Fig. 7: G-to-A mutations in the 3’ LTR alters integration site targeting in vivo.

A LOGO representations of the terminal 27 nucleotides (A, green; C, blue; G, orange; T, red) of the 3’ LTRs of integrated HIV-1 proviruses in HIV-1 infected individuals. B Circa plot showing the integration sites of proviruses in the genome of infected individuals. The outer ring represents the different chromosomes. The chromosomal locations of integration sites of proviruses containing GG (black), GA (red), AG (blue), and AA (brown) at positions 14 and 15 nucleotides from the LTR end are represented as colored ticks. Numbers adjacent to ticks show the number of sites in that region that could not be distinguished by multiple ticks. The number and percentage of total sites are shown inside the circa plots. C Heatmaps depicting the fold-enrichment (blue shading) and depletion (red shading) of integration sites at various distance intervals from common genomic features (left) and non-B DNA features (right). Integration sites from proviral LTR-AG is shown and the fold changes are with respect to proviral LTR-GG integration sites. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; Fisher’s exact test, two-sided. Infinite number (inf) represents 1 or more integrations were observed when 0 integrations were expected by chance. Not a number (nan) represents 0 integrations were observed, and 0 were expected by chance.