Facilitated search for specific genomic targets by p53 C-terminal basic DNA binding domain

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• The p53 protein is a crucial DNA-binding protein involved in cellular responses to stress.
• p53 possesses two DNA-binding domains: a central domain for sequence-specific binding and a C-terminal basic domain (BD) for structure-specific binding.
• The BD domain's role in p53's in vivo DNA binding and transcriptional regulation remains incompletely understood.

Purpose of the Study:

• To investigate the role of the p53 BD domain in binding to the endogenous p21(Waf1) promoter.
• To elucidate the mechanism by which the BD domain influences p53's interaction with genomic DNA in vivo.
• To provide in vivo evidence for non-sequence-specific DNA binding as an intermediate step in target site searching.

Main Methods:

• Global chromatin immunoprecipitation (ChIP) analysis was employed to assess p53 DNA binding in vivo.
• Experiments focused on the p21(Waf1) promoter to evaluate promoter binding and transactivation.
• In vitro DNA binding assays were conducted to compare with in vivo observations.

Main Results:

• The p53 BD domain enhances binding to the endogenous p21(Waf1) promoter and mediates rapid transactivation.
• The BD domain is essential for rapid binding to non-sequence-specific genomic DNA (NS-DNA) in vivo.
• Global ChIP analysis revealed that NS-DNA binding is a prerequisite for efficient sequence-specific DNA recognition by p53.

Conclusions:

• The p53 BD domain plays a critical role in facilitating rapid p53 binding to genomic DNA through an initial NS-DNA interaction.
• This NS-DNA binding mechanism, mediated by the BD domain, supports the model of facilitated diffusion for target site searching in the genome.
• The findings offer a resolution to the paradox of the BD domain's apparent inhibitory effect in vitro versus its enhancing role in vivo, highlighting its importance in genomic surveillance during genotoxic stress.