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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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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 extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
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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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Nucleosome-mediated conformational switches in micro-eccDNAs.

Sarah Harris1, Victor Velasco Berrelleza1, William Sandel2

  • 1School of Mathematical and Physical Sciences, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, UK, S3 7RH and School of Physics and Astronomy, University of Leeds, UK, LS2 9JT.

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Extrachromosomal-circular DNA (eccDNA) can switch between intact and denatured states. Nucleosome binding acts as a topological switch, influencing eccDNA structure and function in genomic processes.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biophysics

Background:

  • Extrachromosomal-circular DNA (eccDNA) are involved in genomic diversification and instability.
  • The structure and chromatinization of eccDNA remain poorly understood.
  • Understanding eccDNA is crucial for comprehending genome dynamics.

Purpose of the Study:

  • To investigate the structural and topological properties of a specific micro-eccDNA molecule.
  • To explore the interaction between eccDNA and nucleosomes.
  • To elucidate the role of nucleosomes in regulating eccDNA topology.

Main Methods:

  • Identification of a 358-bp Titin gene-derived micro-eccDNA.
  • Atomistic molecular dynamics simulations.
  • Analysis of DNA-nucleosome interactions and topological states.

Main Results:

  • A specific micro-eccDNA molecule derived from the human Titin gene was identified.
  • Atomistic molecular dynamics simulations revealed the topological behavior of eccDNA.
  • The presence or absence of bound nucleosomes acts as a topological switch, determining whether the DNA remains intact or denatures.

Conclusions:

  • Nucleosome binding is a key factor in regulating eccDNA structure.
  • This topological switch mechanism influences eccDNA's role in genomic processes.
  • Further research into eccDNA-nucleosome interactions can illuminate mechanisms of genomic instability.