Fig 3. 4C-seq analysis in 6E cells containing integrated HPV31 DNA.

CIN612-6E cervical keratinocytes that contain integrated HPV31 DNA on chromosome 4 were used as a positive control for the 4C-seq assay. Alignment of 6E 4C sequencing reads associated with viewpoint 3 (purple peaks) to host chromosomes (top) and chromosome 4 (bottom). Prominent 4C peaks mark the HPV31 integration site. Numbers in parentheses indicate the range of average normalized 4C reads for 50 Kb windows. No 4C output files were generated for viewpoint 1 and 2 in 6E cells due to deletions within the integrated HPV31 genome at regions targeted by the associated inverse PCR primers (S2 Fig).