Fig. 6: Chromatin conformation enhancer loops depend on AT3:VCP.

a Correlation of AT3 and VCP enrichments aggregated for each target gene in ASPS-1 cells from all narrowly defined peaks localized to the promoter or a looped enhancer (normalized by H3K27ac-HiChIP loop score). b Similar FU-UR-1 plot. c Correlation between log₂fold-change expression from siRNA VCP depletion over control in FU-UR-1 cells, with AT3 depletion or CB-5083 VCPi for the 50 strongest promoter-targeted genes and 50 strongest enhancer-targeted genes. d Principal component (PC) analysis according to the top one percent (n = 99, by AT3 aggregate enrichment) of genes by RNA-seq after siSCR, siTFE3, siVCP, or combinations in FU-UR-1 cells. e K-means cluster heatmaps of PC1-contributing genes (coefficients greater than 0.05, n = 54) in FU-UR-1 cells, showing expression after application of siRNAs or CB-5083 in FU-UR-1 cells as well as expression in human and mouse ASPS tumors compared to skeletal muscle. f Example tracks of H3K27ac-HiChIP loops around a highly targeted gene in baseline FU-UR-1 cells (above, black) and FU-UR-1 cells exposed to siVCP for 6 days (below, cyan; n = 2 siRNAs against VCP). g Negative control example tracks show retained/strengthened H3K27ac-HiChIP loops after filtering out VCP-ChIP-seq-peak-associated loops. h Comparison dot diagrams of the change in VCP-peak-associated or not-associated H3K27ac-HiChIP loops at baseline compared to 6 days of VCP depletion with siVCP (n = 2 for each). i Normalized loop score (NLS) aggregated per promoter for VCP-associated genes in FU-UR-1 cells at baseline (from 6b) or 6 days VCP depletion. Genes with no change or increased NLS per promoter are designated as VCP-associated or not. j Plot of differential H3K27ac ChIP-seq enrichment in FU-UR-1 cells with siRNA-depleted AT3 (left) or VCP (right) at loci defined as VCP-peaks and HiChIP loop ends that are top-ranked for AT3 enrichment as well (above) versus the lowest AT3 enriched HiChIP loop H3K27ac ChIP peaks that are not coincident with VCP peaks (below). (n = 3, biologically independent samples, Wald test p-values, Benjamini-Hochberg correction.).