Fig. 5: CREB5 associates with the chromatin remodeling complex SWI/SNF, leading to oncogenic transcriptional changes in H3.3K27M DIPG.

a CUT&Tag profiles from DIPG17 cells showing the CREB5 binding peaks for CREB5, ATAC-seq, H3K4me3, H3K27ac, H3K27me3, and H3K9me2. Pie charts showing the percentage of CREB5 binding at the genome. b The Venn diagram (top) showing the CREB5 directly regulated genes. Waterfall plot (middle) of 920 genes that exhibited significant CREB5 binding signals within their respective promoter regions, which were also significantly regulated by CREB5. GO analysis of these genes was performed (bottom). c IGV tracks for CREB5, H3K4me3, H3K27ac, H3K27me3 CUT&Tag, and ATAC-seq in DIPG17 cells at ID1 and its neighboring gene COX4I2 gene loci (negative control, in black). d Kaplan-Meier survival curves for DIPG patients in the UCSC Xena patient cohort separated into decreased and increased survival groups. e Heatmaps illustrating CREB5-regulated genes in control (Ctr) or CREB5 KD DIPG17 cells (left panel), alongside clinical DIPG patient RNA-seq dataset depicting subgroups of decreased survival or increased survival (right panel). f GSEA analysis showing enrichment of CREB5_KD_upregulated genes in the “increased survival” group (top) and CREB5_KD_downregulated genes in the “decreased survival” group (bottom). g Heatmap showing the spectral area with log₁₀ normalization of CREB5 interactome. N = 2 independent experiments. h Heatmap representation of CREB5 CUT&Tag signal, ATAC-seq signal and BRG1 CUT&RUN signal with or without CREB5 KD at CREB5 peaks regions sorted by promoter and enhancer region. The right panel showing ATAC-seq signals at CREB5 peaks with or without BRG1 KO. i Correlation plot illustrating the relationship between the differential DNA accessibility at selected genes’ promoter regions following BRG1 KO and the corresponding changes in gene expression upon CREB5 KD. The selected genes represent the overlap between differentially expressed genes (DEGs) identified in CREB5 KD and BRG1 KO, as illustrated in the upper Venn diagrams. The p value and correlation coefficient were calculated using Pearson’s correlation. The error bands indicate 95% CIs as shades based on standard error. j Gene Ontology (GO) and KEGG analysis on genes from (i) using DAVID. The statistical significance was determined by a two-tailed unpaired Student’s t-test (i) or two-tailed hypergeometric test (j).