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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...

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...

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...

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...

Chromatin Packaging

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: Jun 13, 2026

Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy

Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy

Published on: November 11, 2025

Single-base resolution nucleosome mapping on DNA sequences.

I Gabdank¹, D Barash, E N Trifonov

¹Department of Computer Science, Ben Gurion University of the Negev, P.O.B 653 Be'er Sheva 84105, Israel. gabdank@cs.bgu.ac.il

Journal of Biomolecular Structure & Dynamics

|May 19, 2010

Summary

This summary is machine-generated.

Researchers created a DNA bendability matrix from C. elegans data to map nucleosomes on DNA sequences. This computational tool accurately predicts nucleosome positions with +/-1 base uncertainty.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Nucleosomes are fundamental units of DNA organization in eukaryotes.
Understanding DNA bendability is crucial for predicting nucleosome positioning.
Accurate mapping of nucleosomes is essential for studying gene regulation and DNA replication.

Purpose of the Study:

To develop a computational method for sequence-directed nucleosome mapping.
To construct a comprehensive nucleosome DNA bendability matrix.
To provide a tool for predicting nucleosome positions on any DNA sequence.

Main Methods:

Extraction of nucleosome DNA bendability patterns from a large C. elegans database.
Construction of a full-length (116 dinucleotide positions) nucleosome DNA bendability matrix.
Development and testing of a computer program for nucleosome mapping using the matrix.

Main Results:

A robust nucleosome DNA bendability matrix was successfully created.
The computer program accurately predicted known nucleosome positions.
The computational mapping demonstrated an uncertainty of +/-1 base.

Conclusions:

The developed bendability matrix and associated program enable accurate, sequence-directed nucleosome mapping.
The tool is publicly accessible via a server for broad application.
This method advances the study of DNA organization and its functional implications.