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Related Concept Videos

Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
The Nucleosome01:19

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 Nucleosome02:33

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 Nucleosome02:33

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 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...

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Related Experiment Video

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Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

G+C content dominates intrinsic nucleosome occupancy.

Desiree Tillo1, Timothy R Hughes

  • 1Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. desiree.tillo@utoronto.ca

BMC Bioinformatics
|December 24, 2009
PubMed
Summary
This summary is machine-generated.

A simple model using DNA sequence attributes like G+C content accurately predicts nucleosome occupancy. G+C content is the dominant factor, simplifying our understanding of genome packaging and chromatin structure.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Biophysics

Background:

  • Nucleosome formation is crucial for genome packaging.
  • DNA sequence features like motifs and base content influence nucleosome positioning.
  • Previous models, though accurate, were complex and lacked clarity on key determinants.

Purpose of the Study:

  • To identify key DNA sequence properties that determine intrinsic nucleosome occupancy.
  • To develop a simplified model for predicting nucleosome formation.
  • To understand the influence of nucleotide composition on chromatin structure.

Main Methods:

  • Developed a linear model using 14 DNA sequence attributes.
  • Included G+C content, dinucleotide composition, and 4-bp sequence frequencies.
  • Validated the model for both in vitro and in vivo nucleosome occupancy.

Main Results:

  • A simple model with 14 attributes achieved accuracy comparable to complex models.
  • G+C content and AAAA frequency were the most significant features.
  • G+C content alone explained approximately 50% of nucleosome occupancy variation in vitro.

Conclusions:

  • The findings offer a simplified approach to predict and understand nucleosome occupancy.
  • G+C content's dominance may stem from its role in reducing poly-A stretches and correlating with DNA structural properties.
  • Nucleotide composition variations likely have a broad impact on chromatin structure across eukaryotic genomes.