ArticleNature communications2020
Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.
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 26 papers.
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Who cites it
26 citing papers in PubMed, 44 citations in OpenAlex.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- On-Tip Polymerization Method for Multimodal Characterization of Nanoparticles with Electron/Ion Imaging and Atom Probe Tomography.Small methods · 2026Article
- RNA-binding proteins mediate the maturation of chromatin topology during differentiation.Nature cell biology · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Microscopy methods for the in vivo study of nanoscale nuclear organization.Biochemical Society transactions · 2025Review
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 2024Article
- From feulgen to modern methods: marking a century of DNA imaging advances.Histochemistry and cell biology · 2024Review
- DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.Histochemistry and cell biology · 2024Article
- Morphomics via next-generation electron microscopy.Journal of molecular cell biology · 2024Review
- Sample preparation and data collection for serial block face scanning electron microscopy of mammalian cell monolayers.PloS one · 2024Article
- Technological advances in probing 4D genome organization.Current opinion in cell biology · 2023Review
- Large-field-of-view scanning electron microscopy of the paraventricular nucleus of the hypothalamus during diet-induced obesity.Journal of neurophysiology · 2023Article
- A chromEM-staining protocol optimized for cardiac tissue.Frontiers in cell and developmental biology · 2023Article
- Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes.Chromosoma · 2022Article
- Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy.Scientific reports · 2022Article
- The stochastic nature of genome organization and function.Current opinion in genetics & development · 2022Review
- Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Extracting physical characteristics of higher-order chromatin structures from 3D image data.Computational and structural biotechnology journal · 2022Article
- Nuclear envelope mechanobiology: linking the nuclear structure and function.Nucleus (Austin, Tex.) · 2021Review
- Review
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Authors and funding
19 authors at 6 institutions in 2 countries.
Funding
Abstract
The human genome is extensively folded into 3-dimensional organization. However, the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra-resolution imaging capability. Here, we report the development of an electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5 × 5 × 30 nm in xyz dimensions) that is superior to the current super-resolution by fluorescence light microscopy. We apply 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualize a large number of distinctive 3D chromatin folding structures in ultra-resolution. We further quantitatively characterize the reconstituted chromatin folding structures by identifying sub-domains, and uncover a high level heterogeneity of chromatin folding ultrastructures in individual nuclei, suggestive of extensive dynamic fluidity in 3D chromatin states.
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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.