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Related Concept Videos

Nucleosome Remodeling02:54

Nucleosome Remodeling

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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.
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The Nucleosome01:19

The Nucleosome

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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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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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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...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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Chromatin Packaging02:21

Chromatin Packaging

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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...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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. 
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The 3-dimensional positioning of chromatin in the nucleus influences the...
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Related Experiment Video

Updated: Oct 17, 2025

Associated Chromosome Trap for Identifying Long-range DNA Interactions
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Associated Chromosome Trap for Identifying Long-range DNA Interactions

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iNucs: inter-nucleosome interactions.

Mehrdad Oveisi1, Manu Shukla2, Nogayhan Seymen1

  • 1Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London SE5 8AF, UK.

Bioinformatics (Oxford, England)
|October 8, 2021
PubMed
Summary
This summary is machine-generated.

Understanding nucleosome-nucleosome interactions is key for chromatin organization. We created iNucs, a Python tool to compute and visualize these interactions, addressing the lack of public computational resources.

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

  • * Computational biology
  • * Bioinformatics
  • * Molecular biology

Background:

  • * Understanding chromatin organization is crucial for deciphering cellular processes.
  • * Nucleosome-nucleosome interactions play a key role in the mesoscale description of chromatin.
  • * Current computational tools for analyzing these interactions are not publicly available, hindering research.

Purpose of the Study:

  • * To develop a user-friendly and efficient computational tool for analyzing nucleosome-nucleosome interactions.
  • * To provide a publicly accessible resource for researchers studying chromatin organization.

Main Methods:

  • * Development of a Python-based bioinformatics tool named iNucs.
  • * Utilization of standard pairs format input generated from pairtools.
  • * Implementation of computational methods to compute and visualize nucleosome-resolved interactions.

Main Results:

  • * iNucs successfully computes and visualizes nucleosome-nucleosome interactions.
  • * The tool is user-friendly and efficient, making complex analyses accessible.
  • * The software is publicly available, promoting wider adoption and research.

Conclusions:

  • * iNucs addresses the unmet need for accessible computational tools in chromatin organization research.
  • * The developed tool facilitates the study of nucleosome-nucleosome interactions.
  • * iNucs is expected to advance the mesoscale description of chromatin organization.