GSE171723
Broad deregulation of fibroblast activation and wound healing genes within Ezh2 cKO decidua.
Our objective was to identify genes differentially expressed between control and Ezh2 cKO decidua, and to compare this set of genes with a previously identified gene set of H3K27me3-marked decidual genes that are putatively silenced by EZH2/PRC2 (Nancy et al. JCI. 2018). RNA was isolated from whole tissue decidua and myometrium of control and Ezh2 cKO mice. Sequencing provided was 731 million total reads with an average of 84.5% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2. We found that 2530 protein-coding genes were differentially expressed within the decidua and 521 were differentially expressed in the myometrium (FDR<0.05, excluding genes whose normalized read counts were less than 30 averaged across samples). Hypergeometric analysis revealed a strong enrichment for previously identified H3K27me3 targets within genes overexpressed in Ezh2 cKO decidua. Overall design: RNA was prepared from whole tissue myometrium and decidua of control (n=4) and Ezh2 cKO (n=3) and E7.5 of pregnancy. One control myometrial sample was excluded due to failed QC. Decidua was the tissue of primary interest, with myometrium serving as reference tissue. Next generation sequencing was performed using Illumina HiSeq 4000.