Fig. 4

Regulatory signatures of BL6-specific CTCF binding. a Distribution of the distances of CTCF binding sites to the transcription start site (TSS) of the nearest downstream gene based on their evolutionary class and tissue-distribution. The median is marked with a black point. b The distance from musculus-common and BL6-specific CTCF sites to their nearest non-overlapping active regulatory region is shorter than that of random genomic regions. The bar chart inset shows the type of regulatory element that is closest (but non-overlapping) to musculus-common and BL6-specific CTCF sites. c Over 6000 1-to-1 orthologous genes are differentially expressed (DE) between BL6 and CAST. Significant DE genes (FDR < 0.05) are highlighted against background of non-DE genes (grey) [29]. d CTCF binding is observed within a 50-kb distance of the vast majority of DE genes. e BL6-specific CTCF binding associates more with downregulated DE genes than musculus-common CTCF binding, either alone or with other associated active cis-regulatory elements. The bar plots display the proportions of DE genes associated with a CTCF binding sites within 50 kb, with an active promoter, an enhancer, and both