Fig. 1

Characterization of different DNMT3A exon knockouts in iPSCs. a Schematic overview of the protein coding DNMT3A splice variants. Arrows indicate CRISPR/Cas9n target sites. b Western blot analysis of DNMT3A upon knockout of exon 2, exon 19, or exon 23. Arrow corresponds to height of transcript 1/3. WT = wildtype. c Semiquantitative RT-PCR analysis of expression of DNMT3A exons (normalized to GAPDH, measured in duplicate). d Representative phase contrast images of iPSC colonies with DNMT3A knockouts and WT. Scale bar = 150 μm. e Scatter plots show DNAm levels (β-values) for all measured CpG sites (grey) when comparing WT versus knockout of exons 2, 19, or 23, respectively. For exon 2, we only present results for the homozygous knockout of exon 2, whereas for exons 19 and 23 the mean of two homozygous knockout lines is presented. CpGs with more than 50% hypermethylation (red) or hypomethylation (blue) are indicated