ArticleNucleic acids research2022
Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 53 citations in OpenAlex.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Current Challenges of Transcription Compartmentalization Research.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Resolving Sub-Nuclear Architecture from Compartments to Functional Domains.International journal of molecular sciences · 2026Review
- Modern RNA Quantification Methods: From RT-qPCR to Advanced Microscopy.The journal of physical chemistry. B · 2026Review
- Development of a Live-Cell Imaging Assay to Elucidate Spatiotemporal Dynamics of Extracellular Vesicle Fusion with Target Cells.Journal of extracellular vesicles · 2026Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Labeling of nascent RNA in the C. elegans intestine.PloS one · 2026Article
- RNA polymerase II transcription compartments - from factories to condensates.Nature reviews. Genetics · 2025Review
- Role of RNA in genome folding: It's all about affinity.Current opinion in structural biology · 2025Review
- Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Illuminating biomolecular assemblies in gene regulation.Biophysical reviews · 2025Review
- Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking.Nature communications · 2025Article
- Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome.bioRxiv : the preprint server for biology · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Three-color single-molecule localization microscopy in chromatin.Light, science & applications · 2025Article
- Microscopy methods for the in vivo study of nanoscale nuclear organization.Biochemical Society transactions · 2025Review
- Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.Science advances · 2025Article
- Cajal's organization of neuronal nucleus revisited.Frontiers in neuroanatomy · 2025Review
- The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.Nucleic acids research · 2024Article
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Authors and funding
8 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level.
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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.