ArticlePLoS computational biology2013
Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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
33 citing papers in PubMed, 58 citations in OpenAlex.
- Multiscale physical effects of CpG methylation on DNA mechanics, nucleosome wrapping, and chromatin condensates.EMBO reports · 2026Article
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Hydropathy Landscapes of Histone-DNA Interactions in Chromatin Building Blocks.The journal of physical chemistry. B · 2026Article
- Unraveling the interplay of DNA methylation and chromosome organization.Biochemical Society transactions · 2025Review
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Charting epimutation dynamics in human hematopoietic differentiation.Blood science (Baltimore, Md.) · 2024Article
- Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.Polymers · 2023Review
- The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation.Frontiers in molecular biosciences · 2023Review
- Cytosine methylation regulates DNA bendability depending on the curvature.Chemical science · 2022Article
- Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health.International journal of molecular sciences · 2022Review
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Impact of DNA methylation on 3D genome structure.Nature communications · 2021Article
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region.Nucleic acids research · 2019Article
- Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts.International journal of molecular sciences · 2019Article
- Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Article
- How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study.Journal of molecular modeling · 2018Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling.
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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.