ArticleeLife2023
Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes.
Article in eLife, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4Immunity · 2026Article
- Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026Article
- Live-cell imaging of enhancer-promoter dynamics reveals transient contact-driven gene activation.bioRxiv : the preprint server for biology · 2026Article
- A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.PLoS computational biology · 2025Article
- Real-time visualization of reconstituted transcription reveals RNAPII activation mechanisms at single promoters.Cell reports · 2025Article
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Regulation of RNA polymerase II transcription through re-initiation and bursting.Molecular cell · 2025Review
- Regulation of Transcriptional Bursting and Spatial Patterning in EarlybioRxiv : the preprint server for biology · 2025Article
- Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.Science (New York, N.Y.) · 2025Article
- Incorporating spatial diffusion into models of bursty stochastic transcription.Journal of the Royal Society, Interface · 2025Article
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters.bioRxiv : the preprint server for biology · 2025Article
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts.Nature cell biology · 2024Article
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 2024Article
- The method in the madness: Transcriptional control from stochastic action at the single-molecule scale.Current opinion in structural biology · 2024Review
- Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation.Nature reviews. Molecular cell biology · 2024Review
- Chromatin structure and dynamics: one nucleosome at a time.Histochemistry and cell biology · 2024Review
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
Corrections and comments
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2 authors.
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Abstract
The role of the spatial organization of chromosomes in directing transcription remains an outstanding question in gene regulation. Here, we analyze two recent single-cell imaging methodologies applied across hundreds of genes to systematically analyze the contribution of chromosome conformation to transcriptional regulation. Those methodologies are (1) single-cell chromatin tracing with super-resolution imaging in fixed cells; and (2) high-throughput labeling and imaging of nascent RNA in living cells. Specifically, we determine the contribution of physical distance to the coordination of transcriptional bursts. We find that individual genes adopt a constrained conformation and reposition toward the centroid of the surrounding chromatin upon activation. Leveraging the variability in distance inherent in single-cell imaging, we show that physical distance - but not genomic distance - between genes on individual chromosomes is the major factor driving co-bursting. By combining this analysis with live-cell imaging, we arrive at a corrected transcriptional correlation of [Formula: see text] for genes separated by < 400 nm. We propose that this surprisingly large correlation represents a physical property of human chromosomes and establishes a benchmark for future experimental studies.
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