Context dependent activity of p63-bound gene regulatory elements

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.