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Context dependent activity of p63-bound gene regulatory elements.

Abby A McCann1, Gabriele Baniulyte1, Dana L Woodstock1

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The DNA sequence and cellular context significantly influence p63 transcription factor activity, determining whether it activates or represses gene expression. P63 isoform changes dramatically alter regulatory element function, impacting development and tumor suppression.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Cancer Research

Background:

  • The p53 family of transcription factors, including p63, are crucial regulators of cell development, genetic stability, and tumor suppression.
  • While p53 binding typically activates transcription, p63 exhibits dual roles, mediating both gene activation and repression, a mechanism not fully understood.
  • Understanding how DNA sequence dictates p63's diverse transcriptional activities is essential for deciphering its role in biological processes and disease.

Approach:

  • Utilized massively parallel reporter assays (MPRA) across various cellular and genetic contexts to investigate DNA sequence influence on p63-mediated transcription.
  • Analyzed the relationship between p63 response element (p63RE) motifs, binding frequency, sequence similarity to p53 response elements, and transcriptional output.
  • Examined the impact of flanking sequence GC content, p63 abundance, cofactors, and p63 isoform expression on regulatory element activity.

Key Points:

  • Most p63RE-containing regulatory elements activate transcription, with higher activity linked to increased p63 binding or canonical p53 family response element sequences.
  • Regulatory elements also bound by p53 showed the highest activity; elements uniquely bound by p63 displayed varied activity, with repression linked to lower flanking GC content.
  • Differential activity across cell lines suggests regulation by p63 abundance or context-specific cofactors, while altered p63 isoform expression significantly impacts element activity.

Conclusions:

  • The study provides novel insights into how DNA sequence, cellular context, and transcription factor interplay govern p63-dependent transcription.
  • Establishes a framework for understanding how p63 genomic binding locally regulates transcription, offering a basis for future investigations.
  • Findings can be extended to explore the influence of sequence, genomic context, and chromatin structure on p63 isoforms and p53 family paralogs in various biological contexts.