ArticleNature communications2020
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
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- A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.Science (New York, N.Y.) · 2026Article
- Differential analysis of image-based chromatin tracing data with Dory.bioRxiv : the preprint server for biology · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- Tracing the evolution of single-cell 3D genomes in Kras-driven cancers.Nature genetics · 2025Article
- Article
- OLIVE provides rapid visualization and analysis of chromatin tracing experiments.Cell reports methods · 2025Article
- MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart.bioRxiv : the preprint server for biology · 2025Article
- Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE.bioRxiv : the preprint server for biology · 2025Article
- Advancing biological understanding of cellular senescence with computational multiomics.Nature genetics · 2025Review
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
- Extrinsic heterogeneity: Collectivity in isotropic conformational fluctuations of chromosomes.Biophysical journal · 2025Article
- Regulatory roles of three-dimensional structures of chromatin domains.Genome biology · 2025Article
- Article
- Perturb-tracing enables high-content screening of multi-scale 3D genome regulators.Nature methods · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged in the same cell and how they are mutually correlated in different cell types in mammalian tissue are largely unknown. Here, we develop Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We apply this method in mouse fetal liver, and identify de novo cell-type-specific chromatin architectures associated with gene expression, as well as cell-type-independent principles of chromatin organization. Polymer simulation shows that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our results illustrate a multi-faceted picture and physical principles of chromatin organization.
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