ArticleBiophysical journal2012
The effect of DNA CpG methylation on the dynamic conformation of a nucleosome.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 63 citations in OpenAlex.
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- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- IMPACTS OF DNA METHYLATION ON H2A.Z DEPOSITION AND NUCLEOSOME STABILITY.bioRxiv : the preprint server for biology · 2025Article
- Fundamentals of DNA methylation in development.Pediatric research · 2025Review
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- Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.Polymers · 2023Review
- Epigenetics of Thymic Epithelial Tumors.Cancers · 2023Review
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- Enhanced nucleosome assembly at CpG sites containing an extended 5-methylcytosine analogue.Nucleic acids research · 2022Article
- Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction.Nature communications · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- The Relevance of Gender in Tumor-Influencing Epigenetic Traits.Epigenomes · 2019Review
- Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker.Nature communications · 2018Article
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- Optical Trapping Nanometry of Hypermethylated CPG-Island DNA.Biophysical journal · 2017Article
- Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability.Scientific reports · 2016Article
- Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.Open biology · 2015Article
- Computational study of remodeling in a nucleosomal array.The European physical journal. E, Soft matter · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an important epigenetic mark that is known to induce chromatin condensation and gene silencing. We used a time-domain fluorescence lifetime measurement to quantify the effects of DNA hypermethylation on the conformation and dynamics of a nucleosome. Nucleosomes reconstituted on an unmethylated and a methylated DNA both exhibit dynamic conformations under physiological conditions. The DNA end breathing motion and the H2A-H2B dimer destabilization dominate the dynamic behavior of nucleosomes at low to medium ionic strength. Extensive DNA CpG methylation, surprisingly, does not help to restrain the DNA breathing motion, but facilitates the formation of a more open nucleosome conformation. The presence of the divalent cation, Mg(2+), essential for chromatin compaction, and the methyl donor molecule SAM, required for DNA methyltransferase reaction, facilitate the compaction of both types of nucleosomes. The difference between the unmethylated and the methylated nucleosome persists within a broad range of salt concentrations, but vanishes under high magnesium concentrations. Reduced DNA backbone rigidity due to the presence of methyl groups is believed to contribute to the observed structural and dynamic differences. The observation of this study suggests that DNA methylation alone does not compact chromatin at the nucleosomal level and provides molecular details to understand the regulatory role of DNA methylation in gene expression.
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