Global transcriptional program of p53 target genes during the process of apoptosis and cell cycle progression

Area of Science:

• Molecular Biology
• Cancer Genomics
• Gene Regulation

Background:

• The tumor suppressor protein p53 plays a critical role in cellular responses to stress, including apoptosis and cell cycle arrest.
• Understanding the full spectrum of p53-regulated genes is crucial for deciphering its complex functions in cancer.

Purpose of the Study:

• To comprehensively explore the temporal gene expression changes in response to p53 in human ovarian cancer cells.
• To identify direct and indirect p53 target genes involved in apoptosis and cell cycle progression.
• To characterize the regulatory mechanisms, including transcriptional repression, mediated by p53.

Main Methods:

• Utilized cDNA microarrays to analyze the expression of over 33,000 genes in ovarian cancer cells.
• Integrated microarray data with p53 DNA-binding site analysis to identify direct targets.
• Employed hierarchical clustering to analyze temporal expression patterns.
• Performed quantitative chromatin immunoprecipitation (ChIP) to validate p53-DNA interactions in vivo.

Main Results:

• Identified 1501 genes (4.4%) responsive to p53, with approximately 80% showing repression.
• Found that 361 of these responsive genes contain p53 consensus DNA-binding sequences, predominantly repressed by p53.
• Observed distinct temporal patterns: gene activation at early time points and repression after apoptosis onset.
• Validated in vivo p53-DNA interaction for 8 out of 10 tested genes, many repressed early in apoptosis.

Conclusions:

• This study provides the first large-scale identification of p53-repressed genes containing consensus DNA-binding sites.
• Demonstrates that p53 can negatively regulate a significant portion of its target genes through sequence-specific DNA binding.
• The identified genes and regulatory networks offer insights into p53's role in ovarian cancer progression and therapeutic strategies.