Fig. 2

MB-associated DhMRs are implicated in stem-like properties. a Volcano plot showing the hMe-seal data of 16 MB and 6 NC samples. Red dots indicate gain-of-5hmC regions in MB, and blue dots indicate loss-of-5hmC regions in MB. Two-thousand-base-pair binning was performed, and the criteria were set as an absolute value of the log2 fold change (MB/NC) > 2 and FDR < 0.01. b Genomic annotation of identified 5hmC gain or 5hmC loss in MBs using HOMER. Annotations with FDR < 0.001 compared to background are highlighted in blue. c Plot of average 5hmC containing 2 kb bins around previously reported MB active enhancers. d Sequence logos for the highly enriched sequence motifs in 5hmC acquiring genomic regions in MBs. e Top 20 pathways identified by Molecular Signatures Database (MSigDB) enrichment analysis with GREAT using 5hmC gain in MB. Each term shows statistical significance in both binomial test and hypergeometric test (FDR < 0.05). f, g Plots using mapped 5hmC containing bins of fetus and adult samples at either 5hmC gain in MBs (n = 24,006, top) or 5hmC loss in MBs (n = 85,738, bottom). Sequencing reads of fetus and adult are used to generate binned matrices (binsize: 2 kb). Linear regression analysis determines statistical significance (FDR < 0.001, R² = 0.0893 and R² = 0.6118)