Fig. 6

Distinct co-localization of DNA marks with enhancers in NSCs and GSCs. a Scatter plots showing the correlation of each DNA mark with gene expression changes between GSC and NSC. X-axis: average expression change. Y-axis: average DNA mark change. Red dashed line indicates the cutoff for differential modification of 5mC (0.1), 5hmC (0.025), and 5fC/5caC (0.025), and for expression fold change (> 1 or < − 1). N number of events in each quadrant. b Ring-bar graph depicting the observed proportion of highly modified 5mC (top), 5hmC (middle), and 5fC/5caC (bottom) (outer ring) sites relative to the expected proportional distribution (inner ring) at different enhancer histone marked regions. c Integrative ChromHMM model of enhancer marks states (left, red color represents highly enriched), co-localization with tissue-specific enhancers (middle), and DNA mark switching events (right) in five scenarios representing prominent enhancer differences among GSC and NSC lines (far left). Enrichment level for co-localization increases as color migrates from blue to red. Histone marks, tissues, and DNA mark switching events are labeled at the bottom. DNA mark switching is denoted as follows: 0, no change; +, gain; −, loss. d Scatter plots showing the expression correlation between GSC and NSC of genes near state 10 (top) and state 12 (bottom). Red dots indicate genes downregulated in TCGA GBM primary tumors compared with normal tissue. Green dots are upregulated genes. X-axis and Y-axis denote average expression as log2 transformed FPKM in NSCs and GSCs, respectively