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Related Concept Videos

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...
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...
Forces Acting on Chromosomes02:11

Forces Acting on Chromosomes

During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
Microtubules and motor proteins exert two types of forces on...
Forces Acting on Chromosomes02:11

Forces Acting on Chromosomes

During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
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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.
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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Modeling chromatin fractal structure and dynamics: Crosslinked single chain under active forces.

Yam Ben Yaish1, Sadhana Singh1, Rony Granek2

  • 1Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.

Biophysical Journal
|June 19, 2026
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Summary

Chromatin folding is fractal-like, but existing models don't fully capture its crosslinked structure. This study uses simulations to model chromatin, successfully replicating its fractal packing and subdiffusive behavior, offering new insights into genome organization.

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Area of Science:

  • Computational Biology
  • Polymer Physics
  • Genomics

Background:

  • Interphase chromatin exhibits fractal-like folding (df ≈ 2.77), deviating from the ideal fractal globule model (df = 3).
  • In vivo chromatin architecture is characterized by diverse crosslinks (e.g., cohesin, Lamin-A), which are absent in simple polymer models.
  • Understanding chromatin's complex structure is crucial for deciphering genome organization and function.

Purpose of the Study:

  • To develop a computational model that accurately captures chromatin's fractal packing and connectivity, including the effects of crosslinks.
  • To investigate the subdiffusive behavior of chromatin under different nuclear conditions using simulations.
  • To compute and analyze the topological dimension of model chromatin networks.

Main Methods:

  • Utilized Monte Carlo simulations of a self-interacting random-walk model with self-avoidance and Van-der-Waals attractive interactions.
  • Incorporated crosslinks into the polymer model to mimic in vivo chromatin architecture.
  • Performed Langevin dynamics simulations to evaluate mean square displacement (MSD) under active and thermal conditions.

Main Results:

  • The model successfully replicates chromatin's fractal packing and connectivity by tuning attractive interaction strength.
  • Introducing crosslinks yields a spectral dimension (ds = 1.2), matching the Rouse model's subdiffusive behavior (MSD ∼ t0.4).
  • The study computes the topological dimension (dl) and confirms the inequality 1 ≤ ds ≤ dl ≤ df ≤ 3.

Conclusions:

  • The developed model provides a robust framework for simulating chromatin organization, accounting for both fractal properties and crosslinking.
  • The findings elucidate the physical basis for chromatin's subdiffusive dynamics and its complex topological characteristics.
  • This work advances our understanding of genome folding and its implications for nuclear organization.