Extended Data Figure 8. Prominent interactions identified by SLICE co-segregate frequently in raw GAM data.

a, Mean co-segregation frequency of pairs of prominently interacting windows (red line) is consistently higher than the mean co-segregation frequency of all intrachromosomal window pairs (green line ± s.d.; green area) across a wide range of genomic distances. For example, when we consider all genomic loci separated by 10 Mb, we find that they co-segregate on average much less frequently (in 5.3 out of 408 NPs; ± 2.6 s.d.) than locus pairs classified as interacting (in 10.1 out of 408 NPs; ± 2.2 s.d.). b, Prominent interactions identified by SLICE over the Shh, Oct4 and c-Myc loci. Also shown are ChIP-seq tracks for pluripotency transcription factors Sox2, Nanog and Oct4, and for CTCF and H3K27ac, as well as DNAse-seq, positions of predicted enhancers and topological domains and published Hi-C data at 50 kb resolution. c, Number of prominent interactions by overlapping feature present in each window. d, Genomic distances between pairs of prominently interacting windows by overlapping feature. e, Enrichment of genomic features overlapped by prominently interacting 30 kb windows. As for Fig. 3c, but excluding windows overlapping more than one feature (e.g. both an inactive gene and an active gene). f, As for Fig. 3c except enrichments are calculated for the top 5% most interacting pairs of 50 kb windows at each genomic distance ranked by GAM normalized linkage. g, Enrichments calculated from independent 200 NP subsamples of the mESC-400 dataset (n=10, mean ± s.d.). h, A small proportion of 30 kb windows within the broadly inactive compartment B (calculated from Hi-C at 100 kb resolution) overlap active genes or enhancers. i, Prominent interactions involving Active and Enhancer windows are enriched irrespective of A or B compartmentalization, demonstrating that observed enrichments between Active regions and Enhancers are not a trivial consequence of nuclear compartmentalization j, Average linkage from 5 kb windows overlapping an enhancer to prominently interacting 30 kb Active windows (orange), Enhancer windows (purple) or non-interacting Active windows (control windows; grey).