Fig. 4

A Methylation status of probes between IDH1^wt LGG and IDH1^Mut LGG at OBI1-AS1 locus. Most probes were hypermethylated in IDH1^Mut samples (orange point and line). Probes located in the intronic region of OBI1-AS1 showed significant overlap with CTCF binding sites based on glioma ChIP-Seq data. B Correlation of OBI1-AS1 expression with probe methylation. As is presented, there was a positive correlation between OBI1-AS1 expression and methylation of probes that are in overlap with the CTCF binding site. C OBI1-AS1 expression in GBM and LGG based on IDH1 mutation status. Cells were colored in orange and blue for IDH1^wt and IDH1^mut, respectively. Median of each group was shown by a black line. Expression was higher than median in IDH1^mut samples in each group. D Hi-C interactions are shown for a 3-Mb region comprising OBI1-AS1. In GBM, a strong TAD boundary in the intronic region of OBI1-AS1 (blue circle) was seen while this boundary site was eliminated in OBI1-AS1-expressing cells (astrocytes). There are multiple binding sites for CTCF at the boundary region. E Hi-C interactions for astrocytes and GBM are shown in subtracted heatmap. Hot color indicates areas in close contact in astrocytes compared to GBM. The reddest region was located precisely in the middle of OBI1-AS1, where in GBM, CTCF binds DNA with a high affinity. This finding confirmed the close contact between OBI1-AS1 promoter with its downstream region in astrocytes, while CTCF prevented this contact in GBM