Fig. 2: A3F and A3G expression alters integration site targeting of genomic features.

A Frequency of integration sites within or at different distance intervals (1–499, 500–4999, 5000–49,999, or >49,999 bp) away from various common genomic 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 A3F or A3G (‘no A3’ control). Inset numbers refers to the percentage of total integration sites falling directly within the feature. The statistical comparison is with respect to the No A3 control. 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. C Pairwise distance matrix was used to determine the overall similarity between the integration site profiles of CEM-SS cells infected with either the no A3 control virus or A3F-WT, A3F [E251A], A3G-WT, or A3G [E259A] virus. The fold-enrichment and depletion values in each distance bin of each common 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. D, E Percentage of total integration sites located in genes for CEM-SS cells infected with A3F-WT, A3F [E251A], A3G-WT, or A3G [E259A] virus generated from cells expressing increasing concentrations of A3 protein. F, G Percentage of total integration sites located in SINEs for CEM-SS cells infected with A3F-WT, A3F [E251A], A3G-WT, or A3G [E259A] virus generated from cells expressing increasing concentrations of A3 protein. 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. Source data are provided as a Source Data file.