Fig. 1

Oxidization of 5mC to 5hmC occurs globally at gene bodies for brain development-related genes. a Wiggle tracks of the 5hmC, 5mC and total modification (5hmC + 5mC) profiles in a genomic region on chromosome 5. b Average 5hmC and 5mC levels in different genomic elements determined by TAB-seq and oxBS-seq, respectively. The promoter is defined as being 500 bp upstream of the TSS. c Box plots of the 5hmC, 5mC and 5hmC/5mC levels in the active enhancers and poised enhancers in the cerebellum. d Wiggle tracks of the 5hmC, 5mC and total modification (5hmC + 5mC) profiles for a representative region with enriched enhancers. e Venn plot of the co-occurrence of 5hmC and 5mC at the same CpG site in the cerebellum. f Venn plot of the overlap for the co-modified CpG sites among the three brain tissues. g The DAVID Functional Annotation for the top 500 genes enriched in the co-modified CpG sites among the three brain tissues. h The association between gene expression level and the enrichment score of the co-modified CpG sites within gene body regions. The enrichment score was calculated as described in “Methods” section. Non represents that the enrichment score is less than 0. Statistical significances were evaluated by rank-sum test. i Graphical representation of the association between gene expression (depths of RNA-seq) and the average 5hmC, 5mC level in gsk3b gene locus