Fig. 7: Dynamic 3D chromatin structures across single cells demonstrate distinct spatial organizations of gene expression.

a The schematic figure of the jointly profiled single-cell chromatin contacts and the coupled DNA methylation in the snm3C dataset. b Hypomethylated gene promoters are spatially closer in 3D space across single cells. For every single cell, genes are divided into three groups based on their DNA methylation scores around promoters (Low: <30% quantile, n = 105; Medium: 30%–70% quantile, n = 140; High: >70% quantile, n = 105). The pairwise 3D distances between two genes within the same methylation group are calculated across all single cells. The center lines of boxplots show the median; the upper and lower box limits show the 25th and 75th percentiles, respectively. The whiskers extend up to 1.5 times the interquartile range away from the limits of the boxes. c 351 single cells are divided into two clusters based on the similarity of their predicted 3D chromatin structures. Tensor-FLAMINGO delineates the cells into two distinct clusters of chromatin structures (red vs. blue). d Distribution of the spatial distances between the cluster-specific differentially methylated genes across cell clusters. Cluster-specific hypomethylated genes show shorter 3D distances in cells belonging to the matched cluster (n = 77) versus the unmatched cluster (n = 49). The center lines of boxplots show the median; the upper and lower box limits show the 25th and 75th percentiles, respectively. The whiskers extend up to 1.5 times the interquartile range away from the limits of the boxes. e Example of the cluster-specific 3D chromatin structure spatially organizing cluster-specific differentially methylated genes into the dense 3D neighborhood. Source data are provided as a Source Data file.