Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2
Fig 2
Disruption scores highlight impactful epigenomic features.
A) Scatterplots showing disruption scores vs. genomic features at n = 9,991 autosomal CTCF sites, profiled with single-molecule footprinting (SMF) [31] which categorizes sites as: bound, nucleosome occupied, or accessible. We used the complete set of SMF-profiled CTCF sites and disrupted genomic sequence via permutation in silico. The first column displays disruption score vs. (i) frequency of being bound or (ii) accessible. The other subplots show disruption scores vs. following genomic features: (iii) cohesin (Rad21) ChIP-seq signal [60], (iv) CTCF ChIP-seq signal, (v) conservation score (phyloP), and (vi) PWM score, with dots colored by their SMF bound frequency. ChIP-seq signal is quantified as the sum in a ±100bp window around each CTCF site. B) Matrix of pairwise correlations between disruption scores and genomic features of n = 9,991 autosomal CTCF sites. C) Partial correlation coefficients between disruption scores and subsets of genomic features from panel B, adjusting for mutual influences among these features. Partial correlations computed controlling for CTCF and cohesin ChIP-seq either from [60] (left) or [52,61] (right) are similar qualitatively and quantitatively.