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Related Experiment Videos

DNA bending determines Fos-Jun heterodimer orientation

D A Leonard1, T K Kerppola

  • 1Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor 48109-0650, USA.

Nature Structural Biology
|October 23, 1998
PubMed
Summary

Transcription factor heterodimers, like Fos-Jun, bind DNA in specific orientations. DNA structure influences binding orientation, impacting gene regulation.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Heterodimeric transcription factors regulate gene expression by binding to specific DNA sequences.
  • These factors can bind to palindromic elements in opposing orientations, potentially leading to different regulatory outcomes.
  • Understanding binding orientation is crucial for deciphering gene regulation mechanisms.

Purpose of the Study:

  • To investigate the binding orientation of Fos-Jun heterodimers at various AP-1 sites.
  • To determine how DNA sequence and structure influence the orientation preference of transcription factor binding.
  • To elucidate the role of indirect read-out in nucleoprotein complex organization.

Main Methods:

  • Development and application of a novel gel-based fluorescence resonance energy transfer (FRET) assay.
  • Analysis of Fos-Jun binding orientation at different AP-1 DNA sites.
  • Site-directed mutagenesis to alter DNA sequences and protein structures.

Main Results:

  • The orientation preference of Fos-Jun heterodimer binding exhibited significant variability across different AP-1 sites (over a 10-fold range).
  • Single base pair substitutions in flanking DNA sequences altered DNA bending and reversed heterodimer binding orientation.
  • Amino acid substitutions reducing DNA bending differences between Fos and Jun decreased orientation preference.

Conclusions:

  • Indirect read-out, mediated by DNA structural features like bending, plays a significant role in determining transcription factor binding orientation.
  • DNA structure directly influences the assembly and organization of nucleoprotein complexes.
  • This mechanism provides a framework for understanding sequence-specific gene regulation by heterodimeric factors.

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