ArticleNature structural & molecular biology2022
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.
Article in Nature structural & molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 26 citations in OpenAlex.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deep learning in chromatin organization: from super-resolution microscopy to clinical applications.Cellular and molecular life sciences : CMLS · 2025Review
- Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking.Nature communications · 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
- Microscopy methods for the in vivo study of nanoscale nuclear organization.Biochemical Society transactions · 2025Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.bioRxiv : the preprint server for biology · 2024Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming.Cell reports · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 2024Article
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Image-based 3D genomics through chromatin tracing.Nature reviews. Methods primers · 2024Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
Corrections and comments
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Authors and funding
17 authors at 7 institutions in 5 countries.
Funding
Abstract
The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes physically fold in the three-dimensional nuclear space. Here we describe immuno-OligoSTORM, an imaging strategy that reveals the distribution of nucleosomes within specific genes in super-resolution, through the simultaneous visualization of DNA and histones. We combine immuno-OligoSTORM with restraint-based and coarse-grained modeling approaches to integrate super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. The resulting method, called Modeling immuno-OligoSTORM, allows quantitative modeling of genes with nucleosome resolution and provides information about chromatin accessibility for regulatory factors, such as RNA polymerase II. With Modeling immuno-OligoSTORM, we explore intercellular variability, transcriptional-dependent gene conformation, and folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells, thereby obtaining the highest degree of data integration achieved so far to our knowledge.
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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.