Fig. 3

Simulations compare favorably with experimental data. a Plot showing the contacts made with the promoters of the two α globin genes (locations indicated by red asterisks; the positions of the regulatory elements and other gene promoters are also indicated). Simulation results (red) are shown alongside Capture-C data (gray); in both cases the plots 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 (i.e., between captured regions; see Additional file 2: Supplementary Methods and Ref. [14]). Since Capture-C data only give relative contact strength, the height of the experimental data has been scaled so as to best fit the simulation results (see Additional file 2: Supplementary Methods). b As in (a), but now showing the contacts made with the Mpg promoter (position indicated by red asterisk). Although Mpg is roughly the same genomic distance away from the regulatory elements as the α globin genes, it interacts with them less frequently. c Plot showing the distribution of the 3D separation of the α globin promoters and the probe pE located at the regulatory elements R1–3. Simulations are compared with FISH measurements (see Methods and Additional file 7: Figure S5) performed on mature erythroblasts 30 hours after differentiation, when the globin genes are maximally expressed. The inset shows the mean and standard deviation for each case. d As in (c), but showing the separation of the α promoters and a downstream control probe p58 located within the Sh3pxd2b gene