Fig. 1.

HIV genome and the targets for transcription profiling assays and bulk cell-associated HIV RNA levels. a This schematic shows the genetic organization of proviral HIV DNA and the HIV ‘transcription profiling’ assays targeting specific HIV RNA sequence regions suggesting transcriptional interference (Read-through) and progression through blocks to HIV transcriptional initiation (TAR), 5′ elongation (LongLTR), mid transcription (Pol), distal transcription (Nef), polyadenylation (PolyA), and multiple splicing (Tat-Rev). b HIV RNA levels normalized to HIV DNA (provirus) copies (ratio of each HIV RNA to LongLTR HIV DNA) (mean of 2 replicate measures of HIV RNA and DNA). c Ratio of one HIV RNA to another: Read-through normalized to TAR (transcriptional interference), LongLTR to TAR (elongation), Pol to LongLTR (mid transcription), Nef to LongLTR (distal transcription), PolyA to LongLTR (completion) and Tat-Rev to LongLTR (multiple splicing). For PBMCs, CD4+ T cells, and activated CD4+ T cells from HIV-infected ART-suppressed individuals (b, c), each individual is shown as a dot, the column height indicates the median, and bars represent 25–75%