DNA bending determines Fos-Jun heterodimer orientation

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.