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Related Concept Videos

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.
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Histone Modification02:32

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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.
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The Nucleosome Core Particle01:12

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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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.
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Duplication of Chromatin Structure02:05

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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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The Nucleosome01:19

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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Updated: May 15, 2025

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

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A Method for Constructing Nucleosome Arrays with Spatially Defined Histone PTMs and DNA Damage.

Ziyun Liu1, Siqi Xi1, Lauren A McGregor2

  • 1Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Angewandte Chemie (International Ed. in English)
|April 7, 2025
PubMed
Summary

Histone acetylation in the globular domain enhances DNA repair in nucleosomes. This finding reveals how chromatin structure impacts base excision repair (BER) efficiency, crucial for preventing genetic instability and cancer.

Keywords:
Abiotic catalystsBase excision repairChromatinDNA damageHistone acetylation

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Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones
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Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF
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Area of Science:

  • Molecular Biology
  • Epigenetics
  • DNA Repair

Background:

  • Base excision repair (BER) is vital for genomic stability.
  • Chromatin structure, particularly nucleosomes, hinders DNA accessibility for repair factors.
  • The role of histone acetylation in globular domains on BER within nucleosome arrays is largely unknown.

Purpose of the Study:

  • To investigate the impact of histone acetylation in globular domains on DNA repair efficiency within nucleosome arrays.
  • To explore the spatial relationship between histone modifications and DNA damage sites in modulating repair.

Main Methods:

  • Development of an abiotic/enzymatic hybrid catalyst system (ABEHCS) for regioselective histone acetylation.
  • Utilized a plug-and-play strategy to introduce specific DNA damage (deoxycytidine-to-deoxyuridine).
  • Constructed nucleosome arrays with controlled configurations of histone acetylation and DNA lesions.

Main Results:

  • H3K56 acetylation in the histone globular domain was found to enhance BER efficiency.
  • The enhancement of BER was mediated by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1).
  • The efficiency of BER was dependent on the spatial proximity between H3K56 acetylation and the DNA damage site.

Conclusions:

  • Histone acetylation within the globular domain of histones can positively regulate DNA repair.
  • The spatial arrangement of epigenetic marks and DNA lesions is a critical determinant of repair pathway efficacy.
  • Findings provide insights into the mechanisms of DNA repair in the context of chromatin organization.