ArticleNature protocols2021
Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA.
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 45 papers.
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Who cites it
45 citing papers in PubMed, 73 citations in OpenAlex.
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- Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4Immunity · 2026Article
- Single-cell chromatin state transitions during epigenetic memory formation.Science advances · 2026Article
- Promoter reinforcement supports transcriptional resilience in drug-resistant cancer.Nature structural & molecular biology · 2026Article
- autoFISH: a modular toolbox for sequential single-molecule RNA FISH experiments.Communications biology · 2026Article
- The role of cohesin loading at enhancers in the flux of loop extrusion and long-range transcriptional control.bioRxiv : the preprint server for biology · 2026Article
- A developmentally regulated long-range enhancer-promoter contact mediates human neural development.bioRxiv : the preprint server for biology · 2026Article
- YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.Science advances · 2026Article
- Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization.Nature communications · 2026Article
- Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.Nature cell biology · 2026Article
- A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.PLoS computational biology · 2025Article
- BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data.bioRxiv : the preprint server for biology · 2025Article
- OLIVE provides rapid visualization and analysis of chromatin tracing experiments.Cell reports methods · 2025Article
- Enhancer activation from transposable elements in extrachromosomal DNA.Nature cell biology · 2025Article
- Comprehensive Single Molecule View of Transcriptional Dynamics in Development.bioRxiv : the preprint server for biology · 2025Article
- RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging.Science (New York, N.Y.) · 2025Article
- Enhancer activation from transposable elements in extrachromosomal DNA.bioRxiv : the preprint server for biology · 2025Article
- An electrostatic repulsion model of centromere organisation.bioRxiv : the preprint server for biology · 2025Article
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.
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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.