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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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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 Packaging01:32

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, 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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Histone Variants at the Centromere02:30

Histone Variants at the Centromere

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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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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Related Experiment Video

Updated: Nov 4, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Hi-CO: 3D genome structure analysis with nucleosome resolution.

Masae Ohno1,2, Tadashi Ando3,4, David G Priest1,5

  • 1Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.

Nature Protocols
|May 29, 2021
PubMed
Summary

We developed high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology to map 3D nucleosome positions and orientations. This method reveals genome organization at the nucleosome level for a deeper understanding of genome function.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Biophysics

Background:

  • Nucleosomes are fundamental genome organizational units.
  • Nucleosome folding impacts genome functions and protein interactions.
  • Existing methods lack nucleosome-level 3D spatial resolution.

Purpose of the Study:

  • To introduce high-throughput chromosome conformation capture with nucleosome orientation (Hi-CO) technology.
  • To enable 3D mapping of nucleosome positions and orientations genome-wide.
  • To provide high-resolution insights into genome organization.

Main Methods:

  • Developed an improved high-throughput chromosome conformation capture (Hi-C) experimental procedure for nucleosome proximity analysis.
  • Utilized micrococcal nuclease digestion and ligation of DNA entry/exit points.
  • Employed simulated annealing-molecular dynamics for computational 3D modeling.

Main Results:

  • Achieved proximity analysis at individual nucleosome loci, surpassing conventional Hi-C resolution.
  • Successfully excluded unwanted ligation products for cleaner data.
  • Mapped 66,360 nucleosome loci in Saccharomyces cerevisiae at 6.8 nm resolution.

Conclusions:

  • Hi-CO technology provides unprecedented 3D resolution of nucleosome organization.
  • This advancement facilitates detailed studies of genome folding and function.
  • The technique offers a powerful new tool for chromatin biology research.