Fig. 3: A3F and A3G alters integration site targeting of non-B DNA.

A Frequency of integration sites within or in different 50 bp distance intervals (1–500 bp) away from various non-B DNA features in CEM-SS T cells infected with HIV-1 generated in the presence of A3F-WT, A3F [E251A], A3G-WT, or A3G [E259A], or the absence of A3G or A3F (‘no A3’ control). The inset numbers refer to the percentage of total integration sites falling within 500 bp of the feature. The statistical comparison is with respect to ‘no A3’. B Heatmaps depicting the fold-enrichment (blue shading) and depletion (red shading) of integration sites at various distance intervals compared to the ‘no A3’ control virus. Black boxes highlight regions of notable enrichment. C Pairwise distance matrix was used to determine the overall similarity between the different integration site profiles. The fold-enrichment and depletion values in each distance bin for each non-B DNA feature were used in the comparison. The heatmap shows the distance matrix calculated by Euclidean distance as the measurement method. Stronger relationships are indicated by the darker blue color and weaker relationships by darker red color. Shaded triangles represent the different distance bins with the darkest shading representing distances further away from the feature. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; Fisher’s exact test, two-sided.