We measured genome-scale 5hmC in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using oxidative and bisulfite treatments. Tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. A linear model tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1. Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence.
Overall design
BS and oxBS conversions were performed with 1.2 -1.4 _g of DNA according to the TrueMethyl protocol. ssDNA was recovered and quantified with Qubit and were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4 using standard Illumina protocol.
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