FIGURE 2.

Variabilities of back-splice junction (BSJ) loci in KSHV. Frequencies of 5′ and 3′ positions of back-spliced junctions detected in reactivated iSLK-BAC16 (iSLK) and TREx-BCBL1 RTA (BCBL1) cell lines. Total RNAs from KSHV-positive cell lines were RNase R-treated and RT-PCR was performed to amplify BSJ regions. Amplicons were sequenced and mapped to KSHV genome (NC_009333), and 5′ and 3′ BSJs are shown as percentages total detected viral BSJ reads (y-axis) for each divergent primer pairs (shown as red triangles or arrows, Supplementary Table 1) across flanking regions of circRNA-specific primers (x-axis). Human circRNA hsa_circ_0001400 serves as positive control of this analysis (A). For viral circRNAs, genomic regions around ORF61 (B), ORF72 (C), T0.7 (D), ORF36 (E), and PAN (F) are shown with primer locations.