Fig. 6: G-to-A mutations in the 3’ LTR alters integration site targeting in vitro.

A LOGO representations of the terminal 56 nucleotides (A, green; C, blue; G, orange; T, red) of the 3’ LTRs of all integrated HIV-1 proviruses generated in the presence of either A3F, A3F [E251A], A3G, or A3G [E259A]. B Circa plots showing the integration sites of A3F- (left) or A3G- (right) containing viruses in the genome of infected CEM-SS cells. 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. 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 A3F-LTR-GA (top) and A3G-LTR-AG (bottom) proviruses are shown. Fold changes are with respect to A3F-LTR-GG and A3G-LTR-GG, respectively. *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.