Single-cell Hi-C demonstrates that TADs are stable units of Drosophila genome folding that persist in individual cells

The 3D organization of the genome appears to be functionally relevant as it allows establishing of long-range spatial contacts between promoters and remote regulatory elements. However, most of the observations on the 3D genome organization have been made by conventional methods in cell population where only average characteristics of the so-called typical cell can be identified. On the other hand, FISH-based studies demonstrated that the spatial configuration of the genome varies in individual cells. However, the microscopic approaches do not allow performing a genome-wide analysis that is critical to understand better the regulatory events occurring at the level of 3D genome organization. The high throughput chromosome conformation capture protocol (Hi-C) has been modified recently to allow construction of chromatin contact frequency maps for individual cells. Using this modified protocol we constructed Hi-C maps for 20 drosophila cells (line Dm-BG3c2). In the best cell we have captured ~15% of the theoretically available contacts. This allowed constructing of the spatial contact matrices with 10 Kb resolution. Analysis of these matrices demonstrated that topologically-associating domains (TADs) do not represent a computer-generated population average, but exist in individual cells. Importantly, using a number of statistical approaches we show that the observed profile of contact chromatin domains in individual cells cannot be explained by random fluctuations. Furthermore, we show that in individual cells TADs are organized hierarchically, and that this hierarchy closely matches the hierarchy seen in population maps. Finally, we show that genomic regions that frequently harbor the contact domain borders possess specific epigenetic signatures.