A model for the topology of active ribosomal RNA genes
Open accessAbstract
The Christmas tree view of active ribosomal RNA (rRNA) genes suggests a gene topology in which a large number of nascent rRNA transcripts are prevented from intertwining. The way in which this is achieved has remained unclear. By using a combination of chromatin immunoprecipitation and chromosome conformation capture techniques, we show that the promoter, upstream region and terminator R3 of active rRNA genes are held together spatially throughout the cell cycle, forming a stable core around which the transcribed region is organized. We suggest a new core-helix model for the topology of rRNA genes, that provides a structural basis for the productive synthesis or rRNA.
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Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1.
“Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions (91,92) or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1 (93).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [93]
The ‘core-helix model’ section proposes that the transcribed rDNA region wraps around an SL1-based anchoring core. The citing sentence presents that proposed structure as something studies have shown, whereas this paper describes the wrapping as a model, not a demonstrated arrangement. Citation 93 attaches to this core-helix clause, rather than the preceding loop claim. (LLM, conf=0.86)
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Cites
Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes
Németh, A., Guibert, S., Tiwari, V. K., Ohlsson, R., & Längst, G. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.57 · Cited by 94 · see citing works
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Research works printed but not linked: 1
- Bernard W, Granboulan N (1968) Electron microscopy of the nucleolus in vertebrate cells. In Ultrastructure in Biological Systems, Dalton A, Haguenav F (eds) Vol 3, pp 81-149. New York and London: Academic Press
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Epigenetic control of RNA polymerase I transcription in mammalian cells
Grummt, I., & Längst, G. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.10.004 · Cited by 132 · see citing works
Self-citationFefelova, E. A., Pleshakova, I. M., Mikhaleva, E. A., Pirogov, S. A., Poltorachenko, V. A., Abramov, Y. A., Romashin, D. D., Shatskikh, A. S., Blokh, R. S., Gvozdev, V. A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1276 · Cited by 15 · see citing works
“Studies on mammalian cells show that rDNA repeats in the nucleolus form loops connecting promoter and termination regions (91,92) or more complex structures, in which the transcribed rDNA region is wrapped around the core formed by SL1 (93).”
Background
- Authors
- Denissov, S., Lessard, F., Mayer, C., Stefanovsky, V., van Driel, M., Grummt, I., Moss, T., & Stunnenberg, H. G.
- Affiliations
- Radboud University Nijmegen (NL)
- Université Laval (CA)
- German Cancer Research Center (DE)
- Corresponding author
- Stunnenberg, Hendrik G
- Venue
- The EMBO Reports
- Published
- 2011-02-18
- Volume
- 12
- Issue
- 3
- Pages
- 231-237
- ISSN
- 1469-221X (ISSN-L)
- 1469-3178
- PMC
- PMC3059908
- OpenAlex
- W2040679179
- Cited by
- 58
- References
- 1
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 4 · 2021: 6 · 2020: 1 · 2019: 3 · 2018: 3 · 2017: 5 · 2016: 6 · 2015: 1 · 2014: 6 · 2013: 9 · 2012: 5
- FWCI
- 2.72
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- EMBO Reports (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- ribosomal DNA, promoter, gene structure, ribosomal RNA synthesis, cell cycle
- MeSH terms
- Cell Cycle, Chromosomes, Human, DNA, Ribosomal, Fluorescent Antibody Technique, Humans, Models, Genetic, Models, Molecular, Promoter Regions, Genetic, RNA Polymerase I, RNA, Ribosomal, Structure-Activity Relationship, Terminator Regions, Genetic, Transcription, Genetic, Blotting, Northern, Genes, rRNA, TATA-Box Binding Protein, Cell Line, Tumor, Chromatin Immunoprecipitation
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