Fig. 3

CTCF binding is enriched at VM-IAPs relative to other IAPs in the mouse genome. a CTCF motif derived from the top 10% of CTCF ChIP-seq peaks from the combined peak calls of eight individual liver samples. b IAP LTRs are divided into U3 (green), R (orange), and U5 (purple) substructures. Colour boundaries represent the median location of the substructure boundaries; colour gradients represent the middle 50% of the distribution of those boundaries (top plot). The CTCF motif is enriched at the 5′ end of the IAP LTRs (bottom plot), within the U3 substructure. c-e Presence of the CTCF motif within the IAP LTR (horizontal black bars) alongside CTCF ChIP-seq enrichment in liver (heatmaps) at c fully-structured and solo LTR IAPs (excluding VM-IAPs), d cVM-IAPs, and e tsVM-IAPs; circles represent tsVM-IAPs with methylation ranges in liver of 9–10% (orange) and ≥ 10% (red). CTCF enrichment score scale bar in (c) also applies to (d) and (e). For the solo LTR plots, the vertical black lines denote the 5′ and 3′ ends of the solo LTR. For the fully-structured IAP plot, the vertical black lines denote the 5′ and 3′ ends of the entire IAP. Note that the ‘fully-structured’ plots include fragmented IAPs. Heatmaps are ordered by the score in the tile preceding the 5′ edge of each IAP