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Related Concept Videos

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...
Euchromatin01:01

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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...
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,...

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Related Experiment Video

Updated: May 20, 2026

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

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

Published on: January 26, 2018

Chromatin context-dependent deacetylation by the asymmetric Rpd3L.

Heyu Zhao1,2, Huadong Li3, Chi Wang1,4

  • 1State Key Laboratory of Respiratory Disease, Center for Biomedical Digital Science, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.

Nucleic Acids Research
|May 19, 2026
PubMed
Summary
This summary is machine-generated.

The Rpd3 Large (Rpd3L) complex uses a unique structure to bind two nucleosomes, activating its gene silencing function. This substrate-guided mechanism enhances its deacetylase activity for precise chromatin regulation.

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A Method to Study de novo Formation of Chromatin Domains
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A Method to Study de novo Formation of Chromatin Domains

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

Published on: April 11, 2014

Related Experiment Videos

Last Updated: May 20, 2026

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

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

Published on: January 26, 2018

A Method to Study de novo Formation of Chromatin Domains
07:34

A Method to Study de novo Formation of Chromatin Domains

Published on: August 23, 2019

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:

  • Molecular Biology
  • Epigenetics
  • Structural Biology

Background:

  • Gene expression regulation depends on chromatin-associated complexes responding to epigenetic signals.
  • The Sin3 histone deacetylase complex (Rpd3L) dynamically adapts to chromatin states for transcriptional silencing.
  • Mechanisms of Rpd3L catalytic activation within chromatin remain poorly understood.

Purpose of the Study:

  • To elucidate the structural basis of Rpd3L catalytic activation on nucleosome substrates.
  • To uncover the substrate-guided mechanism of Rpd3L allosteric activation.
  • To understand how Rpd3L interprets chromatin context for enzymatic regulation.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine the structure of Rpd3L bound to nucleosomes.
  • Biochemical assays to assess Rpd3L activity and substrate specificity.
  • Mass spectrometry to analyze Rpd3L interactions and modifications.

Main Results:

  • Near-atomic resolution cryo-EM structure of Rpd3L bound to mono- and di-nucleosome substrates.
  • Revealed an asymmetric Rpd3L architecture with dual nucleosome engagement.
  • Demonstrated substrate-guided allosteric activation, enhancing catalytic activity and substrate specificity.

Conclusions:

  • Rpd3L utilizes a hierarchical mechanism involving dual nucleosome binding for activation.
  • The spatial arrangement of nucleosomes dictates Rpd3L enzymatic output at promoter regions.
  • Provides a framework for understanding higher-order chromatin repression by regulatory complexes.