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Related Concept Videos

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...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

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Related Experiment Video

Updated: May 26, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method
11:01

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

The Rpd3 core complex is a chromatin stabilization module.

Xiao-Fen Chen1, Benjamin Kuryan, Tasuku Kitada

  • 1Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.

Current Biology : CB
|December 20, 2011
PubMed
Summary
This summary is machine-generated.

The Rpd3 histone deacetylase (HDAC) complex has a novel nucleosome stabilization function, independent of its deacetylase activity. This function contributes to transcriptional repression by maintaining chromatin stability, particularly at specific genes.

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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

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Last Updated: May 26, 2026

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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
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Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Chromatin Biology

Background:

  • The S. cerevisiae Rpd3 large (Rpd3L) and small (Rpd3S) histone deacetylase (HDAC) complexes are key regulators of transcriptional repression in eukaryotes.
  • Current models propose Rpd3 complexes repress transcription by deacetylating chromatin, limiting transcription factor access.

Purpose of the Study:

  • To investigate the histone deacetylase (HDAC)-independent functions of Rpd3 complexes.
  • To explore the role of Rpd3 in chromatin stabilization and its contribution to transcriptional repression.

Main Methods:

  • Biochemical assays to identify HDAC-independent activities.
  • Investigating Rpd3 core complex (Sin3, Rpd3, Ume1) function.
  • Genomic analysis of histone H3 density in Rpd3 deletion and catalytic mutants.

Main Results:

  • Rpd3 complexes possess chaperone activity promoting histone deposition and prevent nucleosome eviction.
  • These HDAC-independent activities inhibit RNA Polymerase II transcription on nucleosomal templates.
  • Rpd3 deletion mutants show reduced H3 density at promoters, partially restored in catalytic mutants, especially on RSC-enriched genes.

Conclusions:

  • The Rpd3 core complex contributes to transcriptional repression through a novel nucleosome stabilization function.
  • This stabilization activity is independent of its deacetylase function and impacts chromatin structure in vivo.
  • Rpd3's role in chromatin stabilization offers a new perspective on eukaryotic transcriptional repression mechanisms.