Extended Data Fig. 3: Integration site features (Supplementary to Fig. 3).

(a) Correlation between enrichment of histone marks in producer integration sites and transcripts per million (TPM) from CD4⁺ T cell bulk RNA-seq results of each corresponding host gene harboring a provirus. On x-axis, total peak numbers in ± 10 kb flanking regions of n = 11 producer, n = 21 nonproducer and n = 44 defective integration sites from NSV samples were compared to each host gene TPM in their CD4 + T cells on y-axis. Two-sided Spearman correlation tests were used for the comparisons. (b) The distance of integration sites in each class of proviruses to the nearest transcriptional start sites (TSS). (c) The distance between the integration site to the TSS when HIV-1 or host genes are in the same orientation. (d) The distance between the integration site to the TSS when HIV-1 or host genes are in the opposite orientation. For figures b-d, n = 11 producer, n = 21 nonproducer and n = 44 defective integration sites from NSV samples were compared to each other. (e) The distance from the integration sites of different proviral classes to the centromere. Two-sided Kruskal-Wallis and Mann-Whitney U tests were used for comparisons. (f) Fraction of integration sites in speckle-associated domains (SPADs). Chi-squared test was used for comparisons. (g) Transcriptomic level of HIV host genes for producers, non-producers and defectives. For (e)-(g), n = 11 producer, n = 21 nonproducer and n = 44 defective integration sites from NSV samples were compared to each other. (h) Transcriptomic level of host genes for producers, non-producers and defectives categorized by directionality to closest host genes. We compared the number of transcripts per million cells for the host gene of each integrated provirus, including categorizing by the relative direction of the provirus to the host gene. “+” represents human and HIV genome in the same and “- “represents human and HIV in the opposite orientation of their transcriptions. Total of n = 11 producer (5 integrations site in the same and 6 in the opposite orientation), n = 21 nonproducer (7 integrations site in the same and 14 in the opposite orientation) and n = 44 defective (20 integrations site in the same and 24 in the opposite orientation) integration sites from NSV samples were compared to each other. All the boxplots in this figure are in the format of the Tukey boxplot, with the center line indicating median, box limits indicating upper and lower quartiles and the whiskers indicating 1.5x interquartile range. Two-sided Kruskal-Wallis or Mann-Whitney U tests was used for comparisons, if not otherwise specified. For P values, ns, not significant.