Fig. 1

Overview of genomics features and evolutionary conservation of CTCF binding in the BL6 and CAST subspecies. a A schematic example of the contribution of transposable elements novel subspecies-specific CTCF binding. The peaks represent CTCF binding as determined from ChIP-seq experiments, while the boxes denote different groups of transposable elements (black = SINE, green = LTR). The table shows the peak counts (binding sites) retrieved from the three biological replicates for each subspecies. All downstream analysis utilised peaks common to a minimum of two replicates. b The Venn diagram shows the degree of CTCF binding overlap in whole genome alignments between the Mus musculus domesticus (BL6) and Mus musculus castaneus (CAST) mouse subspecies. CTCF binding sites found aligned in orthologous locations are called musculus-common, while those with no alignment in the other species are subspecies-specific. For each evolutionary class of CTCF sites (above Venn diagram) and for all sites regardless of conservation between species (below Venn diagram), the most represented sequence motif and the distance to the nearest downstream genes. c The pie charts show the gene features overlapping CTCF sites for all evolutionary classes in the Venn diagram in b. d The repeat content of all CTCF binding sites, and each evolutionary category described in b is measured as the percentage of a CTCF binding sites’ sequence that overlaps a repeat element. The asterisks indicate the significance of enrichment of SINE B2-B4 elements between subspecies-specific sets and all CTCF binding sites for both species and the musculus-common set (binomial tests, ***p < 0.0001)