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Related Concept Videos

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 Position Affects Gene Expression02:35

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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)
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Spreading of Chromatin Modifications02:25

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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Inheritance of Chromatin Structures03:17

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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CRISPR-Mediated Reorganization of Chromatin Loop Structure
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Chromatin Loop Extrusion and Chromatin Unknotting.

Dusan Racko1,2,3, Fabrizio Benedetti4,5, Dimos Goundaroulis6,7

  • 1Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland. Dusan.Racko@unil.ch.

Polymers
|April 10, 2019
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Summary

Interphase chromosomes avoid knots, defying expectations. Molecular dynamics simulations reveal that chromatin loop extrusion actively unknots and decatenates DNA fibers in a crowded cellular environment.

Keywords:
DNA knotsDNA topoisomerasesbiopolymerschromatinchromatin loop extrusionchromosomescohesin

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Area of Science:

  • Molecular Biology
  • Genetics
  • Computational Biology

Background:

  • Interphase chromosomes are surprisingly unknotted, despite the presence of DNA topoisomerases that could lead to topological equilibrium and knot formation.
  • The observed contact probability decay in interphase chromosomes resembles a 'crumpled globule' state, suggesting an active knot-removal mechanism.

Purpose of the Study:

  • To investigate whether chromatin loop extrusion can actively unknot and decatenate chromatin fibers.
  • To understand the role of chromatin loop extrusion in maintaining the unknotted state of interphase chromosomes.

Main Methods:

  • Coarse-grained molecular dynamics simulations were employed.
  • Simulations focused on the process of chromatin loop extrusion involving knotted and catenated chromatin fibers.

Main Results:

  • Chromatin loop extrusion was found to be effective in actively unknotting chromatin fibers.
  • The process also demonstrated decatenation and demixing capabilities for chromatin fibers.

Conclusions:

  • Chromatin loop extrusion is a viable mechanism for actively removing knots and catenations from interphase chromosomes.
  • This process plays a crucial role in maintaining the topologically simple state of chromatin within the nucleus.