Fig. 3

RNA polymerase depletion caused few or no changes in the local, small-scale chromatin interactions according to the Hi-C data sets. a Hi-C contact maps for the Pol I peak: 38.8–39.8-Mb region of chromosome 1. The yellow line marks regions of insulated domains, and the signals indicated by the blue dashed line mark regions were quantified as illustrated with the box plot in the left panel. Significance was determined using a Wilcoxon test (**p < 0.01). PE-SCAn analysis results (10-kb resolution) depicting the Hi-C contact frequency for the high-density clusters of Pol I under untreated and degraded conditions are displayed in the right panel. The area shown is centered on the respective RNAP-binding sites (including 500 kb upstream and downstream). The y axis indicates the Hi-C contact frequency. b Hi-C contact maps for the mRNA (Tlk2) loci: 105.2–105.7-Mb region of chromosome 11 at 10-kb resolution in the Pol II degron cell line under untreated (left) and auxin-treated (right) conditions with Pol II degron cell line. b is illustrated as a but based on the Pol II degradation Hi-C data sets. c Hi-C contact maps for the tRNA cluster: 21.7–22.1-Mb region of chromosome 13 at 10-kb resolution in the Pol III degron cell under untreated (left) and auxin-treated (right) conditions with Pol III degron cell line. c is illustrated as a but based on the Pol III degradation Hi-C data sets. d Bar graph shows the highest reproducible Hi-C contact intensity (means ± SEM) detected for Pol I-, Pol II-, or Pol III-binding clusters (red bars) and compared with the intensity of each in the degraded cells (blue bars) at each respective region, shown in the left panel. Box plot displaying the changes in the average contact frequency for the Pol I-, Pol II-, or Pol III-binding clusters after auxin treatment, shown in the right panel. For all the box plots, the centerline denotes the median; box limits denote the 25th–75th percentile. p values were calculated using a two-sided Wilcoxon test. e Correlation of Hi-C contact frequency changes in the Pol I clusters (top), Pol II clusters (middle), and Pol III clusters (bottom) after Pol I, Pol II, and Pol III depletion and Pol I, Pol II, and Pol III ChIP-Seq, GRO-Seq, GRID-Seq, and ATAC-Seq signals in the mESCs. f Normalized Hi-C contact maps for 45S rRNA (Chr17:38.4 M–41.3 M). The f is illustrated as a, but based on Pol I degradation Hi-C data sets. g PE-SCAn plots showing the aggregate Hi-C contact maps around pairs of active gene promoters (N = 2649) under untreated and Pol II-degraded conditions, respectively. The values of the central pixel relative to the bottom-left corner are annotated on the maps. h Same as g, but for tRNA (N = 435) under untreated and Pol III-degraded conditions