Fig. 4: Chromatin heterogeneity, compaction, and dynamic changes of a 3-body interaction unit.

a Hierarchical clustering of 3D chromatin configurations of all three stages of cells in the polycomb-repressed region. Aggregated contact heat maps of the 5 clusters are ordered based on their averaged radius of gyration (R_g). b Representative conformations of the 5 clusters shown in a. Proportions are labeled on top of the conformations. c Proportions of the 5 clusters in each cell type. pre-MBT: cycles 9–13; post-MBT: stages 5–8. d The left figure shows the simulated distance distributions of the a–c (Scyl–chrb) interaction and another two control interactions (c–d and c–c'). c–d has the same genomic distance as a–c, while c–c' is a near-range interaction. The right figure shows the distance distributions derived from the DNA FISH measurements⁴⁵. The three interactions are illustrated on the top. e A virtual 4C plot of the region that contains a three-body interaction among two promoters and a putative enhancer, with the anchor shown in red bar. The gene Scyl is located within this anchor region. Two target regions are shown in the blue bar and yellow bar. The gene chrb is localized in the blue region, and a putative enhancer overlapped with a ChIP-defined cis-regulatory module (CRM) CRM4311 is in the yellow region. Tracks of RNA polymerase II, H3K27ac, and RefSeq genes are shown at the bottom. f The left figure shows an example of a two-body interaction between the promoters of genes Scyl and chrb which are labeled in e. The right barplot shows the fractions of this two-body interaction in three different cell types. g The left figure shows an example of a three-body interaction among the two promoters and the enhancer labeled in e. The right barplot shows the fractions of this three-body interaction among all Scyl–chrb interactions in the three cell types. Source data are provided as a Source Data file.