Fig. 4: Gene body (hydroxy-)methylation is positively associated with gene expression but cannot serve as an explanation for the increased transcriptional activity given the lack of differential (hydroxy-)methylation between ASXL1 genotypes.

a Box and strip plots showing the association between the extent of gene body methylation and gene expression (transcriptome-wide) among patients with ASXL1^MT CMML (two-sided Cuzick’s test for trend, raw p-values without adjustment for multiple hypothesis testing shown). b Bar graphs showing the lack of differential gene body methylation between ASXL1^WT and ASXL1^MT CMML for the up-regulated genes. c Bar graphs showing the lack of differential gene body methylation between ASXL1^WT and ASXL1^MT CMML for the down-regulated genes. d Box and strip plots showing the association between the extent of gene body hydroxymethylation and gene expression (transcriptome-wide) among patients with ASXL1^MT CMML. e Bar graphs showing the lack of differential gene body hydroxymethylation between ASXL1^WT and ASXL1^MT CMML for the up-regulated genes. f Bar graphs showing the lack of differential gene body hydroxymethylation between ASXL1^WT and ASXL1^MT CMML for the down-regulated genes. g Scatter plot showing the association between the extent of gene body (hydroxy)methylation and gene expression among patients with ASXL1^MT CMML. Gene expression increases linearly with increases in gene body methylation. While the presence (compared to the absence) of gene body hydroxymethylation is strongly associated with increased gene expression, a greater extent of gene body hydroxymethylation is not associated with further increases in gene expression (threshold). The two-sided Wald test was used to test the model coefficients (raw p-values without adjustment for multiple hypothesis testing are shown). h Signal tracks showing the lack of differential (hydroxy-)methylation between ASXL1^WT and ASXL1^MT CMML for the up-regulated genes HOXA7 and HOXA9. Data are presented as mean values (bars in 4b, c, e, f) or standard Tukey boxplots (with the box encompassing Q1 to Q3, the median denoted as a central horizontal line in the box, and the whiskers covering the data within ±1.5 IQR in 4a–f). The two-sided Mann–Whitney U test was used to compare groups in 4b–f, raw p-values without adjustment for multiple hypothesis testing are shown.