Fig. 5: Relationship between 3D chromatin structure and transcriptional activity.

a, Top, Heatmap of gene–speckle distances in chromosome 13 in 10,000 structures. Each column shows, for a given gene, the gene–speckle distances in all 10,000 structures of the population. In each column, gene–speckle distances are sorted in ascending order from top to bottom, with short distances (dark red) to large distances (dark blue). Bottom, SAF for each chromatin region in chromosome 13. b, Top, Heatmap of single-cell mRNA counts of genes in chromosome 13 in all 4,633 G1 cells measured by scRNA-seq experiment³⁷. For a given gene, each column shows the observed mRNA transcript count in each cell of the population of cells. In each column, mRNA transcript counts are sorted in descending order from top to bottom, with high counts (dark red) to zero counts (dark blue). Bottom, TRF for each gene in chromosome 13 from scRNA-seq data³⁷ (Methods). c, ILF and SAF values for genes with different TRF ranges from scRNA-seq³⁷ (left) and nascent RNA-MERFISH imaging⁶ (right). Error bars show mean ± s.d. of ILF and SAF values in each TRF range. The numbers of regions used in each range in the left plot are (from left to right): 4,940, 960, 669, 478, 352, 280, 220, 204, 167, 301. The numbers of regions used in each range in the right plot are (from left to right): 692, 75, 65, 59, 41, 27, 10, 10. d, Fold-change enrichment of the 17 structural features for chromatin with top 10% highest (T10) and bottom 10% lowest (B10) transcript numbers of actively transcribed genes according to scRNA-seq data³⁷ (Methods). e, Distributions of several structural features for T10 and B10 regions. f, ROC curves for RAD, SpD, ILF, SAF, and trans A/B ratios to distinguish T10 and B10 regions (area under the curve values are 0.65, 0.72, 0.81, 0.85, 0.84, respectively). g, Fold-change enrichment of the 17 structural features for enhancer (EN) and superenhancer (SEN) chromatin regions.