Figure 7. Subcompartment Persistence in the Absence of Transcription.

(A) Mean RNA polymerase II ChIP-seq profiles for expressed genes (FPKM ≥ 0.5) (upper) and heatmap of the ChIP-seq signal for each expressed gene (lower) from TC-797 cells treated with DMSO or triptolide indicate clearance of RNA polymerase II from promoters and gene bodies after triptolide treatment.

(B) Heatmaps of TT-seq signal (nascent transcription) for expressed genes (FPKM ≥ 0.5) from TC-797 cells treated with DMSO or triptolide (4 hours) indicate inhibition of nascent transcription after triptolide treatment.

(C) Immunofluorescence for BRD4-NUT (magenta) and histone H3K27ac (green) from TC-797 cells treated with DMSO or triptolide counterstained with DAPI (blue) indicates that nuclear foci persist in the absence of transcription. Scale bars, 5 μm.

(D) Heatmaps of H3K27ac ChIP-seq signal for each H3K27ac enriched region from TC-797 cells treated with DMSO or triptolide indicate an increase in H3K27ac after inhibiting transcription. H3K27ac enriched regions were normalized to the same length and 50 kb of flanking DNA is shown next to each normalized region.

(E) Hi-C contact maps at 50 kb resolution from TC-797 cells treated with DMSO or triptolide demonstrating persistence of old and formation of new contacts between hyperacetylated loci in the absence of transcription. Histone H3K27ac ChIP-seq (green) and TT-seq profiles (sense transcripts in blue, anti-sense transcripts in red) are aligned with the maps.

(F) Genome-wide aggregate analysis of megadomain-megadomain interactions from TC-797 cells treated with DMSO or triptolide demonstrating no genome-wide change in average megadomain-megadomain interactions after inhibiting transcription. Regions around each megadomain-megadomain interaction were extracted from 5 kb resolution Hi-C contact maps, normalized to the same size, and the resulting submatrices then averaged. Aggregate scores are given at bottom right.

(G) Loci (100 kb bins) within subcompartment M (ovals) are largely preserved after TC-797 cells are treated with triptolide, indicating persistence of the subcompartment in the absence of transcription. 47 of 63 (75%) of subcompartment M intervals remained after triptolide treatment. Colors alternate for successive chromosomes.

See also Figure S7