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Related Concept Videos

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...
Nucleosome Remodeling02:54

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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.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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...
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 Packaging02:21

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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
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Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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Cracking the chromatin code: precise rule of nucleosome positioning.

Edward N Trifonov1

  • 1Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel. trifonov@research.haifa.ac.il

Physics of Life Reviews
|February 8, 2011
PubMed
Summary
This summary is machine-generated.

This study explores DNA packaging in eukaryotic cells, focusing on physical properties and signal processing challenges. It introduces a DNA bendability matrix and a sequence motif representing the "chromatin code" for nucleosome positioning.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • DNA packaging in eukaryotic cells involves complex physical and informational instructions encoded within DNA sequences.
  • Nucleosome positioning signals present significant signal processing challenges due to low signal-to-noise ratio and high degeneracy.
  • Understanding DNA's physical properties is crucial for deciphering its packaging mechanisms.

Purpose of the Study:

  • To review the physical aspects of DNA packaging, emphasizing the role of DNA deformational properties in nucleosome positioning.
  • To derive a DNA bendability matrix that dictates dinucleotide positioning for efficient DNA bending into nucleosomes.
  • To present a simplified DNA deformability sequence pattern derived from the bendability matrix.

Main Methods:

  • Analysis of physical rather than purely biological terms for DNA packaging.
  • Focus on signal processing challenges inherent in DNA sequence information.
  • Development and application of three distinct approaches to derive DNA deformability patterns.

Main Results:

  • Identification of significant challenges in signal processing for nucleosome positioning.
  • Derivation of a DNA bendability matrix to guide dinucleotide placement.
  • Convergence of three approaches to a unique DNA sequence motif (CGRAAATTTYCG) representing the chromatin code.

Conclusions:

  • The deformational properties of DNA play a leading role in nucleosome positioning.
  • A specific DNA sequence motif, termed the 'chromatin code', governs DNA bending and packaging.
  • This work provides a physical framework for understanding DNA organization within eukaryotic cells.