ArticleNature communications2021
Order and stochasticity in the folding of individual Drosophila genomes.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Article
- 3D genome organization in tissue regeneration involves long-range chromatin loops.Science advances · 2026Article
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.bioRxiv : the preprint server for biology · 2025Article
- Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.Bioinformatics (Oxford, England) · 2025Article
- Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.Nature genetics · 2025Article
- Generative inpainting of incomplete Euclidean distance matrices of trajectories generated by a fractional Brownian motion.Scientific reports · 2025Article
- Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.NAR genomics and bioinformatics · 2025Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Article
- Single-Cell Hi-C Analysis Workflow with Pairtools.Methods in molecular biology (Clifton, N.J.) · 2025Article
- ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models.Computational and structural biotechnology journal · 2025Article
- Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization.Current opinion in genetics & development · 2024Review
- Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei.Communications biology · 2024Article
- HiCDiff: single-cell Hi-C data denoising with diffusion models.Briefings in bioinformatics · 2024Article
- The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.Epigenetics & chromatin · 2024Article
- Pairtools: From sequencing data to chromosome contacts.PLoS computational biology · 2024Article
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Authors and funding
18 authors.
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No grant is acknowledged in the PubMed record.
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.
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