Fig 5. Quantitative analysis of transcription start site usage in undifferentiated and differentiated keratinocytes and CTCF-dependent regulation of promoter activity.

The 5’ end of each HPV18 transcript was identified in Nanopore RNA sequencing data sets and relative abundance calculated as reads per million (RPM). Total counts at each nucleotide position were binned into 10 (A and B) or 100 (D) nucleotide regions in the data shown. Transcripts originating around the P₁₀₂ (A), P₈₁₁ (B) and P₃₀₀₀ (C) promoters were identified in HPV18 and ΔCTCF-HPV18 cells in undifferentiated (blue and red, respectively) and methylcellulose differentiated (green and purple, respectively) cultures. Relevant HPV18 genome features are shown alongside each panel. The E2-CTCF binding site is indicated by a blue oval.