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The Nucleosome

The Nucleosome

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...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to 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.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to 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.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

The Nucleosome Core Particle

The Nucleosome Core Particle

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...

The Nucleosome Core Particle

The Nucleosome Core Particle

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.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...

Nucleosome Remodeling

Nucleosome Remodeling

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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Related Experiment Video

Updated: Jun 21, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Stable G-quadruplexes are found outside nucleosome-bound regions.

Han Min Wong¹, Julian Leon Huppert

¹Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge, UK.

Molecular Biosystems

|July 9, 2009

Summary

Regulatory G-quadruplexes form in vivo within nucleosome-depleted regions. This finding clarifies how these unusual DNA structures, important for gene regulation, can assemble within the cell.

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Published on: May 12, 2023

Area of Science:

Molecular Biology
Genetics
Epigenetics

Background:

Unusual DNA structures like G-quadruplexes form in vivo and regulate biological processes.
DNA is typically packaged into chromatin by wrapping around histone proteins, posing a challenge for G-quadruplex formation.
The precise location and formation mechanism of G-quadruplexes within chromatin remain incompletely understood.

Purpose of the Study:

To investigate the relationship between G-quadruplex formation and nucleosome occupancy in vivo.
To determine if G-quadruplexes preferentially form in specific chromatin regions.
To elucidate the accessibility of G-quadruplex forming sites within the cellular environment.

Main Methods:

Analysis of G-quadruplex locations relative to nucleosome-bound regions in Caenorhabditis elegans and human genomes.
Computational modeling to assess the stability and formation potential of G-quadruplexes in different chromatin contexts.

Main Results:

Regulatory G-quadruplexes upstream of transcription start sites are located in nucleosome-depleted regions.
Stable G-quadruplexes are generally found outside of nucleosome-bound DNA in both model organisms.
Nucleosome depletion facilitates the in vivo formation of stable G-quadruplex structures.

Conclusions:

G-quadruplex formation in vivo is spatially regulated by chromatin structure.
Nucleosome-depleted regions provide accessible sites for G-quadruplex assembly and function.
This spatial organization is crucial for the regulatory roles of G-quadruplexes in gene expression.