Fig. 2: The K258R mutation in IN has minimal effect on integration site distribution into low-copy number sequences.
From: A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats
Integration sites were mapped to the GRCh38 human reference genome assembly using Bowtie end-to-end alignment. Frequency of integrations falling within (A) RefSeq genes, or within 1 kb of (B) CpG islands, (C) DNase hypersensitivity sites, and (D) RNA polymerase II binding sites was calculated using BedTools. The frequency of integrations expected to be located near these features by random chance (matched random control, MRC) is shown as a dashed line. E Distribution of integrations around transcription start sites (TSS). Integrations in a 10 kb window around TSS are shown. F Frequency of integrations within 1 kb of select pre-infection histone modification sites. Data shown is the average of three independent biological replicates ± SEs. Statistical significance of average integration frequency relative to MRC as gauged by a one-sample, two-tailed t test is shown (*p < 0.05). Additional statistical analysis comparing the integration site pattern of WT and K258R mutant IN is shown in Table S1. Source data are provided as a Source Data file.
