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Analysis of p53-regulated gene expression patterns using oligonucleotide arrays
1Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
Abstract:
Oligonucleotide microarrays were employed to quantitate mRNA levels from a large number of genes regulated by the p53 transcription factor. Responses to DNA damage and to zinc-inducible p53 were compared for their transcription patterns in cell culture. A cluster analysis of these data demonstrates that genes induced by gamma radiation, UV radiation, and the zinc-induced p53 form distinct sets and subsets with a few genes in common to all these treatments. Cell type- or cell line-specific p53 responses were detected. When p53 proteins were induced with zinc, the kinetics of induction or repression of mRNAs from p53-responsive genes fell into eight distinct classes, five different kinetics of induction, and three different kinetics of repression. In addition, low levels of p53 in a cell induced or repressed only a subset of genes observed at higher p53 levels. The results of this study demonstrate that the nature of the p53 response in diverse mRNA species depends on the levels of p53 protein in a cell, the type of inducing agent or event, and the cell type employed. Of 6000 genes examined for p53 regulatory responses, 107 induced and 54 repressed genes fell into categories of apoptosis and growth arrest, cytoskeletal functions, growth factors and their inhibitors, extracellular matrix, and adhesion genes.
Insights
The p53 transcription factor
Area of Science:
- Molecular Biology
- Genetics
- Cell Biology
Background:
- The p53 transcription factor plays a critical role in cellular responses to DNA damage.
- Understanding p53's regulatory network is crucial for deciphering cellular fate decisions.
Purpose of the Study:
- To compare the transcriptional patterns of p53-regulated genes in response to DNA damage versus zinc-induced p53.
- To investigate how p53 protein levels and inducing agents influence gene expression kinetics.
Main Methods:
- Oligonucleotide microarrays were used to quantify mRNA levels for thousands of genes.
- Cluster analysis was employed to identify distinct gene expression patterns.
- Cell cultures were treated with gamma radiation, UV radiation, or zinc to induce p53.
Main Results:
- Genes regulated by gamma radiation, UV radiation, and zinc-induced p53 formed distinct sets, with some overlap.
- p53 responses were found to be cell type-specific.
- The kinetics of mRNA induction or repression varied, with distinct classes observed based on p53 levels and inducing agents.
- Among 6000 genes, 107 were induced and 54 repressed, falling into categories like apoptosis, growth arrest, and cell adhesion.
Conclusions:
- The transcriptional response mediated by p53 is complex and depends on p53 protein levels, the nature of the stimulus, and the cell type.
- p53 regulates a diverse set of genes involved in critical cellular processes, including apoptosis, growth control, and cell adhesion.
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