Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• The tumor suppressor p53 protein regulates cellular responses to stress, including cell cycle arrest and apoptosis.
• p53 function relies on binding to specific DNA sequences called response elements (REs).
• The precise sequence code dictating p53's selective binding to high-affinity (cell cycle arrest) versus low-affinity (apoptosis) REs is not fully understood.

Purpose of the Study:

• To elucidate the molecular mechanisms underlying p53's selective binding to high- and low-affinity DNA response elements.
• To identify the role of DNA shape in mediating differential p53-DNA interactions.
• To demonstrate the functional consequences of DNA shape-mediated binding in vivo.

Main Methods:

• Analysis of DNA sequence and shape features of p53 response elements.
• Investigating p53 DNA-binding modes using structural biology insights.
• Utilizing genome editing to alter BAX RE sequence and assess functional outcomes.

Main Results:

• Key determinants of p53 binding selectivity are embedded in DNA shape, specifically minor/major groove widths.
• Specific base pair content (G/C vs. A/T) at positions 3, 8, 13, and 18 of REs dictates DNA shape.
• Distinct p53 DNA-binding modes, influenced by Arg248 and Lys120 conformations, correlate with DNA shape.
• In vivo genome editing at the BAX RE successfully altered binding modes, transcription patterns, and cell fate.

Conclusions:

• DNA shape is a critical determinant of p53 binding affinity and selectivity.
• The identified DNA shape code provides predictive power for p53-mediated transcription and cell fate.
• This work reveals a novel layer of gene regulation by the tumor suppressor p53.