Fig. 3: Enhancer-promoter neoloops in GSC-specific gene regulation.
a Exemplary Hi-C contact map from G275R around a 1.24-Mbp inversion in the IFIT1 locus. Enhancer-promoter neoloops forming across the breakpoint are indicated (blue circles). The same locus of G412, where no inversion occurs, provides a control. b Plot showing mean (line) ±SEM and GSC-specific IFIT1 RNA-seq levels (circles) in lines with (orange; n = 2) or without the inversion (gray; n = 8) or in astrocytes (black; n = 2). *: P = 0.0042, unpaired two-sided Student’s t-test. Source data for this panel are provided as a Source Data file. c Bar plot showing the fraction of neo- or non-neoloops around EagleC SVs representing enhancer-promoter (E-P), enhancer-enhancer (E-E), promoter-promoter (P-P) or other loops. *: P = 6.34e-34 (E-P), 0.1e-99 (E-E), 9.08e-34 (P-P) and 0.1e-99 (other), two-sided Fisher’s exact test. Source data for this panel are provided as a Source Data file. d Box plots (bands show the mean, each box extends between 1st and 3rd quartile, and whiskers extend 1.5x the interquartile range) comparing expression of genes involved in enhancer-promoter (E-P), promoter-promoter (P-P) or other neoloops with and without filtering out loci with >1.5 CNV. *: P = (left to right) 0.0007, 0.0447 and 0.0053, two-sided Mann-Whitney U-test. Source data for this panel are provided as a Source Data file. e As in panel (d) but showing expression of E-P neoloop-associated genes in GSCs with (green) or without neoloops (gray) or in astrocytes (black). *: P = (left to right) 4.55e-20, 4.47e-20, 0.023, 0.039, and 1.82e-10, two-sided Wilcoxon rank-sum test. Source data for this panel are provided as a Source Data file. f GO terms associated with genes involved in E-P (red) or P-P neoloops (blue); P-values calculated using two-sided Fisher’s exact tests without multiple comparison adjustments. g Heatmap showing duplication, deletion, neoloop, or gene fusion occurrence for 43 known cancer-associated gene loci.
