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Related Concept Videos

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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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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Epigenetic Regulation01:46

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Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Phase II Reactions: Methylation Reactions01:17

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Methylation is a phase II biotransformation process involving the attachment of a methyl group to a substrate. Enzymes known as methyltransferases orchestrate this reaction.
The mechanism of methylation unfolds in two stages. The first stage sees a methyltransferase enzyme facilitating the transfer of a methyl group from S-adenosylmethionine (SAM) to the substrate, forming S-adenosylhomocysteine (SAH). The second stage involves further metabolism of SAH into homocysteine, which can be recycled...
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Histone Modification02:32

Histone Modification

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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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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Updated: May 1, 2026

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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Methylome diversification through changes in DNA methyltransferase sequence specificity.

Yoshikazu Furuta1, Hiroe Namba-Fukuyo2, Tomoko F Shibata3

  • 1Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan; Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.

Plos Genetics
|April 12, 2014
PubMed
Summary
This summary is machine-generated.

Helicobacter pylori DNA methylation patterns vary significantly between strains. These epigenetic changes influence gene expression and genome evolution, offering potential targets for selection.

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Targeted DNA Methylation Analysis by Next-generation Sequencing
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Targeted DNA Methylation Analysis by Next-generation Sequencing

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Area of Science:

  • Microbiology
  • Epigenetics
  • Genomics

Background:

  • DNA methylation is a key epigenetic mechanism influencing gene expression and genome stability.
  • Helicobacter pylori, a pathogen, possesses numerous DNA methyltransferase genes with strain-specific variations.
  • Domain movement in methyltransferases is a proposed mechanism for altering DNA sequence specificity.

Purpose of the Study:

  • To investigate the methylome variability in closely related H. pylori strains.
  • To identify DNA methylation motifs and link them to specific methyltransferase domains.
  • To explore the functional impact of DNA methylation on gene expression and evolution.

Main Methods:

  • Single-molecule real-time sequencing to detect N6-methyladenines and N4-methylcytosines.
  • Comparative analysis of methylomes across multiple H. pylori strains.
  • Identification of DNA sequence motifs and assignment to methyltransferase homology groups.
  • Gene knockout experiments to assess the impact on the transcriptome.

Main Results:

  • The methylome of H. pylori is highly variable among closely related strains.
  • Specific hypermethylated regions were identified, including within the rpoB gene.
  • DNA sequence motifs for methylation were mapped to target recognition domains of Type I restriction-modification systems.
  • Disruption of a Type I specificity gene resulted in significant transcriptome alterations.

Conclusions:

  • The findings support domain movement as a mechanism for DNA methyltransferase sequence-specificity evolution.
  • DNA methylation in H. pylori plays a role in gene expression regulation.
  • Changes in the methylome can drive transcriptome and phenotypic evolution, presenting targets for selection.