Fig. 4: DNAme plays a more important role in silencing of DMS germline genes in EpiLCs than nESCs. | Nature Communications

Fig. 4: DNAme plays a more important role in silencing of DMS germline genes in EpiLCs than nESCs.

From: Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing

Fig. 4

a Violin plots showing the distribution of DNAme levels in the promoter regions (TSS −0.9/+0.4 kb) of the 137 DMS germline (blue filled), 8 GGD (red data points) and all other gene loci (open) in E3.5 ICM, WT, Dnmt1-, Dnmt3a-, Dnmt3b-, or Dnmt3a/3b double KO (DKO) E6.5 epiblast cells and E8.5 embryos. Data for nESCs, EpiLCs, and exEpiLCs are also shown. b Genome browser tracks showing % DNAme in the promoter regions (TSS ±3 kb) of GGD gene loci at the developmental time points shown in panel (a). For each WGBS track, regions highlighted in gray reflect the absence of DNAme data. c A schematic representation of the induction of Dnmt1/3a/3b conditional triple KO (cTKO) in nESCs and derived EpiLCs. To induce Dnmt cTKO, 4-hydroxytamoxifen (4OHT) was added at the indicated time points and cells were harvested for RNA-seq analysis at the time points indicated. d Scatterplots showing the fold-change (FC) of gene expression in Dnmt cTKO nESCs (n = 2) and EpiLC (n = 2) vs % DNAme in the promoter region (TSS −0.9/+0.4 kb). All, DMS germline and GGD genes are color-coded as shown and the number of genes in each category showing % DNAme >30 and a concomitant >2-fold increase in expression is included at the top right of each plot. e Bar graph showing the mean FC of expression of GGD genes (red) and control genes (black) in nESCs and EpiLCs with Dnmt cTKO relative to WT cells. Data points show biological duplicates. % DNAme in nESCs, EpiLCs and exEpiLCs in the promoter regions (TSS −0.9/+0.4 kb) of each gene are also shown.

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