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An intrachromosomal repeating unit based on DNA bending

Y Wada-Kiyama1, R Kiyama

  • 1Department of Physiology, Nippon Medical School, Sendagi, Japan.

Molecular and Cellular Biology
|October 1, 1996
PubMed
Summary

DNA bending sites occur at regular intervals in globin gene regions, influencing nucleosome positioning. These periodic DNA bends are conserved across species, indicating a role in chromosome organization.

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Area of Science:

  • Genetics
  • Molecular Biology
  • Genomics

Background:

  • DNA bending is implicated in fundamental genetic processes like transcription, replication, and recombination.
  • Nucleosome positioning in eukaryotic cells is mediated by DNA bending, highlighting its role in chromosome organization.
  • Previous studies identified DNA bend sites at approximately 680 bp intervals in human globin gene regions.

Purpose of the Study:

  • To investigate the periodicity and conservation of DNA bend sites in the G gamma-A gamma-psi beta-globin gene region.
  • To identify the DNA sequences responsible for bending and their role in nucleosome phasing.
  • To understand the hierarchical organization of DNA bending in relation to gene expression and genome rearrangement.

Main Methods:

  • Analysis of DNA sequences in globin gene regions to identify periodic bend sites.
  • Comparative sequence analysis between human and mouse globin genes.
  • In-depth examination of specific DNA sequences associated with bending.
  • Assessment of DNA sequence interaction with core histones to determine nucleosome phasing.

Main Results:

  • DNA bend sites were found at approximately 700 bp intervals in the G gamma-A gamma-psi beta-globin gene region, dividing it into distinct units.
  • These periodic sites were conserved in promoter regions of most beta-like globin genes and between human and mouse beta-globin genes.
  • Periodicity was locally disrupted at duplicated gene junctions and within introns, suggesting lower hierarchical importance than gene rearrangement or expression.
  • A 20-bp sequence with periodic (dA)n tracts was identified as a key contributor to DNA bending and nucleosome phasing through histone binding.

Conclusions:

  • Periodic DNA bending sites are a conserved feature of beta-like globin gene regions, playing a role in organizing genomic DNA.
  • Specific DNA sequences, characterized by periodic (dA)n tracts, drive DNA bending and influence nucleosome positioning.
  • The observed periodicity of DNA bending sites is subordinate to genome rearrangement and gene expression in genomic organization hierarchy.

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