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Related Concept Videos

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 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...
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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

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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

Predicting human nucleosome occupancy from primary sequence.

Shobhit Gupta1, Jonathan Dennis, Robert E Thurman

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

Plos Computational Biology
|August 30, 2008
PubMed
Summary
This summary is machine-generated.

Sequence-based models accurately predict nucleosome positioning in human and yeast chromatin, revealing shared mechanisms. Nucleosome-free regions and specific DNA sequences influence nucleosome organization in eukaryotes.

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Published on: December 12, 2017

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Nucleosomes are key structural units of eukaryotic genomes.
  • Micrococcal nuclease (MNase) is used to map nucleosome organization.
  • Previous studies in yeast identified sequence-directed nucleosome positioning.

Purpose of the Study:

  • To apply computational models of sequence-directed nucleosome positioning to human chromatin.
  • To investigate shared mechanisms of nucleosome occupancy between yeast and humans.
  • To identify sequence features of nucleosome-forming and nucleosome-disfavoring regions.

Main Methods:

  • Training computational models on yeast and human nucleosome positioning data.
  • Analyzing MNase-digested chromatin samples (weak vs. heavy).
  • Applying classifiers to human ENCODE regions to identify sequence characteristics.

Main Results:

  • Human and yeast models show strong correlation, indicating conserved sequence-based positioning.
  • Complementary classifiers identify nucleosome-forming and nucleosome-free sequences.
  • Nucleosome-disfavoring sequences have dinucleotide repeats; nucleosome-forming sequences have GC periodicity.
  • Nucleosome phasing is often predicted flanking nucleosome-free regions.

Conclusions:

  • Sequence-based mechanisms for nucleosome positioning are conserved across species.
  • Nucleosome organization is influenced by sequence composition and periodicity.
  • Boundary-event-driven mechanisms and statistical positioning theory are supported by the findings.