ArticleNucleic acids research2013
Effects of DNA methylation on nucleosome stability.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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.
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Who cites it
52 citing papers in PubMed, 98 citations in OpenAlex.
- Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Review
- IMPACTS OF DNA METHYLATION ON H2A.Z DEPOSITION AND NUCLEOSOME STABILITY.bioRxiv : the preprint server for biology · 2025Article
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation.Nature communications · 2024Article
- DNA Methylation in the Adaptive Response to Exercise.Sports medicine (Auckland, N.Z.) · 2024Review
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.Nature communications · 2024Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.bioRxiv : the preprint server for biology · 2024Article
- Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer.Epigenetics & chromatin · 2023Article
- DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation.Nature communications · 2023Article
- Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors.International journal of molecular sciences · 2022Review
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts.PLoS computational biology · 2022Article
- Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules.Molecular biotechnology · 2021Review
- Prevention of Chromatin Destabilization by FACT Is Crucial for Malignant Transformation.iScience · 2020Article
- Integrative computational epigenomics to build data-driven gene regulation hypotheses.GigaScience · 2020Article
- A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer.PloS one · 2020Article
- Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted nucleosome reconstitution experiments in conjunction with high-throughput sequencing on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin.
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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.