Fig. 3

Effect of TET2 germline mutation on methylation and hydroxymethylation at different genomic regions. A Volcano plot showing the effect of TET2 mutation status on average methylation in different cell types (Additional file 1: Table S1 and Additional file 3: Table S3) and genomic annotations. Model lm(average methylation ~ mutation status + lymphoma status + genome-wide average methylation) was fitted over each cell type and annotation separately. Each point represents results related to mutation status from one cell type and annotation. Colored and labeled points showed FDR-corrected p value < 0.05. The result from PBMC enhancers is depicted with a red outline. Mutation status seems to increase the observed methylation average especially on enhancer (Enh) regions in multiple cell types. B Average DNA methylation levels before the vitamin C trial across different genomic annotations originating from peripheral blood mononuclear primary cells. Mutation carriers showed high methylation levels compared to those of the control individuals especially on enhancer regions. C Average hydroxymethylation levels across the annotations. Note the different Y-scales in panels (B) and (C). Abbreviations: BivFlnk Flanking bivalent TSS/enhancer, Enh Enhancers, EnhBiv Bivalent enhancer, EnhG Genic enhancer, Het Heterochromatin, Quies Quiescent/Low, ReprPC Repressed PolyComb, ReprPCWk Weak repressed PolyComb, TssA Active TSS, TssAFlnk Flanking active TSS, TssBiv Bivalent/Poised TSS, Tx Strong transcription, TxFlnk Transcribed at gene 5′ and 3′, TxWk Weak transcription, ZNF/Rpts ZNF genes and repeats