Fig. 6: Order and stochasticity in the Drosophila 3D genome.

a Schematic representation of the ordered and stochastic components in the Drosophila genome folding. Positions of TAD boundaries are largely conservative between individual cells and determined by active chromatin. Chromatin fiber path within a particular TAD and within the whole chromosome territory is largely stochastic and demonstrate prominent cell-to-cell variability. b Determined positions of active regions along the Drosophila genome define TAD boundaries persistent in individual cells. Inactive region is folded into chromatin globule due to interactions between non-acetylated “sticky” nucleosomes. This region adopts different configurations in individual cells (and at different time points in a particular cell). In a cell 1, it is folded into two globules separated with stochastically formed fuzzy boundary. In a cell 2, one part of the region is compact (left) and the other part (right) is transiently decondensed. In a cell 3, the entire region forms one densely packed globule. Averaging of these configuration results in a TAD containing two sub-TADs in a population-based Hi-C map. Note, that the hierarchical structure of the TAD emerging in a population Hi-C map reflects different configuration of the region in individual cells. We note that the absence of any structure at inactive TAD borders denotes ambiguity of folding of these regions with snHi-C, but not the absence of this structure. c Extended active regions serving as barrier elements for potential loop extrusion complex (LEC) in Drosophila cells. It has been previously shown that transcription might interfere with loop extrusion^71,72. Since stable TAD boundaries in Drosophila are enriched with transcribed genes, we propose that extended regions of active chromatin but not binding sites of architectural proteins represent barrier elements for LEC in Drosophila cells. In this scenario, LEC is looping out a TAD and terminates within flanking active regions colliding with RNA-polymerases, large chromatin-remodeling complexes and other components of active chromatin. In different individual cells, termination occurs accidentally at different points within these regions. In a population-based Hi-C map that results in a compartment-like signal but not in a conventional pointed loop observed in mammalian cells where CTCF binding sites serve as barrier elements for LEC.