CTCF-cohesin colocalisation analysis

Genomic regions where at least two cohesin subunits peaks overlap were merged using BEDOPS version 2.4.30 [96], and cohesin merged regions overlapping with musculus-common/BL6-specific/BL6-tissue-shared from our CTCF liver binding sites were identified. The intersection analysis was done for CTCF co-occupancy with two and three subunits, owing to the significantly fewer number of ChIP-seq peaks retrieved from the STAG1 data.

To investigate the correlation between the evolutionary/tissue-specificity type and cohesin-recruitment by CTCF, we divided each set of CTCF binding sites into ten 10% bins based on descending ChIP-seq signal. ChIP signal in this context referred to the read pileup per peak from the replicate where the peak signal was at its highest, for each of the three evolutionary/tissue-specific classifications: musculus-common/BL6-specific/BL6-tissue-shared. CTCF ChIP-seq signal intensity was then compared to the level of cohesin recruitment, defined as the fraction of CTCF sites belonging to each evolutionary/tissue-specific type that falls within a 2-subunit cohesin-bound region.