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Related Experiment Videos

Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure

P Blomquist1, S Belikov, O Wrange

  • 1Laboratory of Molecular Genetics, Department of Cell and Molecular Biology, Medical Nobel Institute,Karolinska Institute, S-171 77 Stockholm, Sweden.

Nucleic Acids Research
|December 24, 1998
PubMed
Summary

DNA A-tracts flanking binding sites modulate transcription factor NF-1 affinity within nucleosomes. Their positioning influences DNA curvature, affecting histone interactions and accessibility for gene regulation.

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Gene Regulation

Background:

  • DNA organization into chromatin regulates transcription by controlling transcription factor access.
  • Nuclear factor 1 (NF-1) binds DNA with high affinity, but this is reduced within nucleosomes.

Purpose of the Study:

  • To investigate how flanking adenine-tracts (A-tracts) affect NF-1 binding to nucleosomal DNA.
  • To determine the role of A-tract positioning relative to DNA bending sequences in modulating NF-1 affinity.

Main Methods:

  • Synthesized DNA sequences with NF-1 binding sites flanked by A-tracts and a TG-motif bending sequence.
  • Measured NF-1 binding affinity to both free and nucleosomal DNA using varying A-tract positions.
  • Assessed DNA curvature and histone octamer binding affinity.

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Main Results:

  • A-tracts significantly altered NF-1 binding to nucleosomal DNA, but not free DNA.
  • NF-1 affinity was seven times higher when A-tracts were positioned out-of-phase with the TG-motif compared to in-phase.
  • Observed correlations between A-tract positioning, DNA curvature, and histone octamer affinity.

Conclusions:

  • DNA curvature, influenced by flanking A-tracts, modulates local histone-DNA interactions.
  • This modulation affects the accessibility of NF-1 binding sites within nucleosomes, impacting transcription factor binding and gene regulation.