Fig. 3

DNAm signature identified by nanopore long-read sequencing. A, B Genome-wide screening of DMRs in Sotos syndrome (A) or ATR-X syndrome (B). Y-axis is limited to (0,10,000) and one and two datapoints with high areaStat values have been removed to aid visualization in (A) and (B), respectively. DMRs are plotted as in Fig. 2D. Arrow indicates NSD1 CpGi shown in Fig. 3G in (A). C Heatmap visualization of sets of differential methylation marks for Sotos syndrome and ATR-X syndrome (Sotos and ATR-X LR-DNAm signatures). The methylation level is colored from yellow (indicating high DNA methylation) to blue (indicating low DNA methylation). Sotos syndrome (n = 3, SoS1 to SoS 3), ATR-X syndrome (n = 3, ATRX-1 to ATRX-3), and healthy controls (n = 8, Ctr1 to Ctr8) are labeled red, blue, and green, respectively, in the bottom. D Multi-dimensional scaling (MDS) plot showing the similarity of DNA methylation pattern in Sotos syndrome and ATR-X syndrome. Each point represents one subject colored red, blue, and green for Sotos (n = 3), ATR-X (n = 3), and healthy controls (n = 8), respectively. E The median methylation difference at LR-DNAm signatures and reported DNAm signatures. Sotos LR-DNAm (n = 44 DMRs); reported DNAm signatures (n = 36 DMRs); ATR-X LR-DNAm signatures (n = 26 DMRs); 40 reported DNAm signatures (n = 40 DMRs). ****: significant differences with p-value < 0.0001 by Mann–Whitney test. F The number of CpGs available for analysis within regions of Sotos and ATR-X LR-DNAm signatures by nanopore sequencing and EPIC methylation array in the same DNA samples (SoS1 and ATRX-1). Each point represents a region of 44 Sotos and 26 ATR-X LR-DNAm signatures. Black bars represent mean values of the number of CpGs. G DNA methylation profiles at NSD1 CpGi DMR by two different technologies: nanopore sequencing and EPIC methylation array. Data were obtained from the same DNA samples (Ctr1, Ctr2, SoS1, and SoS2). CpGi: CpG island annotation from UCSC (http://genome.ucsc.edu/); DMR: DMR detected by DSS. NSD1: NM_022455.5. Sample information is listed in Supplementary Table 1