Fig. 3

5hmC signature in SmoA1 mouse model recapitulates human MB signature. a 5hmC dot blot analysis using SmoA1-MBs (n = 4) and surrounding NCs (n = 4). b Boxplot showing relative 5hmC levels in SmoA1-MBs (n = 8) and NCs (n = 4) (****p < 0.001). c Relative expression level of Tet1 and Tet2 in SmoA1-MBs compared to NC. Each region is normalized using Gapdh signal (****p < 0.001 and **p < 0.01). d Volcano plot showing the hMe-seal data of 4 SmoA1-MB and 5 NC samples. Red dots indicate gain-of-5hmC regions in SmoA1-MB, and blue dots indicate loss-of-5hmC in SmoA1-MB. The same binning and criteria used in hMe-seal data analysis for human MB samples were applied. e Bar graphs displaying commonly identified genes in both human MBs (either 16 MBs or 4 SHH-MBs) and SmoA1-MBs (n = 4). Gray indicates genes associated with human MBs (n = 2430) and SHH-MBs (n = 285) only, pink indicates genes which have mouse orthologs (human MBs n = 1191, SHH-MBs n = 318) but were not identified in mouse MBs, and red indicates genes which are commonly identified in both human and mouse MBs (human MBs n = 3514, SHH-MBs n = 461). Mouse orthologs from both human MBs and SHH-MBs are significantly identified in SmoA1-MBs and the percentage are indicated above each bar (p < 0.01). f Pie charts illustrating the annotation summary of 5hmC gain in SmoA1-MB (n = 22,368) using HOMER. Annotations with FDR < 0.001 compared to background are highlighted in blue. g Sequence logos are shown for the highly enriched sequence motifs in 5hmC acquiring genomic regions in SmoA1-MB. h Top 20 pathways identified by Molecular Signatures Database (MSigDB) enrichment analysis with GREAT using 5hmC gain in SmoA1-MB. All statistical tests were performed using the same parameters used in human MB data analysis