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Related Concept Videos

The Nucleosome Core Particle01:12

The Nucleosome Core Particle

915
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
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The Nucleosome01:19

The Nucleosome

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
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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.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
13.3K
Nucleosome Remodeling02:54

Nucleosome Remodeling

9.1K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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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Heterochromatin02:38

Heterochromatin

12.8K
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...
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Related Experiment Video

Updated: Jul 4, 2025

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
10:40

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Published on: September 10, 2013

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Nucleosome conformation dictates the histone code.

Matthew R Marunde1, Harrison A Fuchs2,3, Jonathan M Burg1

  • 1EpiCypher, Durham, United States.

Elife
|February 6, 2024
PubMed
Summary
This summary is machine-generated.

Histone post-translational modifications (PTMs) form codes that regulate gene expression. Our study reveals these codes depend on nucleosome context, not just isolated peptides, refining the histone code concept.

Keywords:
PHD fingerbromodomainchromosomesgene expressionhistone PTMhistone codehumanmolecular biophysicsnucleosomestructural biology

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Area of Science:

  • Epigenetics and Molecular Biology
  • Chromatin Biology
  • Gene Regulation

Background:

  • Histone post-translational modifications (PTMs) are crucial for chromatin regulation.
  • The 'histone code' hypothesis suggests PTMs are recognized by protein domains (reader domains) on chromatin-associated proteins (CAPs).
  • Previous studies often used simplified models like isolated reader domains and histone peptides.

Purpose of the Study:

  • To investigate the role of nucleosome context in the interaction between reader domains and histone PTMs.
  • To determine if the specificity of the BPTF tandem reader (PHD finger and bromodomain) for histone PTMs is influenced by the nucleosome structure.
  • To refine the 'histone code' concept by considering higher-order chromatin factors.

Main Methods:

  • In vitro binding assays using isolated reader domains and histone peptides.
  • Nucleosome reconstitution and biochemical assays to assess BPTF tandem reader binding specificity.
  • Cellular context experiments to validate in vitro findings.

Main Results:

  • The interaction of the BPTF PHD finger and bromodomain with histone PTMs is dependent on the nucleosome context.
  • The tandem reader selectively binds to nucleosomes with specific combinations of PTMs (H3K4me3 with H3K14ac or H3K18ac).
  • This nucleosome-specific binding is not predictable from isolated peptide assays and is recapitulated in cells.

Conclusions:

  • The 'histone code' needs refinement to incorporate nucleosome context and higher-order chromatin factors.
  • Histone tail accessibility and reader domain binding potential are influenced by the nucleosome structure.
  • Future research should interrogate histone codes at the nucleosome level for a comprehensive understanding of epigenetic regulation.