Intermediate-abundance clones in ATL cases contained proviruses with distinct genomic marks. (A) The OR of integration in proximity to specific TFBSs compared with AC is illustrated for 2 TFBSs, P300/CBP-associated factor binding sites (PCAFbsites) and Rad21. (See supplemental Figure 1 for full list of TFBSs tested). The y-axis shows the OR compared with ACs. The x-axis shows the distance in base pairs (logarithmic scale) from the integration site upstream (left-hand side) or downstream (right-hand side). “Upstream” and “downstream” are defined with respect to the sense strand of the HTLV-1 provirus. The junction of the x-axis and y-axis represents the integration site. There were no independent TFBS predictors for small clones (blue squares) or large clones (green triangles) in ATL cases compared with ACs (OR = 1) or when compared with each other or to random data sets (not illustrated). Independent TFBSs associated with intermediate-abundance clones in ATL cases (red circles) (PCAFbsites, Rad21) at 100 bp upstream or downstream compared with ACs are illustrated. (B) OR of integration in proximity to activatory epigenetic marks compared with random sites. AC, small, and large clones in ATL cases showed a significant bias toward integration in proximity to activatory epigenetic marks. There was no such bias in the intermediate-abundance clones. (C) OR of integration in proximity to inhibitory epigenetic marks compared with random. AC, small, and large clones in ATL cases showed no bias toward integration in proximity to inhibitory marks compared with random sites, whereas intermediate-abundance clones showed a bias toward inhibitory epigenetic marks (see supplemental Figure 1 for details of epigenetic marks tested). IS, integration site.