Fig. 6

Simulations also correctly predict looping for a less studied locus. Simulations of the Slc25a37 gene (Mitoferrin1) were performed for mouse erythroblasts and embryonic stem cells, using similar input data as for the globin loci (DNase-seq, and ChIP-seq for CTCF and the H3K4me1 histone modification). a Contact map from the simulations of erythroblasts showing the frequency of contacts between each chromatin bead in 500 simulated configurations. b Similar contact map for the same locus in mES cells. c Difference between the contact maps in panels (a) and (b). Blue regions indicate contacts that were present in erythroblasts, but not mES cells, and yellow indicates contacts present in mES cells but not erythroblasts. d Browser view showing the genes across the 400-kb simulated region. e Plots showing the interaction profiles for the Slc25a37 promoter in each cell type, comparing simulation results (upper panels) with new Capture-C data (lower panels). Note that the genomic coordinates are aligned with the browser view in (d)