Host chromatin architecture constrains the cis-regulatory effect of HPV integrations in cervical tumors.

By using HeLa as our model system, which has integration in the most recurrently integrated TAD in the cervical tumors i.e. TAD3189, we show most of the interactions of integrated HPV18 DNA is constrained within the TAD with integration. Similarly, TAD3189 also showed very high and most significant allele specific expression among all the TADs on chr8, in HeLa. The integrated HPV18 DNA also showed strong chromatin looping interactions with the oncogenes present in the TAD3189 which were ~500kb away from the integration. These oncogenes in the TAD3189 further showed high allele specific expression from the haplotype with HPV18 integration, possibly representing the cis-regulatory potential of integrated HPV DNA. 4C-seq in HeLa, using the integrated HPV18 DNA as the bait region.