Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking
Open accessAbstract
By using formaldehyde cross-linking of histones to DNA and gel retardation assays we show that formaldehyde fixation, similar to previously established psoralen photocross-linking, discriminates between nucleosome- packed (inactive) and nucleosome-free (active) fractions of ribosomal RNA genes. By both cross-linking techniques we were able to purify fragments from agarose gels, corresponding to coding, enhancer and promoter sequences of rRNA genes, which were further investigated with respect to DNA methylation. This approach allows us to analyse independently and in detail methylation patterns of active and inactive rRNA gene copies by the combination of Hpa II and Msp I restriction enzymes. We found CpG methylation mainly present in enhancer and promoter regions of inactive rRNA gene copies. The methylation of one single Hpa II site, located in the promoter region, showed particularly strong correlation with the transcriptional activity.
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Only a part of rDNA units is transcriptionally active at any time, while the rest, or even the majority of rDNA repeats, are in a repressed state.
“Numerous genetic, microscopic and biochemical studies have demonstrated that only a part of rDNA units is transcriptionally active at any time, while the rest, or even the majority of rDNA repeats, are in a repressed state (6–14).”
From Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon (2022) · cites this paper as [10]
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- Authors
- Stancheva, I., Lucchini, R., Koller, T., & Sogo, J. M.
- Affiliations
- ETH Zurich (CH)
- Corresponding author
- Sogo, J. M.
- ORCID
- Stancheva, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-05-01
- Volume
- 25
- Issue
- 9
- Pages
- 1727-1735
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC146648
- OpenAlex
- W2028863816
- Cited by
- 51
- References
- 39
- Citations by year
- 2025: 1 · 2024: 1 · 2022: 1 · 2021: 2 · 2020: 2 · 2019: 3 · 2018: 1 · 2016: 3 · 2015: 2 · 2014: 1 · 2013: 3 · 2012: 6
- FWCI
- 0.12
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- reroDoc Digital Library (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, other-oa)
- ETH Zürich Research Collection
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- ribosomal DNA, chromatin structure, DNA methylation, CpG methylation, nucleosome packing, rDNA transcription, enhancers, promoter, transcriptional activity, rats
- MeSH terms
- Animals, Cell Line, Cell Nucleus, Chromatin, Cross-Linking Reagents, Enhancer Elements, Genetic, Formaldehyde, Liver, Methylation, Promoter Regions, Genetic, Furocoumarins, RNA, Ribosomal, Deoxyribonuclease EcoRI, Deoxyribonuclease HpaII, Rats
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