Fig. 2

Local visualization modes. a A cartoon representation of the three-dimensional conformation of a putative DNA loop tethered by two CTCF proteins. CTCF binding sites are colored in blue and pink on the black DNA strand. Below the cartoon, a one-dimensional representation of the DNA fragment that forms the loop is placed above an Epigenome Browser visualization of a ∼1Mb locus, displaying the genes, CTCF binding, and interactions detected by ChIP-seq [50] and ChIA-PET assays (unpublished, GEO ID:GSM970216), and three-dimensional interactions as measured by Hi-C [28]. Two bins containing putative binding sites (pink and blue bars) show an enrichment of Hi-C contacts in the heat map visualization [28] (indicated by the red arrow). CTCF tethered interactions measured by ChIA-PET in an arcs view also indicate an interaction between these two putative binding sites. b A circular plot that shows the chromosome-wide long range contacts of the CTCF loop in panel a; the locus of interest is highlighted by a red arrow. The contacts are displayed as arcs, and only contacts above a certain threshold are visualized. c A putative promoter–enhancer interaction around the NANOG gene is displayed as a cartoon, which includes the PolII complex (yellow oval). Red and green bars in these cartoons represent the promoter and enhancer elements, respectively. Below the cartoon representations, a virtual 4C plot from the three-dimensional genome browser is shown, which visualizes the Hi-C signal around the NANOG promoter with a 1D representation of this region aligned above the plot. The bin in focus (the “anchoring point”) corresponds to the promoter of the NANOG gene. The height of the blue line indicates, for each locus, the read count for contacts between the current locus and the anchor point. In particular, the series shows an upstream enrichment of signal from a capture Hi-C experiment specifically targeting the NANOG promoter [51], which suggests a promoter–enhancer interaction. This observation is further supported by enrichment of DNaseI linkage data [41] (shown in grey below the primary plot) around the promoter and upstream regions. The NANOG gene is shown in the UCSC Genome Browser track under the virtual 4C plot