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Related Concept Videos

Nucleosome Remodeling02:54

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 Particle02:10

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 Particle01:12

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 Position Affects Gene Expression02:35

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...
Chromatin Packaging02:21

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.
Chromatin Packaging01:32

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...

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Related Experiment Video

Updated: May 9, 2026

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
10:40

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

Published on: September 10, 2013

Modeling nucleosome position distributions from experimental nucleosome positioning maps.

Robert Schöpflin1, Vladimir B Teif, Oliver Müller

  • 1Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.

Bioinformatics (Oxford, England)
|July 13, 2013
PubMed
Summary

This study introduces a new computational method to analyze nucleosome positioning data, revealing specific DNA configurations from population averages. This helps understand nucleosome dynamics and genome organization.

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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

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Related Experiment Videos

Last Updated: May 9, 2026

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
10:40

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

Published on: September 10, 2013

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

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

Published on: September 6, 2024

Area of Science:

  • Genomics
  • Computational Biology
  • Molecular Biology

Background:

  • Nucleosome occupancy maps are population averages, obscuring individual DNA configurations.
  • Understanding nucleosome organization and translocation requires analyzing specific conformations.

Purpose of the Study:

  • To develop a method for retrieving specific nucleosome configurations from population-averaged data.
  • To analyze nucleosome positioning at regulatory genomic elements.

Main Methods:

  • A novel method combining binary-variable analysis and Monte Carlo simulation with simulated annealing.
  • Application to experimental nucleosome positioning data.

Main Results:

  • Identified non-overlapping nucleosome configurations from heterogeneous cell populations.
  • Compared nucleosome positioning at transcription factor binding sites across different mouse cell types.
  • Modeled nucleosome translocations and generated configurations for spatial folding simulations.

Conclusions:

  • The developed method successfully deconvolutes complex nucleosome positioning patterns.
  • Enables detailed study of nucleosome dynamics and genome organization at single-cell resolution.