Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

The discovery that genomes are partitioned into self-interacting modules or topologically associated domains (TADs) has revolutionized our understanding of the multiscale organization of chromatin. TADs are often considered as stable structures over time, however this view contrasts with the structural dynamics needed for DNA to cope rapidly and accurately with cell-specific and developmental programs regulation. Here, we combine super-resolution microscopy with state-of-the-art DNA labeling methods to reveal the variability in the multiscale organization of chromosomes in Drosophila . We find that TAD borders display very low contact frequency independently o f TAD size, epigenetic state, or cell type. Moreover, long range interactions and assemble of epigenetic domains into active/repressed compartments display different degrees of stochasticity that globally depended on cell-type. Overall, our results show that stochasticity is specifically modulated by sequence and epigenetic state at all levels of chromatin organization, revealing a novel mechanism for the spatial organization and regulation of genomes. Hi-C experiments in drosophila S2 cell