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Related Concept Videos

Epigenetic Regulation01:37

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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Related Experiment Video

Updated: Jan 17, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.

Shinya Yoshida1, Ikuo Uchiyama2, Masaki Fukuyo3

  • 1Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.

DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
|September 19, 2025
PubMed
Summary

This study introduces a new framework for analyzing molecular evolution, incorporating DNA methylation alongside nucleotide changes. It reveals high demethylation rates and insights into methylation patterns in Helicobacter pylori.

Keywords:
Helicobacter pyloriDNA methylationepigenome evolutionsubstitution rate

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Area of Science:

  • Molecular Biology
  • Genomics
  • Evolutionary Biology

Background:

  • Genomic DNA is typically represented by four bases (ATGC).
  • Epigenetic modifications like DNA methylation are crucial and detectable with advanced sequencing.
  • Understanding epigenetic modifications is key to a comprehensive view of genome evolution.

Purpose of the Study:

  • To develop an integrated framework for analyzing the molecular evolution of nucleotide substitution and DNA base methylation/demethylation.
  • To expand the nucleotide code to include methylated bases for evolutionary analysis.
  • To investigate methylation and substitution rates in Helicobacter pylori.

Main Methods:

  • Developed an expanded nucleotide code incorporating methylated bases.
  • Analyzed substitution rates between unmethylated and methylated bases.
  • Utilized Helicobacter pylori methylomes as a model system.
  • Compared methylation and demethylation frequencies with base substitution rates.

Main Results:

  • Demethylation rates were found to be remarkably high.
  • Methylation rates were comparable to substitution rates between unmethylated bases.
  • Genes for ribosomal proteins showed high methylation/demethylation frequencies, unlike DNA methyltransferase genes.

Conclusions:

  • This study pioneers molecular evolutionary epigenomics.
  • The findings provide a foundation for understanding epigenome evolution.
  • The integrated framework offers new insights into the dynamics of DNA methylation in evolution.