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Fig. 6 | Retrovirology

Fig. 6

From: HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA

Fig. 6

Identification of HERV-K proviral transcripts from total and cytoplasmic RNAseq data. SupT1 cells were transduced with retroviral vectors expressing a fluorescent protein marker and Rev, Tat, Rec, a combination of Rev and Tat, or only the fluorescent protein (EV). The fluorescent transduced cells were isolated by flow cytometry. SupT1 cells that were mock transduced and subjected to collection by flow cytometry were also included as a control (−). At 48 h post transduction, both total and cytoplasmic RNA was prepared and stranded RNAseq libraries were constructed. Illumina sequencing was performed yielding ×2 150 bp paired-end reads. Reads were then mapped to the human genome (hg19) using HISAT2 and HERV-K loci were quantified with DESeq2 using a custom GTF file. Normalized read counts that mapped uniquely to each HERV-K locus are shown for a total RNA or b cytoplasmic RNA. The reads mapping to 11q22.1 in the Rec sample are derived from the vector that expressed Rec and not the proviral locus. Quantitation of these reads and the reads mapping to 6p21_1 are presented in the right panel because they are expressed at a higher level than the others

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