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DNA sequence influences hexasome orientation to regulate DNA accessibility.

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Hexosomes, formed by removing a histone dimer from nucleosomes, regulate DNA accessibility. Specific DNA sequences influence hexasome orientation, impacting transcription factor access and gene regulation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Nucleosomes are the basic units of eukaryotic genome organization.
  • Hexosomes are formed by removing a histone H2A-H2B dimer from nucleosomes.
  • Hexasome formation and its regulatory role in DNA accessibility are not well understood.

Purpose of the Study:

  • To investigate the influence of hexasomes on DNA accessibility.
  • To understand the regulation and functional consequences of hexasome formation.
  • To identify DNA sequence elements controlling hexasome orientation and function.

Main Methods:

  • Utilized the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneous hexasomes in vitro.
  • Assessed DNA accessibility to transcription factors (TF) on hexasomes.
  • Determined the DNA region responsible for homogeneous hexasome formation.
  • Analyzed ChIP-exo data and performed ExoIII mapping studies.

Main Results:

  • DNA accessibility on the hexasome H2A-H2B distal side is similar to naked DNA.
  • DNA accessibility on the H2A-H2B proximal side is reduced 2-fold due to decreased hexasome unwrapping.
  • A 23 bp region of the Widom-601 NPS is crucial for homogeneous hexasome formation.
  • Identified DNA sequence motifs correlating with hexasome orientation in vivo and in vitro.

Conclusions:

  • Hexasome orientation, influenced by DNA sequence, modulates DNA accessibility.
  • Hexasome orientation plays a role in regulating gene transcription.
  • Understanding hexasome formation and orientation provides insights into genome regulation.