Order and stochasticity in the folding of individual Drosophila genomes

Ulianov, S.V.; Zakharova, V.V.; Galitsyna, A.A.; Kos, P.I.; Polovnikov, K.E.; Flyamer, I.M.; Mikhaleva, E.A.; Khrameeva, E.E.; Germini, D.; Logacheva, M.D.; Gavrilov, A.A.; Gorsky, A.S.; Nechaev, S.K.; Gelfand, M.S.; Vassetzky, Y.S.; Chertovich, A.V.; Shevelyov, Y.Y.; Razin, S.V.

Авторы: Ulianov Sergey V., Zakharova Vlada V., Galitsyna Aleksandra A., Kos Pavel I., Polovnikov Kirill E., Flyamer Ilya M., Mikhaleva Elena A., Khrameeva Ekaterina E., Germini Diego, Logacheva Mariya D., Gavrilov Alexey A., Gorsky Alexander S., Nechaev Sergey K., Gelfand Mikhail S., Vassetzky Yegor S., Chertovich Alexander V., Shevelyov Yuri Y., Razin Sergey V.
Журнал: Nature communications
Том: 12
Номер: 1
Год издания: 2021
Издательство: Nature Pub. Group
Местоположение издательства: United Kingdom
Номер статьи: 41
DOI: 10.1038/s41467-020-20292-z
Аннотация: Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.
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Order and stochasticity in the folding of individual Drosophila genomesстатья

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