Fig. 3

CYTOR promoter is hypermethylated and not accessible in a majority of nuclei in IDHmut-codel gliomas. a Promoter accessibility for several non-coding RNAs (LINC001193, CCT8L2, MIR4436A, and MALAT1), and coding RNAs (KLF12, OLIG2) are indicated on the t-SNE plot. Maroon, IDHmut-noncodel; Teal, IDHmut-codel; False, no peak detected; True peak present, b t-SNE plot indicating nuclei with open CYTOR promoter. Gray category includes nuclei that were not well-distinguished. In the upper trajectory, the blue arrow indicates branching of IDHmut-codel samples, and the blue category is the top of the branch. In the lower trajectory, the red arrow indicates a longer branch that largely includes IDHmut-noncodel samples, and the red circle is the top part of the branch. Maroon, IDHmut-noncodel; Teal, IDHmut-codel; False, no peak detected; True peak present, c Heatmap shows the reads within and upstream of the CYTOR transcription start site. While most of the IDHmut-noncodel nuclei (red) have open chromatin, only a small percentage of IDHmut-codel nuclei have the same pattern (blue), d Heatmap of CYTOR peaks and top correlated peaks. It shows that most of astrocytoma cells and a small population of oligodendroglioma cells Have an open chromatin peak at CYTOR promotor and other correlating peaks, e Overlap of CpG locations on the EPIC array (green) with the peaks from pseudo-bulk snATAC-seq data (black) within and upstream of the CYTOR locus, f Box-plot showing methylation b-values for the overlapping probes, cg22535363, and cg23944790 for IDHmut-noncodel and IDHmut-codel tumors