Fig. 2

Comprehensive mapping of KSHV genomic loop formation in TREx-K-Rta BCBL-1 cells with Capture Hi–C. a Circos diagrams depicting KSHV genomic links detected by Capture Hi–C. Each arc connects two BamHI fragments and represents a distinct interaction. Blue- and Red-colored lines indicate genomic links occurring before or after of K-Rta induction, respectively. Black outer hatches mark genomic positions. ORF names are indicated in the outer circle. Positions of non-coding RNA are shown by gray shading in the outer circle and position of BamHI sites are also indicated. b Regulation of genomic loops by KSHV reactivation in TREx-K-Rta BCBL-1. The relative increase/decrease of genomic links by induction of K-Rta was obtained by subtracting the relative sequence reads of non-reactivated TREx-K-Rta BCBL-1 cells from those in reactivated TREx-K-Rta BCBL-1 cells, and visualized in a heatmap by using R package ggplot2. Values are sequence reads at each position divided by the total sequence reads contained within the KSHV genome and multiplied by 10³. The numbers indicate positions of the BamHI sites, which correspond to the BamHI site numbering shown with in the Circos plot in panel a. Several BamHI sites and their corresponding column in the heatmap are labeled, and genomic loops that increased during reactivation are marked by black squares. P-values for selected loops are listed in Table 2 part A (constitutive) and part B (induced). c Enriched Capture-C DNA (BamHI ligation products) was analyzed by qPCR for the contacts listed using DNA from TREx-K-Rta BCBL-1 cells±dox. Values (mean±SD, n = 3) represent signals obtained relative to a BAC16 BamHI random ligation matrix. Fold increase (+dox/−dox) is listed. (*p < 0.05; **p < 0.01, Student’s t-test)