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Multimodal bHLH-PAS DNA binding controls specificity and drives obesity.

David C Bersten1,2, Daniel P McDougal1,3, Adrienne E Sullivan1,4,5

  • 1The Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5001, Australia.

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Summary
This summary is machine-generated.

The basic-helix-loop-helix Per-Arnt-Sim (PAS) transcription factor (TF) family

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • The basic-helix-loop-helix Per-Arnt-Sim (bHLH-PAS) transcription factor (TF) family are crucial regulators of physiological and environmental responses.
  • Specificity mechanisms for DNA binding and target gene regulation by bHLH-PAS TFs are not fully understood.

Purpose of the Study:

  • To systematically analyze the DNA binding hierarchies and specificity mechanisms of key bHLH-PAS TF family members.
  • To elucidate the role of DNA shape and flanking sequences in TF binding specificity.
  • To investigate the functional significance of SIM1 PAS-loop/DNA interactions in TF activity and disease.

Main Methods:

  • Systematic analysis of cognate DNA binding hierarchies for prototypical bHLH-PAS TFs (ARNT, ARNT2, HIF1α, HIF2α, AhR, NPAS4, SIM1).
  • Investigation of DNA binding footprints and sequence preferences.
  • Analysis of TF-DNA interactions, including DNA shape and flanking sequence contributions.
  • Functional studies in a SIM1.R171H knock-in mouse model.

Main Results:

  • Identified large DNA binding footprints (12-15 bp) for bHLH-PAS TFs.
  • Revealed flank-encoded DNA binding specificity, distinguishing SIM1 and HIF TF binding through N-terminal interactions.
  • Demonstrated a relationship between DNA shape, core, and flank TF binding, enabling motif sequence flexibility.
  • Discovered novel SIM1 PAS-loop/DNA interactions with AT-rich sequences critical for DNA binding and transcriptional activity.
  • Established a monogenic cause for hyperphagic obesity linked to SIM1 function in a mouse model.

Conclusions:

  • bHLH-PAS TF binding specificity is achieved through multimodal mechanisms involving core motifs, flanking sequences, and DNA shape.
  • SIM1 PAS-loop/DNA interactions are essential for TF function and linked to hyperphagic obesity.
  • This study resolves key aspects of bHLH-PAS TF DNA binding specificity and its implications for homeostasis and disease.