(A) Scatter plot showing transcript expression levels in Ehmt2Cntr and Ehmt2Mat 8C (E2.5) stage embryos. Blue points are differentially expressed genes (adjusted p<0.05 in DEseq2). Shown is the average from ten biological replicates. (B) Venn diagram showing the overlap between upregulated genes upon maternal loss of G9a (Ehmt2Mat) at 8C (E2.5) and those upregulated in zygotic Ehmt2 deletion in E6.25 epiblast (Zylicz et al., 2015). (C) Expression profiles of genes within specific clusters during wildtype development from 2C to 8C (left panels). Dotted line represents mean expression within the cluster. Data from GSE22182 (Tang et al., 2011) was used and within all expressed genes 14 specific clusters were identified. Shown are clusters most enriched for genes becoming derepressed (Clusters 1 and 6) or downregulated (Cluster 11) at 8C in Ehmt2Mat. Right panel of bar plots shows the percentage of genes upregulated (Green) or downregulated (Red) at 8C in Ehmt2Mat, which belong to identified clusters. Significance of enrichments was calculated using Chi2 test (* 10−5 < p < 0.05; ** 10−10 < p < 10−5; ***p<10−10). (D) Fold expression changes of PrE (Fgfr1, Gata6, Gata4) and TE (Tead4, Tfap2c) marker genes in Ehmt2Matcompared to Ehmt2Cntr 8C embryos. Box plots show median and interquartile range (IQR), with whiskers drawn 1.5xIQR away from the lower and upper quartiles. Each dot is a single embryo and data was normalised to median expression levels in Ehmt2Cntr. (*adjusted p<0.05 in DEseq2). 2C: 2 cell embryo, 4C: 4 cell embryo; 8C: 8 cell embryo; Ehmt2Cntr: control embryos with maternally inherited G9a; Ehmt2Mat embryos maternally depleted of G9a; Fgfr1: fibroblast growth factor receptor 1; Gata4: GATA binding protein 4; Gata6: GATA binding protein 6; IQR: interquartile range; Tcfap2c: Transcription factor AP-2 gamma; TE: trophectoderm; Tead4: TEA domain transcription factor 4. Also see Figure 3—figure supplements 1–3 and Figure 3—source data 1–3.