Repression of new p53 targets revealed by ChIP on chip experiments

Area of Science:

• Molecular Biology
• Cell Biology
• Genetics

Background:

• The tumor suppressor p53 plays a critical role in cellular responses to DNA damage.
• p53 regulates gene expression by activating some genes and repressing others, including those involved in cell cycle progression.
• p53's repression mechanism, particularly its interaction with NF-Y, is not fully understood.

Purpose of the Study:

• To identify novel p53 target genes involved in DNA-damage and ER-stress responses.
• To investigate the role of p53 and NF-Y in promoter association under normal conditions.
• To elucidate the mechanism of p53-mediated transcriptional repression.

Main Methods:

• Oligo-based array encompassing 179 human promoters.
• ChIP on chip experiments for p53 and NF-Y.
• Conventional ChIP, RT-PCR, and transfection assays in various cell lines (HCT116 wt, E6, p53-/-).

Main Results:

• Identified 46 new p53 targets, with significant enrichment in ER-stress response genes (e.g., XBP1, C/EBPbeta).
• Observed p53 association with promoters in unstressed cells and DNA-damage-dependent acetylation.
• Demonstrated p53-mediated repression of most identified promoters upon DNA damage or p53 activation, with significant overlap (66%) between p53 and NF-Y targets.

Conclusions:

• p53 directly recognizes and represses specific promoters, including those involved in ER-stress and p53 regulation, as a key mechanism to cope with DNA damage.
• NF-Y is a frequent partner of p53 in transcriptional repression.
• The findings highlight the physiological importance of p53's direct transcriptional repression activity.