Fig. 4

TAD boundaries harbor clusters of both conserved and divergent CTCF binding sites. a Both Mus-conserved and species-specific CTCF binding sites are highly enriched around TAD boundaries. CTCF sites shared by two to four species are also enriched around TAD boundaries. b TAD boundary-associated sites lie significantly closer to each other compared to non-TAD boundary-associated CTCF sites (Mann-Whitney U test: p < 2.2e−16). c CTCF binding sites that belong to a cluster (clustered) are more enriched at TAD boundaries than singleton CTCF sites. d The violin plots correspond to TAD boundary regions categorized according to the maximum conservation level of CTCF binding they contain. A TAD boundary region separating two adjacent TADs is defined as the first nucleotide of the downstream TAD ± 50 kb. Each violin plot shows the distribution of the total number of CTCF sites that occur at the TAD boundary regions in the category. TAD boundary regions with at least one Mus-conserved site (right-most violin plot) also have a higher number of CTCF sites overall (higher redundancy). In contrast, TAD boundaries that do not contain any species-conserved CTCF sites (left-most violin plot) have much lower numbers of CTCF binding sites. There is a progressive association between the presence of individual conserved CTCF sites with higher abundance of CTCF sites. e The bars correspond to TAD boundary regions categorized according to the maximum conservation level of CTCF binding they contain. Dark green demarcates TAD boundaries with clustered CTCF sites; light green shows TAD boundaries with only singleton sites. TAD boundaries that harbor species-conserved CTCF sites also contain CTCF site clusters. f Schematic representation of evolutionarily dynamic clusters of CTCF sites that commonly occur at TAD boundaries. TAD borders usually have at least one 5-way conserved CTCF site that is clustered with other sites of lower conservation, including species-specific ones. These CTCF clusters preserve CTCF binding potential at TAD boundaries