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Related Concept Videos

Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

7.6K
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...
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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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Chromatin Packaging02:21

Chromatin Packaging

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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.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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Author Spotlight: Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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Computational strategies to address chromatin structure problems.

Ognjen Perišić1, Tamar Schlick

  • 1Big Blue Genomics, 11000 Belgrade, Serbia.

Physical Biology
|June 28, 2016
PubMed
Summary

Chromatin fiber structure is dynamic and diverse, impacting gene expression. Computational modeling complements experimental methods to better understand this complex biological polymer and its epigenetic regulation.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • Gene expression relies on complex chromatin structures, including nucleosomes and chromatin fibers.
  • The dynamic and diverse nature of chromatin fiber structure, essential for DNA packing and gene accessibility, remains incompletely understood.
  • Existing experimental techniques offer insights but have limitations in resolution and scope for compact chromatin structures within cells.

Purpose of the Study:

  • To review current approaches in understanding chromatin structure, with a focus on computational modeling.
  • To highlight the complementary role of modeling techniques alongside experimental methods.
  • To illustrate how these approaches address key biological questions, particularly epigenetic modulation of chromatin.

Main Methods:

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

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  • Review of experimental techniques (in vitro biochemistry, in vivo imaging, chromosome capture technology).
  • Discussion of computational modeling approaches, including molecular dynamics and coarse-grained methods.
  • Integration of experimental and computational findings to interpret chromatin dynamics.

Main Results:

  • Chromatin fibers exhibit significant structural diversity, influencing DNA packing and accessibility.
  • Experimental methods provide valuable data but are limited in resolving compact chromatin structures.
  • Computational modeling is essential for analyzing the behavior of large, flexible polymers like chromatin fibers.

Conclusions:

  • A combination of experimental and computational modeling techniques is crucial for a comprehensive understanding of chromatin structure and dynamics.
  • Understanding chromatin's dynamic behavior is key to interpreting gene expression patterns across different tissues and organisms.
  • Computational approaches, especially when focused on epigenetic modulation, offer powerful tools to complement experimental data in chromatin research.