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Related Concept Videos

Histone Modification02:32

Histone Modification

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.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Histone Modification02:32

Histone Modification

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.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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.
Writers
The writer is an enzyme that can...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...

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Related Experiment Video

Updated: May 25, 2026

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

Hydroxylation mediates chromatin demethylation.

Yu-ichi Tsukada1

  • 1Division of Molecular Immunology, Research Center for Infectious Diseases, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan. ytsukada@bioreg.kyushu-u.ac.jp

Journal of Biochemistry
|January 17, 2012
PubMed
Summary

Chromatin methylation, once thought stable, is dynamically regulated by hydroxylation. This process, crucial for cell fate, impacts human diseases and regenerative medicine.

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
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The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Published on: April 11, 2014

Area of Science:

  • Epigenetics and Molecular Biology
  • Biochemistry and Enzymology

Background:

  • DNA and histone methylation are critical epigenetic marks involved in fundamental biological processes.
  • Historically, chromatin methylation was considered a static and stable modification.
  • Emerging evidence reveals dynamic regulation of chromatin methylation through demethylation pathways.

Purpose of the Study:

  • To highlight the dynamic nature of chromatin methylation.
  • To elucidate the role of hydroxylation in demethylating DNA and histones.
  • To underscore the implications of dynamic chromatin methylation for human health and regenerative medicine.

Main Methods:

  • Review of biochemical mechanisms involved in chromatin demethylation.
  • Focus on hydroxylation reactions catalyzed by Fe(II) and α-ketoglutarate (KG)-dependent hydroxylase/dioxygenase.
  • Analysis of the role of these enzymes in regulating epigenetic marks.

Main Results:

  • Hydroxylation is identified as a key chemical reaction mediating the demethylation of both DNA and histones.
  • Fe(II) and α-ketoglutarate (KG)-dependent hydroxylase/dioxygenase enzymes catalyze this crucial demethylation process.
  • This enzymatic activity demonstrates that chromatin methylation is a more dynamically regulated process than previously understood.

Conclusions:

  • Chromatin methylation is a dynamic epigenetic mark, not static, with active demethylation mechanisms.
  • Hydroxylation by specific dioxygenases is a key pathway for reversing methylation marks.
  • Understanding these dynamic epigenetic regulations is vital for advancing human disease research and regenerative medicine.