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Related Concept Videos

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.
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The Nucleosome02:33

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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.
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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 process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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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.
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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Nucleosomes shape DNA polymorphism and divergence.

Sasha A Langley1, Gary H Karpen2, Charles H Langley3

  • 1Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

Plos Genetics
|July 4, 2014
PubMed
Summary
This summary is machine-generated.

Natural selection shapes genome evolution by favoring specific DNA sequences within nucleosomes. These sequence preferences influence genomic divergence and polymorphism, particularly in introns, revealing how chromatin structure impacts DNA sequence changes.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Eukaryotic DNA is packaged into nucleosomes, forming higher-order chromatin structures.
  • Nucleosomal DNA sequences show periodic variations in dinucleotide frequencies (AA, TT, GC).
  • These periodicities are linked to DNA curvature and histone-DNA interactions.

Purpose of the Study:

  • To investigate if histone core's DNA sequence preferences drive natural selection on genomic divergence and polymorphism.
  • To examine the interplay between chromatin organization and genome evolution.

Main Methods:

  • Isolation of nucleosomal DNA sequences from Drosophila melanogaster embryos.
  • Analysis of genomic variation (divergence and Single Nucleotide Polymorphism - SNP) within and between species.
  • Examination of dinucleotide frequencies and their periodicities across nucleosomal and intergenic regions.

Main Results:

  • Divergence in D. melanogaster shows periodicity in nucleosome regions, with base changes favoring preferred nucleotides.
  • SNP frequency spectra exhibit striking periodicities in nucleosomal regions, mirroring divergence patterns.
  • Preferred alleles are at higher frequencies in natural populations, indicating natural selection.
  • Patterns are stronger in introns than intergenic regions, suggesting stronger selection in transcribed areas.
  • Large-scale periodicity (∼180 bp) of AA/TT dinucleotides linked to nucleosome occupancy, with GC peaking in linker regions.

Conclusions:

  • Nucleosome-associated sequence periodicities are under selective pressure.
  • Structural interactions between nucleosomes and DNA sequence significantly shape sequence evolution.
  • Natural selection plays a key role in generating and maintaining these super-nucleosomal patterns, especially within introns.