Predicting three-dimensional genome organization with chromatin states
Fig 2
Comparison between simulated and experimental contact probability maps for a 20 Mb segment of chromosome 1 from GM12878 cells.
(A) Results from simulation and the Hi-C experiment performed in Ref. [7] are shown in the upper and lower triangle respectively on a log scale. Also shown on the left and top panels are the sequence of chromatin states and the genomic positions of CTCF binding sites. (B) A zoomed-in view of the contact maps along the diagonal region to highlight the formation of TADs. TAD boundaries detected using the software TADbit are plotted on the top of the contact map, with the simulation shown in cyan and experiment in grey. (C) Zoomed-in view of several representative regions along the diagonal to highlight the formation of chromatin loops. (D) A representative chromatin structure predicted by the computational model is drawn in a tube representation and colored by chromatin states. (E) The average contact probability as a function of the genomic separation is shown below on a log-log scale for the simulated (blue) and experimental (red) contact maps respectively.