title: Global transcriptional program of p53 target genes during the process of apoptosis and cell cycle progression.
abstract: 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.
authors.affiliation: Tumor Biology Department, Schering-Plough Research Institute, 2015 Galloping Hill Road, K-15-4 (4600), Kenilworth, NJ 07033, USA.
authors.forename: Asra
authors.initials: A
authors.lastname: Mirza
authors.forename: Qun
authors.initials: Q
authors.lastname: Wu
authors.forename: Luquan
authors.initials: L
authors.lastname: Wang
authors.forename: Terri
authors.initials: T
authors.lastname: McClanahan
authors.forename: W Robert
authors.initials: WR
authors.lastname: Bishop
authors.forename: Ferdous
authors.initials: F
authors.lastname: Gheyas
authors.forename: Wei
authors.initials: W
authors.lastname: Ding
authors.forename: Beth
authors.initials: B
authors.lastname: Hutchins
authors.forename: Tish
authors.initials: T
authors.lastname: Hockenberry
authors.forename: Paul
authors.initials: P
authors.lastname: Kirschmeier
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Greene
authors.forename: Suxing
authors.initials: S
authors.lastname: Liu
mesh_terms: D000256:Adenoviridae / Q000235:genetics; D000595:Amino Acid Sequence; D017209:Apoptosis / Q000235:genetics*; D001665:Binding Sites; D002453:Cell Cycle / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism; D016000:Cluster Analysis; D017124:Conserved Sequence; D005260:Female; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000473:pathology; D011233:Precipitin Tests; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D014162:Transfection / Q000379:methods; D014407:Tumor Cells, Cultured; D016159:Tumor Suppressor Protein p53 / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D012097:Repressor Proteins; D016159:Tumor Suppressor Protein p53