Fig. 1

SETDB1 is pivotal for ERV silencing in naïve ESCs. a Deep amplicon sequencing from oxBS-treated DNA was used to measure 5mC levels at ERVs in primed and naive ESCs; each data point represents the average value from two biological replicates at a given CpG within the amplicon (ANOVA with Tukey’s multiple comparison test, *p < 0.01, ****p < 0.0001). b RNA-seq data using inclusive mapping from primed and naïve cells was overlayed with the RepeatMasker annotation to determine repeat classes that are differentially expressed upon SETDB1 removal (highlighted in red, n = 3). c Analysis of IAP expression by RT-qPCR in SETDB1 knockdown primed and naïve ESCs. The error bars show standard deviation (n = 6–12; ANOVA with Tukey’s multiple comparison test, *p < 0.05, **p < 0.01, ****p < 0.0001; ns not significant). d H3K9me3 ChIP-qPCR at IAPs upon SETDB1 loss (ANOVA with Tukey’s multiple comparison test, *p < 0.05, **p < 0.01). Data are shown as mean ± standard deviation of seven independent experiments. e Expression data from uniquely mapped RNA-seq reads at truncated and full-length (>5 kb) IAP elements