Packaging of transcripts from repetitive elements. (A) Composition of repeat element-derived reads in the HIV-1 data set. (B–D) Reads aligning to a full-length L1Hs (B; chr8:73787793–73793823), to a consensus AluY (C; chr14:31943010–31943320) and to RN7SL1, one of two genes encoding 7SL RNA (D; chr14:50,053,298–50,053,597) were visualized with the University of California at Santa Cruz (UCSC) genome browser. Arrows, transcription direction. Y-axis, read depth. (E,F) Reads aligning to a truncated and divergent LINE element (E; chr17:70,697,347–70,697,477) and a divergent AluSc element (F; chr2:141,573,687–141,573,984) were visualized using the UCSC genome browser. (G,H) RT-qPCR was used to determine the enrichment of consensus L1Hs and AluY transcripts (G) and the divergent LINE (H) in virions, compared to 7SL RNA. Virions were produced in CEM-SS cells. Actin, a nonselectively packaged mRNA (Onafuwa-Nuga et al. 2006), was a negative control.
