Fig. 3: Loss of DNA methylation in ExE results in de-repression of germline genes. | Nature Communications

Fig. 3: Loss of DNA methylation in ExE results in de-repression of germline genes.

From: Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B

Fig. 3: Loss of DNA methylation in ExE results in de-repression of germline genes.

a The principle component plot shows the distribution of gene expression replicates for Dnmt3a, Dnmt3b, Dnmt3l, Dnmt3a/b DKO and wildtype (WT) extra-embryonic ectoderm (ExE). Gene expression was quantitated for autosomal genes, using log2(RPKM). b The scatterplot compares gene expression between Dnmt3a/3b DKO and WT littermate control ExE for autosomal genes. Up- and down-regulated differentially expressed genes (DEGs) are highlighted. c The bar plot shows significant gene ontology categories enriched among Dnmt3a/b DKO up-regulated genes in E7.5 ExE, using Fisher Exact Test with Benjamini-Hochberg correction for multiple comparisons. d The scatterplot shows the linear correlation between change in DNA methylation (KO-WT) of 100-CpG windows overlapping gene promoters with log2(fold change) in gene expression (RPKM + 0.1) in the Dnmt3a/b DKO, Dnmt3b KO, Dnmt3a KO and Dnmt3l KO (p < 0.0001, linear correlation test statistic).

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