The tumor suppressor p53 has defined roles in varied cellular processes including apoptosis and DNA repair. While conventional genomic approaches have suggested a large number of p53 targets, there is a need for a systematic approach to validate these putative genes. We developed a method to identify and validate p53's transcriptional behavior by utilizing 16 non-synonymous p53 single-nucleotide polymorphism (SNP) variants. Five SNPs located within the DNA-binding domain of p53 were found to be functionally null, whereas the other 11 SNPs were p53WT-like in behavior. By integrating p53 ChIP-seq analysis with transcriptome data from the p53 SNP variants, 592 genes were identified as novel p53 targets. Many of these genes mapped to previously less well-characterized aspects of p53 function, such as cell signalling, metabolism, central nervous system, and immune system. These data provide pivotal insights into the involvement of p53 in diverse pathways of normal physiological processes and open new avenues for investigation of p53 function. Cell Death and Differentiation (2014) 21, 521-532; doi:10.1038/cdd.2013.132; published online 27 September 2013The tumor suppressor p53 acts as a master regulator of cellular stress responses through transcriptionally regulating specific target genes involved in diverse cellular functions including cell cycle arrest, apoptosis, and DNA repair. 1 With the aid of large-scale screening techniques, it has become clear that the scope of p53 functions is much broader than previously thought, 2,3 expanding to cellular and physiological processes such as metabolism 4 and development. 5 To have a better understanding of this important tumor suppressor, we must be able to study the full complexity of its downstream effects and this requires the efficient identification and validation of genes directly regulated by p53. To date, there are fewer than 150 validated p53 target genes 6-8 and at the same time validation studies have been slow, which is a limitation on the progress in this field.In order to be regulated by p53 a gene must possess the appropriate cognate response element (RE) within its regulatory region. However, our previous study has shown that simple sequence motif identification is not sufficient, as the p53RE exhibits variable binding kinetics that are dependent upon the dinucleotide core 'CWWG' combinations. 9 These variables often result in spurious outcomes and hence we are in need of more robust approaches to accurately identify p53 transcriptional networks.Here, we describe an unbiased method to review 135 reported p53 target genes and at the same time identify new p53 targets on a genome-wide scale. We utilized wild-type (WT) p53 together with 16 allelic replicates comprising all reported non-synonymous single-nucleotide polymorphism (SNP) variants of p53. As the transcriptional functions of these 16 SNPs have not been well studied, we first developed a customized luciferase assay with promoter reporter vectors encompassing all combinatorial forms of the dinucleotide ...