Extended Data Fig. 2: Assessment of single cell chromosome structures.
From: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
a, Comparison of selected structures of chromosome 6 modeled in our simulations and imaged in DNA-MERFISH experiments6. 3D chromosome structures are shown to the right of the corresponding normalized distance matrix for structures from DNA MERFISH experiments (top row) and structure modeling (bottom row). Modeled structures at 200 kb base pair resolution have higher coverage than those from experiment. To allow direct comparison, we highlight those genomic regions that are imaged in DNA-MERFISH by opaque ball and stick representations, while other genomic regions are shown as translucent genomic regions. b, Comparison of distance matrices for single cell structures of chromosome 6 from DNA-MERFISH experiments (top) and structure models (bottom); models reproduce folding patterns of different chromosome conformations observed in experiment. c, Comparison of distance matrices for single cell structures of chromosome 2 from DNA-MERFISH experiments (top) and structure models (bottom). d, Comparison of chromosome structures between models from Dip-C experiment25 (top row) and our structure population (bottom row) for chromosome 2 (left) and chromosome 6 (right). Shown are the normalized distance matrices for chromosome structures in different conformational states. Both experimental and modeled structures show high degree of similarity. In b, c, and d, the numbers indicate the Pearson correlation between the experimental and the predicted distance matrices.
