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Related Concept Videos

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Related Experiment Video

Updated: Dec 13, 2025

Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
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Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy

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Nucleosome movement analysis based on second-order information entropy and density functional theory.

Deliang Zhou1, Jianli Liu2

  • 1Bei Jing Zhongdianyida Technology Co., Ltd, Andingmenwai Street NO.1th, Beijing 100190, China.

Biophysical Chemistry
|July 31, 2020
PubMed
Summary

Nucleosomes near transcription start sites move dynamically to regulate gene transcription. Their movement, influenced by interaction intensity, controls whether genes are turned on or off.

Keywords:
Density functional theoryGene transcription regulationNucleosome movementSecond-order information entropy

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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Gene transcription is tightly regulated by the precise positioning and movement of nucleosomes.
  • Understanding nucleosome dynamics near transcription start sites (TSS) is crucial for deciphering gene regulation mechanisms.

Purpose of the Study:

  • To analyze the dynamics of +1 and -1 nucleosomes relative to the TSS in yeast chromosome 2.
  • To investigate the relationship between nucleosome movement and gene transcription.
  • To explore the role of nucleosome-histone interactions in regulating nucleosome positioning.

Main Methods:

  • Utilized second-order information entropy to quantify nucleosome sequence-histone interactions.
  • Employed density functional theory (DFT) to determine global interaction intensity and analyze binucleoside pair states.
  • Analyzed nucleosome positioning and movement patterns near the TSS of yeast chromosome 2.

Main Results:

  • Observed asymmetry in interaction intensity around the nucleosome's central site.
  • +1 nucleosomes showed a tendency to move towards the 5'-end, while -1 nucleosomes moved towards the 3'-end.
  • Nucleosome movement dynamics were linked to gene transcription: covering TSS silences transcription, while exposing TSS activates it.

Conclusions:

  • Nucleosome sequences contain dynamic information that dictates nucleosome movement.
  • The interplay between nucleosome positioning and TSS accessibility governs gene transcription.
  • Findings provide a mechanistic basis for gene transcription regulation through nucleosome dynamics.