Fig. 1

Mus-conserved CTCF binding sites commonly occur at TAD borders. a CTCF ChIP-seq tracks around the Chrna1 locus in C57BL/6J and in orthologous regions of the other Mus species. The raw data from three independent biological replicates are shown for each species. The majority of peaks are reproducible among the replicates, while a substantial fraction of them is also cross-species conserved. b Conservation of CTCF binding sites across the five studied Mus species. Conservation levels, i.e., the number of species CTCF sites are shared in, are noted at the bottom of the panel (phylogenetic distances are from Thybert et al. [35] c Graphical representation of using orthologous alignments of the CTCF sites identified in each Mus species to project them on the genome of C57BL/6J (Mmus, GRCm38) where TADs are available. d Distances of CTCF sites with different conservation levels to their closest TAD boundary. CTCF sites with a distance ≤ 50 kb are considered TAD boundary associated, while sites with a distance > 50 kb are referred to as non-TAD boundary associated. For clarity, when referring to the distance to a TAD boundary, we define the boundary as a single nucleotide separating adjacent TADs; when we analyze genomic elements a TAD boundary harbors, we define a window of ± 50 kb around this single nucleotide and refer to this as a “TAD boundary region”