Extended Data Fig. 7: Accessory features of chromosomal integration sites of intact proviral sequences from elite controllers.
From: Distinct viral reservoirs in individuals with spontaneous control of HIV-1
a, Expression of host genes that contain intact proviral sequences in elite controllers and long-term ART-treated individuals, as determined by autologous RNA-seq data in total, central memory and effector memory CD4+ T cells. Gene expression percentiles are indicated. b, c, Orientation of intact proviruses relative to host genes in elite controllers and long-term ART-treated individuals. All data for genic integration sites are included, except for integration sites in genic regions associated with multiple genes in opposing orientations. Integration site data from previous studies of elite controllers9 and ART-treated individuals15,17 are shown for comparative purposes. d, e, Proportion of intact proviruses from elite controllers and long-term ART-treated individuals in lamina-associated domains, determined using Lamin B1–DNA adenine methyltransferase identification (DamID)61 for resting Jurkat cells. Integration site data from previous studies of elite controllers9 and ART-treated individuals15,17 are shown for comparative purposes. b, d, Clonal proviruses were counted once. c, e, Clonal proviruses were counted as individual sequences (FDR-adjusted two-sided Fisher’s exact tests). f, Expression of LEDGF (also known as PSIP1 or p75) and CPSF6 mRNA in autologous total CD4+ T cells from elite controllers and long-term ART-treated individuals, as determined by RNA-seq. Gene expression percentiles are indicated. a, f, Horizontal lines show the geometric mean. All comparisons were made between elite controllers and reference groups.
