ArticleNature protocols2021
Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Spatially resolved chromatin architectures in mammalian brain tissues.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Deep Learning-Assisted Prioritization of Candidate Drug Targets in Tumors Using Spatial Multi-Omics.Biology · 2026Review
- A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.Science (New York, N.Y.) · 2026Article
- Lamin A/C directs nucleosome-scale chromatin remodeling to define early lineage segregation in mammals.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic priming promotes tyrosine kinase inhibitor resistance and oncogene amplification.Nature structural & molecular biology · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.bioRxiv : the preprint server for biology · 2025Article
- Article
- OLIVE provides rapid visualization and analysis of chromatin tracing experiments.Cell reports methods · 2025Article
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome.Nature communications · 2025Article
- Non-disruptive 3D profiling of combinations of epigenetic marks in single cells.bioRxiv : the preprint server for biology · 2025Article
- Perturb-tracing enables high-content screening of multi-scale 3D genome regulators.Nature methods · 2025Article
- Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications.International journal of molecular sciences · 2025Review
- Feeling the force from within - new tools and insights into nuclear mechanotransduction.Journal of cell science · 2025Review
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain.Molecular cell · 2024Article
- Reconstructing human-specific regulatory functions in model systems.Current opinion in genetics & development · 2024Review
- Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome.Research square · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
The genome is hierarchically organized into several 3D architectures, including chromatin loops, domains, compartments and regions associated with nuclear lamina and nucleoli. Changes in these architectures have been associated with normal development, aging and a wide range of diseases. Despite its critical importance, understanding how the genome is spatially organized in single cells, how organization varies in different cell types in mammalian tissue and how organization affects gene expression remains a major challenge. Previous approaches have been limited by a lack of capacity to directly trace chromatin folding in 3D and to simultaneously measure genomic organization in relation to other nuclear components and gene expression in the same single cells. We have developed an image-based 3D genomics technique termed 'chromatin tracing', which enables direct 3D tracing of chromatin folding along individual chromosomes in single cells. More recently, we also developed multiplexed imaging of nucleome architectures (MINA), which enables simultaneous measurements of multiscale chromatin folding, associations of genomic regions with nuclear lamina and nucleoli and copy numbers of numerous RNA species in the same single cells in mammalian tissue. Here, we provide detailed protocols for chromatin tracing in cell lines and MINA in mammalian tissue, which take 3-4 d for experimental work and 2-3 d for data analysis. We expect these developments to be broadly applicable and to affect many lines of research on 3D genomics by depicting multiscale genomic architectures associated with gene expression, in different types of cells and tissue undergoing different biological processes.
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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.