Order and stochasticity in the folding of individual Drosophila genomes

Sergey V Ulianov,Elena A Mikhaleva,Sergey V Razin,Ekaterina E Khrameeva,Kirill E Polovnikov,Alexander S Gorsky,Aleksandra A Galitsyna,Vlada V Zakharova,Yegor S Vassetzky,Pavel I Kos,Yuri Y Shevelyov,Alexey A Gavrilov,Ilya M Flyamer,Mariya D Logacheva,Alexander V Chertovich,Sergey K Nechaev,Mikhail S Gelfand,Diego Germini

doi:10.1038/s41467-020-20292-z

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.

Highlights

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs)
To investigate the nature of TADs in single cells and to characterize individual cell variability in Drosophila 3D genome organization, we performed single-nucleus Hi-C32 (Fig. 1a) in 88 asynchronously growing Drosophila male Dm-BG3c2 (BG3) cells (Supplementary Fig. 1a) in parallel with the bulk BG3 in situ High-throughput chromosome conformation capture (Hi-C) analysis and obtained 2–5 million paired-end reads per single-cell library
To select the libraries for deep sequencing, we subsampled the single-nucleus Hi-C (snHi-C) data to estimate the expected number of unique contacts that could be extracted from the data (Supplementary Fig. 2a; see “Methods”)

Summary

Introduction

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). We use a single-nucleus Hi-C technique to construct high-resolution HiC 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. High-throughput chromosome conformation capture (Hi-C) studies demonstrated that chromosomal territories were partitioned into partially insulated topologically associating domains (TADs)[3,4,5]. High-resolution studies demonstrated that the genome was partitioned into relatively small compartmental domains bearing distinct chromatin marks and comparable in sizes with TADs15. The formation of TADs by active DNA loop extrusion partially overrides the profile of compartmental domains[15,16]. The results of computer simulations suggest that Drosophila TADs are assembled by the condensation of nucleosomes of inactive chromatin[24]

Methods

Results

Conclusion