Fig. 2

TETs target and control the activity of TE-derived ESC enhancers. a Heatmap of ChIP-seq and HiC data on individual copies of TE classes enriched for TET1 and NOS; data are uniquely mapped, except for TET1, where data from both inclusive and unique mapping are shown; each line in the HiC data depicts an interaction with a gene promoter. b RNA-seq data (average values from n = 5) shows that genes interacting with NOS+ TEs are expressed at a higher level than NOS- TEs of the same classes. c RNA profiles at enhancer-associated TE classes reveal bidirectional eRNAs emanating from TEs bound by NOS. d TET1 and TET2 ChIP-qPCR (representative replicate from n = 3), confirming their enrichment at TE classes associated with enhancer activity. e Changes in the RNA levels of genes interacting with TE-derived enhancers in TET1- or TET2-depleted ESCs; TET2 helps to maintain the expression of genes interacting with NOS+ TEs. f BS-seq data on WT, Tet1 KO and Tet2 KO cells shows that TET2 helps to maintain the hypomethylated state of NOS+ enhancer TEs. g TAB-seq data show that both TET1 and TET2 contribute to the 5hmC levels at enhancer-derived TEs. * p < 0.05, ** p < 0.01, *** p < 0.001, t-test (b, e) or Wilcoxon tests with Benjamini–Hochberg correction (f, g)