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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...

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...

Chromatin Packaging

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 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 26, 2026

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

Published on: September 6, 2024

Nucleosome DNA bendability matrix (C. elegans).

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.

Journal of Biomolecular Structure & Dynamics

|December 26, 2008

Summary

This summary is machine-generated.

Researchers identified DNA sequence patterns that influence nucleosome positioning in C. elegans. This nucleosome DNA bendability matrix reveals specific dinucleotide preferences crucial for genome organization.

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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

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In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Nucleosomes are fundamental units of DNA packaging in eukaryotes.
Understanding DNA sequence preferences for nucleosome formation is key to deciphering genome organization.
Previous studies have explored nucleosome positioning, but a comprehensive bendability matrix for C. elegans was lacking.

Purpose of the Study:

To derive a nucleosome DNA bendability matrix for C. elegans.
To identify positional preferences of dinucleotides within the nucleosome DNA repeat.
To establish a basis for sequence-directed mapping of nucleosome positions.

Main Methods:

Application of an original signal extraction procedure to 146 C. elegans nucleosome core DNA sequences.
Calculation of positional preferences for dinucleotides within the 10.4 base nucleosome DNA repeat.
Derivation of a 16x10 nucleosome DNA bendability matrix and a "consensus" repeat pattern.

Main Results:

A nucleosome DNA bendability matrix for C. elegans was successfully derived.
The pattern showed that dinucleotides AT and CG have the strongest affinity at specific positions, separated by 5 bases.
All six chromosomes of C. elegans were found to conform to this derived bendability pattern.

Conclusions:

The derived nucleosome DNA bendability matrix provides a foundation for sequence-directed nucleosome mapping in C. elegans.
This matrix represents the first complete bendability pattern available and can be used for iterative calculations of species-specific matrices.
The findings offer insights into the sequence-directed organization of the C. elegans genome at the nucleosome level.