(A) PCA plot of RNA-Seq results of uterine stromal cells from Pbrm1^fl/fl and Pbrm1^cKO mice. (B) MA plots of differentially expressed RNAs in Pbrm1^fl/fl and Pbrm1^cKO mUSCs. Upregulated and downregulated RNAs are shown as red and blue dots, respectively (>1.5-fold, P <0.01, Padj < 0.1). (C) The top 10 GO terms of downregulated transcripts. (D) Genes directly associated with uterine receptivity and implantation that were significantly downregulated (log₂ fold change and P value) from Pbrm1^fl/fl and Pbrm1^cKO uterine stromal cell RNA-Seq. (E) Venn diagram showing overlap among genes (n = 168) with reduction of RNA expression and differential ATAC accessibility by Pbrm1 deletion and genes with PBRM1/BRG1 direct binding. (F) Genomic distribution of overlapping genes (n = 168) that are most likely to be direct targets of the PBRM1/BRG1 complex. (G) Genome browser view of normalized RNA-Seq signals, ATAC-Seq, and PBRM1/BRG1 ChIC-Seq tracks for Hand2 in Pbrm1^fl/fl and Pbrm1^cKO primary mUSCs. Green rectangle, newly identified uterine specific enhancer regulated by SWI/SNF complex; blue rectangle, known branchial arch enhancer; black rectangle, cardiac-specific enhancer; red rectangle, promoter of Hand2; Rep 1, 2 and 3, 3 biological replicates. (H) Schematic representation of enhancer regions of Hand2 in different tissues. Hand2 uterine (site 1, red), branchial arch enhancer (site 2, green), and cardiac enhancer (site 3, blue). (I) Prediction of DNA-binding site motifs for PBRM1/BRG1 derived from ChIC-Seq data. Graph to right indicates the probability of the binding motif. (J) Renilla-normalized luciferase reporter assay to evaluate Hand2 promoter activation transfected with Hand2 WT or motif mutation vectors. Values are represented as mean ± SEM (n = 3). P values were calculated by post hoc pairwise t test after 1-way ANOVA. *P < 0.05; **P < 0.01.