Fig. 4

Retrotransposons distinguish mouse naïve from primed state. A Heatmap of RNA-seq expression data from CBA × C57 naïve mESCs and primed mEpiSCs. Data shown include 1000 differentiated expressed transposable elements (TEs) with the highest standard deviation (SD) between the samples. B TE signatures of naïve or primed mESCs. The most four heavily primed or naïve-biased TE families are represented as columns split into three segments: overexpressed integrants in naïve cells (1.5-fold cut-off, P < 0.01), overexpressed integrants in primed cells, and no change. C The top 20 TE families with the highest fold change between naïve and primed cells are heavily enriched for LINE1 family (naïve) and ERVK family (primed). The triangles highlight the high expression of MERVL in naïve mESCs. D Left panel of boxplot showing the expression of integrant of L1Md_A and related families according to Dfam database. Right panel of boxplot showing the expression integrant of IAPEz-int and related families according to Dfam database. The significance is calculated by Wilcoxon Test. *P < 0.05; **P < 0.01; ***P < 0.001. E Representative immunofluorescence of 2C marker MuERVL Gag (red) in naïve and primed cells. DAPI-stained nuclei in blue. Scale bars = 10 μm. F Proportion of MuERVL Gag+ cells based on immunofluorescence images in Fig. 4E