Fig. 3

Criteria of promoter and extended regions for enhancer-promoter association and features of chromatin interactions. a Computationally-defined regulatory domains [11]. The transcription start site (TSS) of each gene is indicated as an arrow. The corresponding regulatory domain for each gene is shown in a matching color as a bracketed line. The basal plus extension association rule assigns a basal regulatory domain to each gene regardless of genes nearby (thick line, Association rule 1 and 2) (see Methods). The domain is then extended to the basal regulatory domain of the nearest upstream and downstream genes. The two nearest genes association rule extends the regulatory domain to the TSS of the nearest upstream and downstream genes (Association rule 3). The single nearest gene association rule extends the regulatory domain to the midpoint between this gene’s TSS and the nearest gene’s TSS both upstream and downstream (Association rule 4). b Forward–reverse orientation of CTCF-binding sites are frequently found in chromatin interactions. CTCF can block the interaction between enhancers and promoters limiting the activity of enhancers to certain functional domains. Figures adapted from [28, 69,70,71] with permission