GSE159945
Genome-wide occupancy of conditionally-expressed wild-type and Lys120-to-Arg (K120R) p53 in H1299 cells.
The tumor suppressor p53 integrates stress response pathways, triggering the appropriate cell fate by selectively engaging one of a diverse set of transcriptomes (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to response elements (REs) in the genome, of the consensus sequence (RRRCWWGYYYN0-13RRRCWWGYYY). This unusually long and degenerate RE provides a potential mechanism for contextually activating distinct sets of downstream targets. However, the RE code underlying this selectivity remains undeciphered. p53 REs exhibit the highest sequence variability at the triplets RRR/YYY, which flank the core (CWWG) sequence, and p53 tetramers interact with REs at those bases via Arg248 from the DNA minor groove and Lys120 from the DNA major groove. This set of observations triggered our hypothesis that the interplay of Lys120 and Arg248 residues with variable sequences of REs might be a potential source of p53 selectivity. To gain insight into the role of Lys120 integrity in the recognition of specific RE sequences, we performed a ChIP-seq experiment and analyzed genome-wide occupancy of conditionally-expressed wild-type (WT) and K120R forms of p53 in isogenic human cell lines that are null for endogenous p53. Using an optimized data analysis workflow, we mapped about 35 million unique sequence reads per sample to the human genome, and the number of significantly enriched peaks in each replicate was detected by setting an enrichment cutoff of 0.3 counts per million reads. This study presents a foundation for analysis of differences in sequences between K120R-sensitive and K120R-insensitive p53 binding sites. Overall design: ChiP-seq profiles of WT and K120R-p53 forms in untreated [Tet(-)] and Tetracycline treated [(Tet(+)] 1299 cells.