Fig. 5

Interactions involving MER41 elements. a Overlap of MER41 anchors with ChIP-Seq peaks from ENCODE. Only STAT1 and FAIRE-Seq data were derived from HeLa cells treated with interferon-γ. b Breakdown of the MER41 anchors that do not overlap with any ChIP-Seq peaks. c Interactions are classified whether they are in cis (same chromosome) or trans (other chromosomes) and cis interactions are further divided based on whether they are in the same TAD as the MER41 anchor element. d Histogram of the distance between MER41 anchors and their cis interactions. e Overlap of interactions (± 1 kb) with STAT1 ChIP-Seq peaks, FAIRE-Seq peaks and gene bodies ± 3 kb. The background regions were generated based on randomly shuffling the position of the interactions on the same chromosome and calculated the overlap with each feature (median of 1000 iterations displayed). Significance was calculated based on the number of times an overlap with the randomized interaction positions is greater than observed and divided by 1000. f Representation of the number of promoters each MER41 element was found to interact with (top panel) and the number of MER41 elements contacting each promoter (bottom panel). g Number of TSS interactions that overlap with STAT1 or FAIRE-Seq peaks. h Genomic tracks of STAT1 ChIP-Seq signal, FAIRE-Seq signal and Capture 4Tran data from HeLa cells with (T) and without IFNγ treatment. Black boxes below Capture 4Tran data represent interactions identified by Chicago (C). Red arrow represents the MER41B anchor and the orange dotted rectangle represents the interaction at the IFI6, IL4R, IFITM1, and IFITM3 promoter