ArticleNature communications2021
High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis.
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 26 papers.
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Who cites it
26 citing papers in PubMed.
- Effects of chromatin-lamina attachment on extra-long-range chromatin interactions.Biophysical journal · 2026Article
- SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.Bioinformatics (Oxford, England) · 2026Article
- Igh nuclear speckle association promotes V(D)J recombination.Nature communications · 2026Article
- ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics.Nucleic acids research · 2026Article
- ecPICK: A deep learning-enabled spatial diagnostic platform for direct ecDNA identification and clinical prognosis across pan-cancer histopathology.Theranostics · 2026Article
- 3D chromatin structures precede genome activation in Drosophila embryogenesis.Cell genomics · 2025Article
- ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics.bioRxiv : the preprint server for biology · 2025Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- ChromoGen: Diffusion model predicts single-cell chromatin conformations.Science advances · 2025Article
- Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation.Nature communications · 2023Article
- The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases.Cell regeneration (London, England) · 2022Review
- Chromatin as self-returning walks: From population to single cell and back.Biophysical reports · 2022Review
- Modeling and simulation of cell nuclear architecture reorganization process.Journal of computational physics · 2022Article
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5 authors.
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Abstract
Single-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5-6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.