Fig. 7

Simulations predict the effect of protein knock-outs in the α globin locus. Plots showing the effect of a CTCF knock-out and a DHS knock-out (equivalent to knocking out all protein complexes involved in looping the α globin locus except CTCF). a–c Contact maps showing the interactions between different chromosomal locations for conformations within each group identified by clustering analysis. Maps from three sets of simulations are shown; the positions of the known regulatory elements and gene promoters are indicated above each plot. d Schematics showing the structure of the locus within each group. e Plot showing the percentage of conformations that belong to each group identified by the clustering analysis. The color key is given in (d). f Plot showing in what percentage of conformations the two α globin gene promoters are interacting with one or more of the known regulatory elements. g Plot showing the distribution of the radius of gyration of the locus across the simulated conformations. The radius of gyration is defined as \({R_{g}^{2}}=(1/N) \sum _{i=1}^{N} (\mathbf {r}_{i}-\bar {\mathbf {r}})^{2}\), where r _i is the position of the ith chromatin bead in the polymer, and \(\bar {\mathbf {r}}\) is the mean position of all N chromatin beads