Fig. 2

SINE transposable elements drive CTCF subspecies-specific binding. a The proportion of sequence mismatches/substitution from consensus in SINE TEs for all TE superfamilies in the different evolutionary categories of CTCF sites, compared to a matched random set. b The proportion of sequence masked by SINE repeat elements in conserved/subspecies-specific CTCF sites, compared to a matched random set. The boxplots within each violin plot show the variation in extent of sequence masking for each category. The dashed grey line denotes the average genomic sequence occupied by SINE TEs in all TE-masked sequences of the mouse genome. c Comparison of the total repeat element content in CTCF, CEBPA and FOXA1 transcription factor binding sites between sites with orthologous binding in the other subspecies (musculus-common) and subspecies-specific sites (BL6- and CAST-specific). All differences between subspecies-specific binding enrichment in repeat content with either the repeat content of all TF sites or the musculus-common set where found to be statistically significant (Binomial test, all p values < 2.2e−16). d Comparison of the total content of the SINE B2-B4 transposable element subfamily in CTCF, CEBPA and FOXA1 transcription factor binding sites between sites with orthologous binding in the other subspecies (musculus-common) and subspecies-specific sites (BL6- and CAST-specific). e The dependence of repeat element content of binding sites on signal strength for all CTCF binding sites, the subset of CTCF sites within SINE B2-B4 elements, CEBPA and FOXA1 transcription factors. Within each transcription factor set, the data is binned in 10% bins based on binding site signal strength as estimated from the number of ChIP-seq reads mapped