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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...

Chromatin Position Affects Gene Expression

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area.
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...

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

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 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...

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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

Sequence-dependent nucleosome positioning.

Ho-Ryun Chung¹, Martin Vingron

¹Max-Planck-Institut für molekulare Genetik, Department of Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany. chung@molgen.mpg.de

Journal of Molecular Biology

|December 17, 2008

Summary

This summary is machine-generated.

DNA sequence features significantly influence where nucleosomes form on eukaryotic DNA. Specific patterns of AT and GC base pairs dictate nucleosome positioning in vivo, impacting gene regulation.

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

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

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Area of Science:

Molecular Biology
Genomics
Biophysics

Background:

Eukaryotic DNA is organized into chromatin, with nucleosomes as the basic repeating unit.
Nucleosome positioning is crucial for DNA-dependent processes, making its determinants a key research area.
The DNA sequence is a proposed major factor influencing nucleosome positioning.

Purpose of the Study:

To identify specific DNA sequence features that guide nucleosome formation in vivo.
To analyze a large dataset of nucleosomal DNA sequences for positioning determinants.
To develop a predictive model for nucleosome formation based on sequence characteristics.

Main Methods:

Analysis of over 860,000 nucleosomal DNA sequences.
Identification of periodic and oscillating base pair enrichments (AT and GC).
Development and evaluation of a sequence model for nucleosome formation.

Main Results:

Periodic AT enrichment and out-of-phase oscillating GC enrichment are key determinants.
Overall GC base pair preference also plays a significant role.
A model incorporating both AT and GC signals achieved maximal genome-wide predictive performance.

Conclusions:

DNA sequence composition is a major determinant of nucleosome positioning in vivo.
The energetic cost of DNA deformation around histones may explain GC preference.
The developed sequence model offers superior predictive power for nucleosome formation.