Fig. 2

Comparative analysis of TE-derived 3D genome configuration in the in vitro model of early embryonic cells revealed higher SINE-looping in the naive state. A TE family enrichment in enhancer loop anchors of ESC and EPSC. Enhancer loop anchors were defined by the presence of H3 K27ac ChIP-seq peaks at Hi-C loop anchors. Color represents fold enrichment (see “Methods”). *, FDR < 0.05; **, FDR < 0.01; ***, FDR < 0.001. B Metaplot of H3 K27ac and ATAC-seq signal over Alu- and MIR-enhancer loop anchors in ESC. The number of Alu-derived and MIR-derived enhancer loop anchors were 1254 and 175, respectively. C Comparison of ATAC-seq and H3 K27ac ChIP-seq signal on MIR-enhancer loop anchors in ESC and EPSC. D Pileup Hi-C maps at ESC MIR-enhancer loops showed reduced interactions in EPSC state. E TE-enhancer enrichment within state-specific loop domain. Only significantly enriched TE family with p-value < 0.01, fold change (FC) of enrichment > 1 and number of involved specific loops > 100 were shown. Colour of the bar indicates the enrichment significance. Chi-squared test was used to determine the P-value (see “Methods”). F Enriched GO-terms for genes involved in ESC-specific MIR-loops