Fig. 3: Global chromatin accessibility and DNA methylation changes in NrESC.
From: Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts
a PCA showing the chromatin accessibility divergence between ESC, EPSC, and NrESC at 1st and 16th passage. b Heatmap showing ATAC-seq signal intensity across upregulated accessible peaks with Tead4 motif in NrESC. c Histogram displaying the global CpG methylation levels of ESC, NrESC (Passage 16), and EPSC based on WGBS. d PCA analysis of ESC, NrESC (Passage 16), EPSC, mouse early embryos129, and PSC in serum condition23 based on the genome-wide methylomes. e, f Enrichment of genomic features at transposable element families on NrESC differentially hypermethylated bases. Empirical P-values were calculated by a two-sided permutation test (e) and hypomethylated bases (f). The y-axis represents the log2-enrichment for each genomic feature, and the value labelled on the bar represents the significance p-value, calculated with the Genomic Association Test (GAT) tool128. g Genome browser view showing the WGBS and RNA-seq signal profiles for NrESC and ESC surrounding upregulated genes Scd2 and Ring1 with lower methylation signal in NrESC, and differentially methylated region (DMR)-enriched ERVKs annotated downregulated genes Clca3b and Ercc4.
