Folding of individual drosophila genomes

Abstract

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The current vision of the eukaryotic genome 3D organization is mainly based on the Hi-C data obtained in population studies. These data suggest that, in mammals, birds and Drosophila, chromosomes are partitioned into self-interacting (topologically-associating) chromatin domains (TADs) that represent structural-functional blocks of the genome [1]. In particular, TAD borders appear to restrict the area of enhancer action. Consequently, disruption of these borders cause deregulation of gene expression. Of note, however, folding of individual genome may differ to a certain extend from the population average. To get further inside into biological significance of the 3D genome organization it is thus necessary to estimate the degree of cell to cell variations of this organization. Taking into account the proposed role of the 3D genome folding in establishing regulatory networks, it is easy to see how instability of this organization may cause abnormal events resulting in generation of clones of cancer cells. To this end it is of note that previous studies demonstrated that, in individual mammalian cells, the chromatin contact domains frequently cover the population TAD borders [2]. It is unclear, however whether the contact domains annotated in single cell Hi-C maps are biologically relevant or represent random fluctuation of captured contacts in sparse Hi-C matrices. Here, using a Hi-C protocol, we have produced Hi-C matrices of Drosophila individual cells (line Bg3) with 10 Kb resolution. To analyze the 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 do exist in individual cells and that profiles of chromosomes partitioning into TADs are largely conserved between individual cells and closely match these observed in population studies. Similar to TADs observed in population Hi-C studies, high levels of active chromatin marks determine strong boundaries of contact domains in individual Drosophila cells. At the same time, the shape of individual TADs shows significant cell-to-cell variability, as demonstrated by computer modeling. At macroscale, the path of DNA within a 3D chromosome territory is also variable and is likely directed by stochastic interactions of active chromatin regions and of polycomb TADs.