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Order and stochasticity in the folding of individual Drosophila genomes.

Abstract：

: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.

journal_name

Nat Commun

journal_title

Nature communications

authors

Ulianov SV,Zakharova VV,Galitsyna AA,Kos PI,Polovnikov KE,Flyamer IM,Mikhaleva EA,Khrameeva EE,Germini D,Logacheva MD,Gavrilov AA,Gorsky AS,Nechaev SK,Gelfand MS,Vassetzky YS,Chertovich AV,Shevelyov YY,Razin SV

doi

10.1038/s41467-020-20292-z

subject

Has Abstract

pub_date

2021-01-04 00:00:00

pages

41

issue

1

issn

2041-1723

pii

10.1038/s41467-020-20292-z

journal_volume

12

pub_type

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