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Figure 6 | Genome Biology

Figure 6

From: Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

Figure 6

Transcriptome of Dnmt3b -/- embryos. (A) Scatter plot of normalized read counts per gene (average of three replicates) calculated by DESeq2 in WT and Dnmt3b-/- E8.5 embryos. The red dots represent the genes called differentially expressed with a false discovery rate-adjusted P-value <0.05 and fold change >2. The numbers of genes upregulated and downregulated are indicated. (B) Consequences of reduced CGI methylation on gene expression. The boxplot shows Fragments Per Kilobase of exon per Million fragments mapped (FPKM) scores for genes with reduced methylation (>50% decrease of methylation in Dnmt3b-/- compared with WT embryos) of a CGI covering a TSS, exon or intron, as well as genes with a pmCGI in the TSS. **P < 0.01, ***P < 0.001 (Wilcoxon test). (C) RNA-Seq read coverage at the germline-specific gene Mael in three WT and Dnmt3b-/- embryos. (D) RT-qPCR validation of the upregulation of germline genes in Dnmt3b-/- E8.5 embryos. The heatmap on the left depicts the extent of TSS CGI hypomethylation in Dnmt3b-/- embryos. Gene expression is depicted in the bar graphs as a ratio relative to the expression of two housekeeping genes (Actb and Rpl13a). The error bars represent mean deviations from measurements in independent embryos (n = 3). As a control we show the expression of Dnmt3b measured with primers that amplify within the Cre-deleted catalytic exons.

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