Genome-wide Determinants of Proviral Targeting, Clonal Abundance and Expression in Natural HTLV-1 Infection
Figure 4
Genomic environment at HTLV-1 proviral integration site associated with proviral expression after 18 h in culture.
CD8-depleted PBMCs were placed in culture overnight and sorted by flow cytometry to isolate Tax+ and Tax− cells, followed by integration site analysis of sorted cells. (A)–(C): proportion of observed integration sites compared to random expectation. (A) Frequency of integration in proximity to transcriptional units (RefSeq) in clones that were 100% Tax+ or 100% Tax−, according to the relative transcriptional orientation of the provirus and the host gene. The peak of integration at 1 kb mirrors that observed in vivo in unsorted cells (Figure 1B). However, the integration site in Tax− clones was more likely than in Tax+ clones to possess a nearby upstream TSS in the same orientation, and less likely to lie nearby a downstream TSS in the same orientation (or any relative position in the opposite orientation). (B) The provirus in Tax− clones (blue) was oriented in the same transcriptional sense as the host gene in which it was integrated more frequently than random. The orientation of Tax+ clones (pink) did not differ from random. (C) Frequency of integration in proximity to CpG islands in clones that were 100% Tax+ or 100% Tax−. The peak of integration at 1 kb mirrors that observed in vivo in unsorted cells and in vitro (Figure S4). (D) Mean fraction of Tax+ cells in clones with a TSS at a given distance (log scale) from the integration site, according to the relative transcriptional orientation of the provirus and the host TSS. The dotted line denotes the mean fraction of Tax+ cells across all clones. (E) Frequency distribution of clones according to the frequency of Tax+ cells in the respective clones. See supplementary Figure S7 for detailed frequency distribution separated according to clone abundance.