ИСТИНА

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 distances between various genomic regions vary significantly in individual cells. However, the microscopic approaches do not allow performing a genome­wide 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 (Hi­C) has been modified recently to allow construction of chromatin contact frequency maps for individual cells. Using this modified protocol we have constructed Hi­C maps for 20 drosophila cells (line Dm­BG3c2). In the best cell we have captured ~12% of the theoretically available contacts. To analyze these sparse contact matrices, we have developed program tools allowing us to take into account the noise by comparing maps from individual cells with artificially generated random matrices. The results of our analysis demonstrate that contact chromatin domains in individual chromosomes are organized hierarchically. Importantly, using a number of statistical approaches we show that the observed profile of contact chromatin domains can not be explained by random fluctuations. We also show that these domains do not coincide in randomly selected pairs of individual cells but tend to occupy some preferential positions in the genome as revealed by the comparison of several cells. Finally, we show that genomic regions that frequently harbor the contact domain borders possess specific epigenetic signatures.