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. Author manuscript; available in PMC: 2026 Apr 3.
Published in final edited form as: Mol Cell. 2025 Mar 26;85(7):1330–1348.e6. doi: 10.1016/j.molcel.2025.03.007

Figure 2. 3D hubs in GBM coordinate and expand known oncogenic transcriptional programs.

Figure 2.

(A) Boxplots showing the distribution and mean connectivity of the most (top decile) or least (bottom decile) connected 3D hubs, as detected in our 4 GSC samples across three independent 3D genomics datasets in GSC/GBM samples (Yost et al, TCGA, 2024; Xie et al., 2024; Chakraborty et al., 2023). The numbers of samples are shown at the top. (B) Heatmap displaying the relative connectivity (z-score) of (proto)oncogene-interacting hubs across samples from this study and additional GSC/GBM 3D datasets (shown in (A)). (C) IGV track depicting H3K27ac HiChIP arcs of a 3D enhancer hub (red) interacting with JUN and other genes across multiple GSC (this study) and GBM (TCGA) samples. (D) Top: Schematic showing all gene promoters connected to the JUN hub (shown in (C)) and the location of the guide RNAs (lightning bolt) used for CRIPSRi targeting. Bottom: Relative mRNA levels of all JUN-connected genes upon CRISPRi silencing of JUN hub (48h) expressed relative (percentage) to the negative control values. Dots indicate independent replicates and experiments (n=3). Error bars indicate mean+/−standard deviation.