Cited by 51Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromosomal and Genetic Variations

Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking

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Stancheva, I., Lucchini, R., Koller, T., Sogo, J. M.·1997·Nucleic Acids Research

Abstract

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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  1. Wisendanger,B. (1995) Dissertation, ETH-Zurich.
  2. Solomon,M.J. and Varshavsky,A. (1985) Proc. Natl. Acad. Sci. USA, 82, 6470-6474.
  3. Jost,J.P. and Hofsteenge,J. (1992) Proc. Natl. Acad. Sci. USA, 89, 9499-9503.

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Authors
Stancheva, I., Lucchini, R., Koller, T., & Sogo, J. M.
Affiliations
ETH Zurich (CH)
Corresponding author
Sogo, J. M.
Venue
Nucleic Acids Research
Published
1997-05-01
Volume
25
Issue
9
Pages
1727-1735
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
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
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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