Fig. 3

TET2 does not affect DNA methylation levels at IAPs in naïve ESCs. a 5mC levels using oxBS at IAPs upon SETDB1 knockdown in naïve ESCs; each data point represents the average value from two biological replicates at a given CpG within the amplicon (ns not significant). b Normalised enrichment of TET2 using a spike-in control at IAPLTR1 and the PBS region in naïve ESCs (representative replicate from n = 3). c 5mC levels at additional ERVs upon SETDB1 knockdown in naïve ESCs (ANOVA with Tukey’s multiple comparison test, ****p < 0.0001). d 5mC + 5hmC levels using bisulphite sequencing at individual IAP copies (scIAPs) upon SETDB1 depletion, in primed and naïve ESCs. e 5mC levels at TET2-bound IAPLTR1 elements; each data point represents the value at a given CpG within the amplicon (ANOVA with Tukey’s multiple comparison test, *p < 0.05)