Fig. 1

Simulating the α globin locus. a Browser view showing genes in the vicinity of the α globin locus, alongside a schematic indicating the coarse-graining used in the simulations. A 110-kbp section of the 400-kbp chromatin fragment that was simulated is shown. As described in the text, simulation chromatin beads were designated as CTCF binding sites, DHS binding, H3K4me1 modified sites and combinations of these. The positions of the set of five regulatory elements are indicated with blue triangles and promoters with green squares. b Example simulated configurations of the locus. CTCF proteins (green) and DHS binding proteins (red) are shown; the chromosome fragment is colored as in (a). See also Additional file 4: Video S1 for a 3D view of the configurations, from which the CTCF proteins are more readily visible. Parameters for the polymer model and the bridge–chromatin affinity are given in full in Additional file 2: Supplementary Methods. c Contact map showing the frequency of contacts between each chromatin bead in 1000 simulated configurations. Note that the color bar shows a logarithmic scale. The blue line to the left indicates the region that is shown in (a). The green line to the left indicates the region that is used for the clustering analysis (Fig. 2 and text)