Fig. 7: Suppression of miRNA expression mediated by DNA methylation fine-tunes gastrulation. | Nature Communications

Fig. 7: Suppression of miRNA expression mediated by DNA methylation fine-tunes gastrulation.

From: Base editing-mediated one-step inactivation of the Dnmt gene family reveals critical roles of DNA methylation during mouse gastrulation

Fig. 7: Suppression of miRNA expression mediated by DNA methylation fine-tunes gastrulation.The alternative text for this image may have been generated using AI.

a Bar plots show the numbers of differently expressed miRNAs related to overlapped HMPs. Numerators/denominators: numbers of significantly up-regulated miRNAs/total numbers of significantly differentiated expressed miRNAs. Black bars mean significantly down-regulated miRNAs. b Bar plots show percentages of overlapped genes between downregulated genes revealed by RNA-seq and predicted target genes of the upregulated miRNAs shown in (a) in Dnmt-null embryos. The top 50% high-confident targets of these miRNAs were chosen. Numerators/denominators: numbers of overlapped down-regulated genes/total numbers of downregulated genes shown in Supplementary Fig. 15a. c Enriched Gene Ontology terms of overlapped downregulated genes in E6.5-epi and E7.5-epi related to (b). P values were calculated by Metascape. d Representative genome browser snapshots of methylation profiles. The IG-DMR was divided into IGCGI (red-shaded box) and IGTRE (blue-shaded box). Resolution, 5kb. e Volcano plot shows the differently expressed Dlk1-Dio3 miRNAs of DKO-AG-haESCs compared to WT-AG-haESCs60. f Volcano plot shows the differently expressed Dlk1-Dio3 miRNAs of SC embryos (E6.5 epiblast) from DKO-AG-haESCs compared to WT SC embryos. g Boxplot shows the expression of Dlk1-Dio3 miRNAs between WT SC embryos and Dnmt-null SC embryos (E6.5 epiblast) produced by IMGZ. P values were determined by Student’s two-sided paired t-test. h Representative images of E7.5 and E8.5 SC embryos carrying Dnmt-null. Control SC embryos were derived from DKO-AG-haESCs60. Dnmt-null SC embryos were derived by inactivation of Dnmt1/3a/3b in SC embryos through IMGZ. Mir−6KO;Dnmt-null SC embryos were generated by injection of DKO-AG-haESCs carrying six miRNA deletions into oocytes, followed by inactivation of Dnmt1/3a/3b by IMGZ. Scale bars, 100 μm in up panels, 200 μm in down panels. i Boxplot shows the expression of Dlk1-Dio3 miRNAs between control SC embryos from DKO-AG-haESCs and SC embryos from Mir−6KO carrying Dnmt-null. P-values were determined by Student’s two-sided paired t-test. j Representative images of RNA in situ hybridization of T probe in E7.5 SC embryos with different mutations. Scale bar, 200 µm. Numerators/denominators in h and j: numbers of SC embryos sustaining the phenotype shown in the image/total numbers of observed embryos. Source data are provided as a Source Data file.

Back to article page