Fig. 7: Integration site hotspots across tissues are located in non-B DNA.
From: Early pandemic HIV-1 integration site preferences differ across anatomical sites
Genomic sequences were extracted from a window of 100 nucleotides upstream and 100 nucleotides downstream of each integration site. Sequences from integration sites located in hotspots were compared to sequences from sites not located in hotspots using DiffLogo. Consensus sequences were analyzed for the presence of non-B DNA motifs and represented by colored lines above each DiffLogo image (black, slipped DNA motif; orange, G4 DNA motif; red, STR; blue, triplex motif). The top half of each DiffLogo represents sequences from hotspots, and the lower half represents sequences from non-hotspots. Vertical dashed line represents the point of integration; grey horizontal dashed lines represent JS divergence values of −0.02 as a reference point for comparison between tissues.
