Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis

Proteome and transcriptome analysis of Ehmt2 cKO and Ehmt1/2 cDKO oocytes. (A) Volcano plot showing differential abundance of proteins in Ehmt1/2 cDKO oocytes compared with the controls. Significantly changing proteins (P < 0.05 and Log₂FC > 0.3) are highlighted in dark blue (decreased abundance) or dark red (increased abundance). Light blue and light red dots indicate proteins changing significantly in Ehmt2 cKO oocytes. Proteins changing significantly and with oocyte function of interest are labeled. (B) Volcano plot showing differential abundance of proteins in Ehmt2 cKO oocytes compared with the controls. Significantly changing proteins (P < 0.05 and Log₂FC > 0.3) are highlighted in dark blue (decreased abundance) or dark red (increased abundance); light blue and light red dots indicate proteins changing significantly in cDKO oocytes. (C) MA plot showing Log₂ fold changes in Ehmt1/2 cDKO versus control oocytes (y-axis) over the mean expression level (x-axis). Differentially expressed genes (DEGs) are highlighted in red (up-regulated) and blue (down-regulated). (D) MA plot showing Log₂ fold changes in Ehmt2 cKO versus control oocytes (y-axis) over the mean expression level (x-axis). DEGs are highlighted in red (up-regulated) and blue (down-regulated). (E) Heatmap showing relative expression levels (Log₂RPKM) of up- and down-regulated Ehmt1/2 cDKO DEGs that overlap with Ehmt2 cKO DEGs. (F) Bar chart showing proportion of DEGs overlapping with histone modifications. DEGs are split according to the clustering analysis of E. (**) P < 0.001, (***) P < 0.0001. (G) Plot showing link between changes in transcript and protein abundance. The x-axis shows Log₂FC (control vs. Ehmt1/2 cDKO) of genes present in both transcriptome and proteome data sets (N = 2933). Blue and red boxes represent down- and up-regulated transcripts, respectively, with a FC > 1.5 (Log₂FC > 0.585). Vertical blue and red lines represent differentially abundant proteins (P < 0.05 and Log₂FC > 0.3; 10 proteins not detected in the RNA-seq data are not represented). Enrichment scores, shown above and below, show that down-regulated proteins are enriched among down-regulated transcripts and up-regulated proteins enriched among up-regulated transcripts (Spearman's correlation R = 0.43; P = 2.2 × 10⁻⁹).