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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...

The DNA Helix

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

The DNA Helix

The DNA Helix

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...

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Related Experiment Video

Updated: Apr 4, 2026

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

A Novel Wavelet-Based Approach for Predicting Nucleosome Positions Using DNA Structural Information.

Yanglan Gan, Guobing Zou, Jihong Guan

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|September 11, 2015

Summary

Researchers developed WaveNuc, a new computational method using continuous wavelet transformation to predict nucleosome positioning. WaveNuc accurately identifies both well-positioned and fuzzy nucleosomes by analyzing DNA

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Last Updated: Apr 4, 2026

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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Published on: January 31, 2019

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Area of Science:

Genomics
Structural Biology
Computational Biology

Background:

Nucleosomes are fundamental units of chromatin, crucial for DNA compaction and accessibility in eukaryotes.
Existing computational methods struggle to predict the positions of 'fuzzy' nucleosomes due to their complex configurations.
Understanding nucleosome positioning is vital for regulating gene expression and DNA-related processes.

Purpose of the Study:

To develop a novel computational approach, WaveNuc, for predicting the positions of both well-positioned and fuzzy nucleosomes.
To analyze nucleosome positioning from a unique structural perspective, focusing on DNA propeller twist characteristics.
To improve the accuracy of whole-genome nucleosome positioning prediction, especially for complex configurations.

Main Methods:

Applied continuous wavelet transformation to analyze DNA structural features, specifically propeller twist.
Developed the WaveNuc computational method to infer nucleosome positions based on propeller twist profiles.
Compared WaveNuc's performance against existing methods using real genomic datasets.

Main Results:

Identified distinct propeller twist structural characteristics between well-positioned (sharp peaks) and fuzzy (broader peaks) nucleosomes.
Demonstrated that the propeller twist profile contains valuable information for nucleosome positioning.
WaveNuc accurately resolved complex fuzzy nucleosome configurations, outperforming existing methods.

Conclusions:

The propeller twist profile is a significant indicator for predicting nucleosome positioning.
WaveNuc offers a robust and accurate method for identifying both well-positioned and fuzzy nucleosomes.
This advancement enhances the prediction of nucleosome positioning across the entire genome, particularly for challenging fuzzy nucleosome arrangements.