Fig. 4

Cis-interactions of the β globin locus. a Browser view showing genes in the vicinity of the β globin locus, alongside a schematic indicating the coarse-graining used in the simulations. A 130-kbp section of the 400-kbp chromatin fragment that was simulated is shown. The positions of the known regulatory elements within the LCR 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). c Contact map showing the frequency of contacts between each chromatin bead in 500 simulated configurations. The color bar shows a logarithmic scale. The blue line to the left indicates the region that is shown in (a); the green line indicates the region that is used in the clustering analysis. d As in Fig. 2, clustering analysis allows conformations to be grouped by their structural features. Schematics of the representative structures are shown, with the percentage of conformations in which they occur. A dendrogram and contact maps for each representative structure are shown in Additional file 10: Figure S8. e Plot showing the contacts made with the promoters of the two β genes (locations indicated by red asterisks; the positions of the regulatory elements and gene promoters are indicated). Simulation results (red) are shown alongside Capture-C data (gray); both cases show the contacts to both genes combined (since each copy of the gene has the same sequence it is impossible to separate these in the experiment). Black bars indicate regions where there is no contact data (see Ref. [14] and Additional file 2: Supplementary Methods). f Similar plot showing the contacts made with the Hbb-y gene (position indicated by red asterisk)