Figure 6.

Transcriptional interference configurations created through proviral insertion. Retroviral integration amidst known transcriptional start sites generates de novo promoter configurations leading to transcriptional interference. For each VIS, CTSS contained within ±1 kb flanking regions are described by their relative orientation to VIS as divergent, convergent, upstream tandem, or downstream tandem. (a) Schematic representation of promoter arrangements between provirus and CTSS. In CTSS-dense regions, multiple CTSS:VIS orientation pairings are possible. (b) Each VIS-flanking region is further grouped according to its total unique configuration multiplexity and plotted against total CTSS per VIS-flanking region. (c) Distribution plot of Stalling Index observed at 6,210 CTSS within 1,210 VIS-flanking regions in either “Resting” or “Activated TCR” states. Each VIS-flanking region is categorized by their relative Stalling Index change concordant with TCR (T-cell receptor) activation as: “activated,” “still stalled,” “arrested,” “low activity.” Threshold for stalling set at 5 per Zeitlinger et al.²⁶ CTSS, CAGE tag clusters; VIS, vector integration sites.