Fig. 7

ESRRB co-binds structural protein YY1 at MIR. A Percentage of YY1-mediated loops involving TE and non-TE based on YY1 ChIA-PET data. B YY1 binding enrichment on MIRs with enhancer marks in ESC. YY1 ChIA-PET and ChIP-seq data were obtained from public dataset [60]. C YY1 binding signal on ESRRB-bound MIRs. D Native YY1-ESRRB and ESRRB-YY1 co-immunoprecipitation followed by Western Blot. E Enriched gene ontology terms for ESRRB-YY1 co-bound MIR regulated genes. F, G Heatmap and metaplot showing ChIP-seq signals at YY1-bound MIRs, and ESRRB-YY1 co-bound MIRs, respectively. H Correlation of ESRRB and YY1 binding at co-bound MIR sites. I Venn diagram of genes regulated by ESRRB-YY1 co-bound MIRs after Esrrb or Yy1 knockdown in ESCs. These MIR-regulated genes were defined by the presence of H3 K27ac loops connecting co-bound MIR and gene region (TSS to gene end). Control genes were defined by genes located at around 100–200 kb distance from the ESRRB-YY1 co-bound MIRs. J Graphical summary of the findings in this study. Our TE-centric 3D genome analysis uncovered the increasing complexity of SINE-TE, especially the SINE-MIR family in ESC. Enriched Esrrb motif and binding on MIR suggests the co-option of MIR by ESRRB in forming enhancer loops, to a certain extent in partnership with YY1. Loss of Esrrb abrogates this loop formation and decreased YY1 occupancy on MIR