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Related Concept Videos

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 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.
Polytene Chromosomes02:04

Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...
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...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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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DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
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DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

Topological interactions between ring polymers: Implications for chromatin loops.

Manfred Bohn1, Dieter W Heermann

  • 1Institute for Theoretical Physics, University of Heidelberg, Philosophenweg 19, D-69120 Heidelberg, Germany. bohn@tphys.uni-heidelberg.de

The Journal of Chemical Physics
|February 2, 2010
PubMed
Summary
This summary is machine-generated.

Chromatin loops exhibit increased repulsion due to ring polymer topology and topological constraints. This suggests chromatin loop formation regulates DNA compaction and order.

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

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DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

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

Published on: May 6, 2010

Area of Science:

  • Biophysics
  • Epigenetics
  • Polymer Physics

Background:

  • Chromatin looping is a key epigenetic mechanism in eukaryotes.
  • Beyond transcription, loops may mediate chromosome segregation.
  • Topological and entropic forces governing loop interactions are poorly understood.

Purpose of the Study:

  • To quantitatively determine the forces between two ring polymers (loops).
  • To investigate how polymer topology (linear vs. ring) affects inter-loop interactions.
  • To explore the role of topological constraints on polymer conformations.

Main Methods:

  • Computational modeling of ring polymers.
  • Calculation of potential of mean force between polymer centers of mass.
  • Analysis of conformational and structural properties.

Main Results:

  • Transitioning from linear to ring polymers significantly increases entropic repulsion.
  • Noncatenation constraints reduce accessible conformations by ~50%, adding effective repulsion.
  • Ring polymers exhibit more ordered and aligned states compared to linear polymers.

Conclusions:

  • Topological and entropic forces between chromatin loops are substantial.
  • Ring polymer topology and constraints contribute to effective repulsion and altered conformations.
  • Dynamic chromatin loop formation may regulate local DNA compaction and order.