ArticleScientific reports2022
Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 44 papers.
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44 citing papers in PubMed, 70 citations in OpenAlex.
- AI-assisted Cryo-ET workflow for 3D visualization of chromatin during cellular differentiation.Biochemistry and biophysics reports · 2026Article
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.Nature genetics · 2026Article
- Chromatin Packing Domain Engineering Through the Manipulation of Nuclear Cationic States.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Gravity as a Boundary Condition for the Evolution of Three-Dimensional Multicellularity.Life (Basel, Switzerland) · 2026Article
- Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells.Science advances · 2026Article
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.bioRxiv : the preprint server for biology · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Probing Nanomechanics by Direct Indentation Using Nanoendoscopy-AFM Reveals the Nuclear Elasticity Transition in Cancer Cells.ACS applied nano materials · 2025Article
- Leveraging chromatin packing domains to target chemoevasion in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome.bioRxiv : the preprint server for biology · 2025Article
- Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.Science advances · 2025Article
- Three-color single-molecule localization microscopy in chromatin.Light, science & applications · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
14 authors at 2 institutions in 2 countries.
Funding
Abstract
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.
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