Figure S4.

Additional distinguishing features of transcriptionally active HIV-1 proviruses, related to Figure 2

(A and B) Chromosomal distance between transcriptionally active (RNA+) and transcriptionally silent (RNA-) proviruses and the most proximal host transcriptional start site (TSS) in same (A) or opposite (B) orientation.

(C and D) H3K4me1- (C) and H3K27me3-specific (D) ChIP-seq reads in linear proximity (±5 kb) to proviral IS.

(E and F) Average numbers of intrachromosomal (E) and interchromosomal (F) proviral chromatin contacts; error bars indicate standard error of the mean.

(G and H) RNA-seq reads (G) and H3K4me1-specific ChIP-seq reads (H) in all proviral 3D contact regions.

(I) Sum of H3K4me3- (upper panel) and H3K27ac-specific (lower panel) ChIP-seq reads in linear proximity and interchromosomal proviral contact regions. (E–I) 3D contacts were determined by Hi-C at 10 kb binning resolution.

(J) Network reflecting chromosomal interactions (p < 0.05, 20 kb binning resolution) between IS of transcriptionally active (red) and silent (blue) proviruses from all six study subjects. Circles suggest transcriptional interactomes between HIV-1 RNA+ proviruses. (A–J) HIV-1 long LTR RNA-expressing proviruses were considered “RNA+”; clonal sequences were counted once and were counted as RNA+ when at least one member of a clonal cluster had detectable expression of HIV-1 long LTR RNA. IS located in chromosomal regions in the ENCODE blacklist (Amemiya et al., 2019) were excluded. (^∗p < 0.05, ^∗∗p < 0.01, Mann-Whitney U tests or Fisher’s exact tests were used for all comparisons).