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The Nucleosome02:33

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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to 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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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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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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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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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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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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Structural analysis of OCT4 binding to human LIN28B nucleosomes.

Kalyan K Sinha1, Mario Halic2

  • 1Department of Structural Biology, MS 311, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. kalyan.sinha@stjude.org.

Scientific Reports
|January 19, 2026
PubMed
Summary

Histones from humans and Xenopus frogs assemble similarly on human DNA. The pioneer transcription factor OCT4 binds to these nucleosomes identically, regardless of histone origin, clarifying structural roles.

Keywords:
ChromatinCryo-EMGene regulationNucleosomePioneer transcription factor

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • Nucleosome structure studies commonly use Xenopus or human histones.
  • Subtle histone sequence differences impact nucleosome assembly, DNA positioning, and transcription factor binding.
  • The precise effects of these sequence variations remain largely unknown.

Purpose of the Study:

  • To investigate the impact of human versus Xenopus histone sequences on nucleosome assembly and transcription factor binding.
  • To compare the interaction of OCT4 with nucleosomes assembled from human and Xenopus histones using the human LIN28B DNA sequence.

Main Methods:

  • Nucleosome assembly using human LIN28B DNA and either human or Xenopus histones.
  • Cryogenic electron microscopy (cryo-EM) for high-resolution structural analysis.
  • Analysis of transcription factor OCT4 binding to assembled nucleosomes.

Main Results:

  • Both human and Xenopus histones efficiently assembled into nucleosomes on the human LIN28B DNA sequence.
  • Cryo-EM revealed that the pioneer transcription factor OCT4 binds to human LIN28B nucleosomes assembled with human histones identically to previous findings with Xenopus histones.
  • Demonstrated conserved binding mechanisms of OCT4 across different histone origins.

Conclusions:

  • Human and Xenopus histones exhibit functional similarity in nucleosome assembly and DNA binding.
  • The interaction between OCT4 and LIN28B nucleosomes is conserved, irrespective of the histone species used.
  • Findings contribute to understanding nucleosome dynamics and transcription factor regulation in different species.