Genome-wide analysis of p53 occupancy. Genome-wide analysis of p53 occupancy. ChIP-Seq analysis was performed with a VSV-specific antibody 16 h after addition of DOX to SW480/pRTR-p53-VSV and SW480/pRTR. A, Localization of called ChIP-peaks obtained after p53-ChIP in SW480/pRTR-p53-VSV. B, Distribution of p53-derived ChIP-Seq peaks 100 kbp up- and downstream of the TSS. C, MEME analyses of p53-derived ChIP-peaks in SW480/pRTR-p53-VSV (± 20 kbp of the corresponding TSS) associated with all genes, induced (log2 fc ≥ 1) and repressed (log2 fc ≤ −1) genes according to RNA-Seq. D, Enrichment of the GATA1 DNA binding motif in the vicinity of p53 ChIP-signals of induced genes detected by SpaMo. E, Scatter plot correlating changes in de novo protein synthesis of all differentially regulated proteins with the corresponding mRNA fold changes after induction of p53 (marked in gray). Molecules showing p53 occupancy near the respective gene promoter are indicated in orange. The respective Pearson correlation coefficient and statistical significance are indicated. F, Proteins, protein-coding mRNAs, lncRNAs and miRNAs that have an occupied p53 binding site within ± 20 kbp of the TSS of their host gene are shown in colors or black as described under Fig. 1. Molecules without promoter-proximal p53 binding are shown in gray. G, Cumulative distribution plot displaying expression changes of (left) p53-occupied, protein-coding genes compared with the normal distribution of all detected proteins as detected by pSILAC, (right) p53-occupied, mRNA-coding genes compared with the normal distribution of all detected mRNAs as detected by RNA-Seq. Sabine Hünten et al. Mol Cell Proteomics 2015;14:2609-2629 © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.