ArticleGenes & development2013
In vivo live imaging of RNA polymerase II transcription factories in primary cells.
Article in Genes & development, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 82 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
82 citing papers in PubMed, 137 citations in OpenAlex.
- 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
- A molecular census to elucidate the demixing mechanism of membraneless organelles.Genome biology · 2025Article
- A single cluster of RNA Polymerase II molecules is stably associated with active genes.bioRxiv : the preprint server for biology · 2025Article
- Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II.Genome biology · 2025Article
- The role of transcription bodies in gene expression: what embryos teach us.Biochemical Society transactions · 2025Review
- Review
- Transcription bodies regulate gene expression by sequestering CDK9.Nature cell biology · 2024Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.Research square · 2023Article
- Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics.Epigenetics & chromatin · 2023Review
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.bioRxiv : the preprint server for biology · 2023Article
- Double-strand break repair and mis-repair in 3D.DNA repair · 2023Article
- Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion.Nucleus (Austin, Tex.) · 2022Article
- CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation.EMBO reports · 2022Article
- Nanoscale nuclear environments, fine-scale 3D genome organization and transcription regulation.Current opinion in systems biology · 2022Article
- Live imaging of transcription sites using an elongating RNA polymerase II-specific probe.The Journal of cell biology · 2022Article
- Liquid-Liquid Phase Separation in Chromatin.Cold Spring Harbor perspectives in biology · 2022Review
- Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription.Journal of molecular biology · 2022Review
- Towards a 'Spot On' Understanding of Transcription in the Nucleus.Journal of molecular biology · 2021Review
- CDK9 keeps RNA polymerase II on track.Cellular and molecular life sciences : CMLS · 2021Review
22 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as "transcription factories," but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9-mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.
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Registered trials
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.