Fig. 5

Distance of genomic features from the site of HIV integration. Following HIV infection of unactivated, CCL19-treated and PHA-IL2 activated CD4⁺ T cells, HIV integration sites were cloned, sequenced and mapped to the human genome. Genomic features were identified using the UCSC genome browser and the distance to the closest instance of each feature was determined. Comparison of the integration sites in each of the three in vitro conditions was made to integration sites previously described in CD4⁺ T cells from HIV-infected patients on cART (n = 4) [24] and randomly selected sites on the genome (n = 10,000; random). The distance for each site was analysed and plotted as log mean distance. Blue represents increased and red represents decreased distance from the genomic feature. The labels on the y-axis are shown in Additional file 1: Table S1. The small boxes on the right of the figure describe the main features of the integration sites and are classified as genomic (grey), methylated (associated with elevated transcription, red; intermediate transcription, pink; and repression, blue) and acetylated (associated with promoters, pink; associated with TSS, red) features