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J. Biol. Chem., Vol. 281, Issue 35, 25134-25142, September 1, 2006

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Identification of Cell Cycle Regulatory Genes as Principal Targets of p53-mediated Transcriptional Repression^*

Kevin B. Spurgers¹, David L. Gold^¶, Kevin R. Coombes^¶, Nicole L. Bohnenstiehl, Brian Mullins, Raymond E. Meyn^||, Christopher J. Logothetis^**, and Timothy J. McDonnell²

From the Departments of Molecular Pathology, ^¶Biostatistics, ^||Experimental Radiation Oncology and ^**Genitourinary Medical Oncology, the University of Texas M. D. Anderson Cancer Center and the University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030

Historically, most studies attribute p53 function to the transactivation of target genes. That p53 can selectively repress genes to affect a cellular response is less widely appreciated. Available evidence suggests that repression is important for p53-induced apoptosis and cell cycle arrest. To better establish the scope of p53-repressed target genes and the cellular processes they may affect, a global expression profiling strategy was used to identify p53-responsive genes following adenoviral p53 gene transfer (Ad-p53) in PC3 prostate cancer cells. A total of 111 genes, 0.77% of the 14,500 genes represented on the Affymetrix U133A microarray, were repressed more than 2-fold (p 0.05). Validation of the array data, using reverse transcription-PCR of 20 randomly selected genes, yielded a confirmation rate of >95.5% for the complete data set. Functional over-representation analysis revealed that cell cycle regulatory genes exhibited a highly significant enrichment (p 5 x 10^–28) within the transrepressed targets. 41% of the repressed targets are cell cycle regulators. A subset of these genes exhibited repression following DNA damage, preceding cell cycle arrest, in LNCaP cells. The use of a p53 small interfering RNA strategy in LNCaP cells and the use of p53-null cell lines demonstrated that this repression is p53-dependent. These findings identify a set of genes not known previously to be down-regulated by p53 and indicate that p53-induced cell cycle arrest is a function of not only the transactivation of cell cycle inhibitors (e.g. p21) but also the repression of targets that regulate proliferation at several distinct phases of the cell cycle.

Received for publication, December 30, 2005 , and in revised form, June 19, 2006.

^* This work was supported by National Institutes of Health Grants P50 CA90270 and R01 CA69003-9. The University of Texas M. D. Anderson Cancer Center microarray core facility is supported by Cancer Center Support Grant CA16672. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental tables and a supplemental figure.

¹ Supported in part by the American Legion Auxiliary Fellowship in Cancer Research.

² To whom correspondence should be addressed: Dept. of Molecular Pathology, Box 089, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030. Tel.: 713-834-6028; Fax: 713-745-6696; E-mail: tmcdonne{at}mdanderson.org.

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