Fig. 5

Loops with bound Pol II but without CTCF or Cohesin were largely unchanged after transcription inhibition. a Heatmap of the ChIP-Seq signals of loops classified by the extent of their overlap with Cohesin or Pol II peaks. “Both” means that both of loop anchors overlap with ChIP-Seq peaks, and “no” means that no anchor overlaps with a ChIP-Seq peak. The number of loops was determined based on the H3K27ac HiChIP data sets. The numbers in each group are 773, 101, 2649, and 787. b Violin plots of the loop peak interaction according to the Hi-C data under untreated and auxin(/inhibitors) conditions. Loops of Pol II bound at both anchors without Cohesin at either anchor were selected out and plotted with all loops included. The number of loops is indicated in parentheses. The dot inside the box plot denotes the mean interaction, and the percentage of change was calculated as the difference in the mean value divided by the untreated mean value. Significance was calculated by Student’s t test (***< 0.001, **< 0.01, *0.05). c Aggregate target-centered Hi-C maps reveal that Pol II degradation slightly increased of super-enhancer (SE) stripe formation. Pile-up maps were plotted with the 10-kb resolution contact matrix and normalized to the distance, with a positive signal in red, and a negative signal in blue. In the right panel, the signal decay curve of the SE stripes. The x-axis shows the enrichment of the SE stripes, and the y-axis shows the distance to the target center, up to 200 kb. d Hi-C contact maps for Dhx9: 152.6–153.7-Mb region of chromosome 1 at 10-kb resolution in the untreated and auxin-treated Pol II degron cell lines. The Cohesin, CTCF, H3K27ac ChIP-Seq signals, and GRO-Seq signals are displayed on the left. The black bars indicate TAD structures. The black lines indicate CTCF/Cohesin loops, and the red lines indicate Pol II-associated loops. e The 4C analyses at the Dhx9 locus after Pol II degradation and transcription inhibition are shown. Transcription was inhibited with flavopiridol, actinomycin D, or DRB treatment for 1 h. The orange background regions indicate the 4C-enriched region, and the quantitative analysis (mean with SD) is shown on the right. The untreated signals indicate the average signals under untreated conditions for mES-WT and mES-Pol II degron cells. Significance was calculated using Student’s t test