ArticleNature2017
3D structures of individual mammalian genomes studied by single-cell Hi-C.
Article in Nature, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 501 papers.
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Who cites it
501 citing papers in PubMed.
- Article
- Spatially resolved chromatin architectures in mammalian brain tissues.Nature methods · 2026Article
- ssJSD: A Fusion of Sparsity and Spatial Information for HiC Single-Cell Clustering.bioRxiv : the preprint server for biology · 2026Article
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- Non-coding DNA dynamics and its roles as a physical barrier in genome safeguarding across early development and evolution.Heredity · 2026Review
- Article
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.International journal of molecular sciences · 2026Article
- Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks.Nature communications · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.Bioinformatics (Oxford, England) · 2026Article
- Article
- szKendall: spatial-structural-zero-aware dissimilarity measures for subtype discovery using single cell Hi-C data.Nature communications · 2026Article
- Article
- TAD boundaries and gene activity are uncoupled.eLife · 2026Article
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data.BMC bioinformatics · 2026Article
- scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features.Briefings in bioinformatics · 2026Article
441 more citing papers are in PubMed but not listed here.
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23 authors.
Funding
Abstract
The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. The technique enables genome folding to be examined at a scale of less than 100 kb, and chromosome structures to be validated. The structures of individual topological-associated domains and loops vary substantially from cell to cell. By contrast, A and B compartments, lamina-associated domains and active enhancers and promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. By studying genes regulated by pluripotency factor and nucleosome remodelling deacetylase (NuRD), we illustrate how the determination of single-cell genome structure provides a new approach for investigating biological processes.
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Registered trials
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.