Fig. 1

Cytosine modification landscape of all CpG sites (n = 2.7 × 10⁷) in a glioblastoma patient. a Hematoxylin and eosin (H&E) staining of the margin (top) and tumour (bottom) samples (see Methods). b Base resolution outlook of 5mC and 5hmC levels, nucleotide alterations and changes in transcript levels between margin (M) and tumour (T) in the ATRX gene. The close view highlights 32 bp of the CpG island (chrX:77041003-77041725) located in the 5′-UTR region (middle) and average levels of modification across the 1 kb promoter (chrX:77041719-77042719) (right). Transcript levels (left) are displayed in transcripts per million (TPM). c Combination of BS and oxBS-seq reveals a severe decrease of 5hmC in tumour accompanied by an increase of 5mC, however BS-seq only cannot distinguish between 5mC and 5hmC, and would suggest tumour hypomethylation. Distribution of 5mC and 5hmC in the margin and tumour samples d across genomic regions and e in a sample of 10⁵ CpG sites colour-coded according to the level of 5hmC in the margin