ArticleProceedings of the National Academy of Sciences of the United States of America2014
Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- CircACVR2A(2-4) regulates stem cell pluripotency by uncoupling CDK-activating kinase functions.Nucleic acids research · 2026Article
- Versatile and Scalable Reflective Micromirrors for Single-Objective Light Sheet Microscopy.Nano letters · 2026Article
- Transcription condensates are promoter hubs that enhance transcriptional bursts.bioRxiv : the preprint server for biology · 2026Article
- Versatile and Scalable Reflective Micromirrors for Single-Objective Light Sheet Microscopy.bioRxiv : the preprint server for biology · 2026Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.Nature communications · 2026Article
- RNA polymerase II transcription compartments - from factories to condensates.Nature reviews. Genetics · 2025Review
- In-depth single molecule localization microscopy using adaptive optics and single objective light-sheet microscopy.Nature communications · 2025Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.bioRxiv : the preprint server for biology · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell.Journal of applied physics · 2024Article
- Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics.Nature communications · 2024Article
- Real-time imaging of axonal membrane protein life cycles.Nature protocols · 2024Review
- Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.Nature cell biology · 2024Article
- Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.bioRxiv : the preprint server for biology · 2023Article
- Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei.Scientific reports · 2023Article
- Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton.Science China. Life sciences · 2023Article
- Variations in Intracellular Organometallic Reaction Frequency Captured by Single-Molecule Fluorescence Microscopy.Angewandte Chemie (International ed. in English) · 2023Article
- Resolution doubling in light-sheet microscopy via oblique plane structured illumination.Nature methods · 2022Article
- Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications.International journal of molecular sciences · 2022Review
- Transcription factor dynamics in plants: Insights and technologies for in vivo imaging.Plant physiology · 2022Review
16 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.
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