Fig. 3
Chromosomal and regional distribution of differential methylation consistent in NPCs and DiffNPCs with T21. a Genomic coordinate dot plot (Manhattan plot) of CpGs detected by 500 DMPs in T21 neural NPCs and DiffNPCs showing methylation changes of known CpG regions and promoters and clustering at annotated genes (arrows and boxes). X axis represents chromosomes ranked by number, Y axis represents –log10 (p values) and the red line indicates significance level (Bonferroni; p < 5 × 10−7). b, c Zoom-in of boxed regions in a showing the hypo-methylated HIST1 gene cluster on chromosome 6 (b) and the hyper-methylated ZNF cluster on chromosome 19 (c). d Details on the DMP pattern (arrows) of three HOX genes (top). Differential methylation of HOXD3 and HOXA3 genes are located in shores and shelves of CGIs. In contrast, differential methylation of genes belonging to the HIST1- and ZNF-clusters (mid and bottom) were specific to CGIs. Each DMP is colored according to methylation state (β values) ranging from low (blue) to high (red) methylation in T21 cells