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Yeast As a Chassis for Developing Functional Assays to Study Human P53

Yeast As a Chassis for Developing Functional Assays to Study Human P53

Published on: August 4, 2019

Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements.

Omari J Bandele¹, Xuting Wang, Michelle R Campbell

¹Environmental Genomics Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

Nucleic Acids Research

|September 7, 2010

Summary

This summary is machine-generated.

Single-nucleotide polymorphisms (SNPs) in p53 response elements can alter DNA binding and gene expression. This study developed a method to identify and evaluate SNPs impacting p53-mediated stress responses.

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Area of Science:

Genetics
Molecular Biology
Cancer Research

Background:

The tumor suppressor protein p53 regulates gene expression in response to cellular stress.
Sequence-specific DNA binding by p53 is crucial for its tumor-suppressive functions.
Single-nucleotide polymorphisms (SNPs) in p53 response elements (p53REs) may affect p53's regulatory activity.

Purpose of the Study:

To investigate the impact of SNPs in p53REs on p53 DNA binding and subsequent gene expression following DNA damage.
To develop and validate a bioinformatics and experimental strategy for assessing SNP effects on p53 function.

Main Methods:

Bioinformatic analysis incorporating p53 binding strength into a position weight matrix to select 32 candidate SNPs in p53REs.
Microsphere assay for protein-DNA binding (MAPD) to measure p53 binding affinity to polymorphic p53REs.
Allele-specific expression analysis and chromatin immunoprecipitation-sequencing (ChIP-seq) to assess gene expression changes and in vivo binding.

Main Results:

Most polymorphic p53REs showed significant p53 binding, with some comparable to the established p21 RE.
SNPs predicted to decrease p53 binding reduced binding in 25 out of 32 tested sequences.
ChIP-seq confirmed p53 binding to seven polymorphic p53REs, and five SNPs were associated with altered gene expression after doxorubicin treatment.

Conclusions:

The study presents an effective strategy for identifying and evaluating the functional impact of SNPs in p53REs.
These findings highlight the potential for specific SNPs to modulate p53-mediated stress responses and tumor suppression.
Understanding these genetic variations is important for assessing individual susceptibility and therapeutic responses related to p53 pathways.