Analyses of p53 target genes in the human genome by bioinformatic and microarray approaches

The completion of the human genome sequence (International Human Genome Seq uence Consortium (2001) Nature 409, 860-921; Venter, J. C., et al (2001) Sc ience 291, 1304-1351) allows for new ways to analyze global cellular regula tory mechanisms. Here we present a strategy to identify genes regulated by specific transcription factors in the human genome, and apply it to p53. We first collected promoters or introns of all genes available using two meth ods: GenBank (TM) annotation and a computationally derived transcript map. 4,852 genes analyzed in this way contained at least one p53 consensus bindi ng sequence. Of 13 genes randomly selected for mRNA analysis, 11 were shown to respond to p53 expression. Five promoters were analyzed by chromatin im munoprecipitation, which revealed that all were bound by p53 in vivo. We th en analyzed 33,615 unique human genes on cDNA microarrays, identifying 1,50 1 genes that respond to p53 expression. A parameter was derived that demons trates that in silico prediction greatly enriches for genes that are activa ted and repressed by p53 and assists us to suggest other signaling pathways that may be connected to p53. The methods shown here illustrate a novel ap proach to analysis of global gene regulatory network through the integratio n of human genomic sequence information and genome-wide gene expression ana lysis.