools.