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

The temporal gene expression profile during the entire process of apoptosis and cell cycle progression in response to p53 in human ovarian cancer cells was explored with cDNA microarrays representing 33 615 individual human genes. A total of 1501 genes (4.4%) were found to respond to p53 (approximately 80% of these were repressed by p53) using 2.5-fold change as a cutoff. It was anticipated that most of p53 responsive genes resulted from the secondary effect of p53 expression at late stage of apoptosis. To delineate potential p53 direct and indirect target genes during the process of apoptosis and cell cycle progression, microarray data were combined with global p53 DNA-binding site analysis. Here we showed that 361 out of 1501 p53 responsive genes contained p53 consensus DNA-binding sequence(s) in their regulatory region, approximately 80% of which were repressed by p53. This is the first time that a large number of p53-repressed genes have been identified to contain p53 consensus DNA-binding sequence(s) in their regulatory region. Hierarchical cluster analysis of these genes revealed distinct temporal expression patterns of transcriptional activation and repression by p53. More genes were activated at early time points, while more repressed genes were found after the onset of apoptosis. A small-scale quantitative chromatin immunoprecipitation analysis indicated that in vivo p53–DNA interaction was detected in eight out of 10 genes, most of which were repressed by p53 at the early onset of apoptosis, suggesting that a portion of p53 target genes in the human genome could be negatively regulated by p53 via sequence-specific DNA binding. The approaches and genes described here should aid the understanding of global gene regulatory network of p53.

[1]  D. Latchman,et al.  p53 Suppresses the Activation of the Bcl-2 Promoter by the Brn-3a POU Family Transcription Factor* , 1999, The Journal of Biological Chemistry.

[2]  Yaolin Wang,et al.  Analyses of p53 Target Genes in the Human Genome by Bioinformatic and Microarray Approaches* 210 , 2001, The Journal of Biological Chemistry.

[3]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[4]  K. Kinzler,et al.  A model for p53-induced apoptosis , 1997, Nature.

[5]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  A. Levine,et al.  Surfing the p53 network , 2000, Nature.

[7]  E. Lam,et al.  The p53 Tumor Suppressor Inhibits Transcription of the TATA-less Mouse DP1 Promoter* , 1998, The Journal of Biological Chemistry.

[8]  Luquan Wang,et al.  Transcriptional Regulation during p21 WAF1/CIP1 -induced Apoptosis in Human Ovarian Cancer Cells* , 2002, The Journal of Biological Chemistry.

[9]  J. Trent,et al.  WAF1, a potential mediator of p53 tumor suppression , 1993, Cell.

[10]  T. Soussi,et al.  ATF/CREB site mediated transcriptional activation and p53 dependent repression of the cyclin A promoter , 1996, FEBS letters.

[11]  John Calvin Reed,et al.  Tumor suppressor p53 is a direct transcriptional activator of the human bax gene , 1995, Cell.

[12]  S. N. Agoff,et al.  Regulation of the human hsp70 promoter by p53. , 1993, Science.

[13]  M. Mathews,et al.  Transcriptional activation of the human proliferating-cell nuclear antigen promoter by p53. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[14]  W. R. Bishop,et al.  Human survivin is negatively regulated by wild-type p53 and participates in p53-dependent apoptotic pathway , 2002, Oncogene.

[15]  R. A. Johnson,et al.  Transcriptional Repression by p53 through Direct Binding to a Novel DNA Element* 210 , 2001, The Journal of Biological Chemistry.

[16]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[17]  K. Kinzler,et al.  Definition of a consensus binding site for p53 , 1992, Nature Genetics.

[18]  A. Levine,et al.  Human TAFII31 protein is a transcriptional coactivator of the p53 protein. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. Maxwell,et al.  Differential gene expression in p53-mediated apoptosis-resistant vs. apoptosis-sensitive tumor cell lines. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Madden,et al.  SAGE transcript profiles for p53-dependent growth regulation , 1997, Oncogene.

[21]  K. Kinzler,et al.  Identification and classification of p53-regulated genes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Jiandong Chen,et al.  Transcriptional Repression of the Anti-apoptoticsurvivin Gene by Wild Type p53* , 2002, The Journal of Biological Chemistry.

[23]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[24]  S. Velasco-Miguel,et al.  Induction of the growth inhibitor IGF-binding protein 3 by p53 , 1995, Nature.

[25]  G. Zambetti,et al.  Wild-type p53 binds to the TATA-binding protein and represses transcription. , 1992, Proceedings of the National Academy of Sciences of the United States of America.