@article {bioinflmu-1297,
	title = {{p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses.}},
	journal = {Molecular \& cellular proteomics : MCP},
	year = {2015},
	month = {2015 Jul 16},
	abstract = {We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct targets that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3\% mRNAs, 7.2\% miRNAs, 6.3\% lncRNAs, 5.9\% proteins) than repressed genes (2.4\% mRNAs, 3.2\% miRNAs, 0.8\% lncRNAs, 1.9\% proteins), suggesting indirect mechanisms of repression. Around 50\% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 which provides new insights and leads into the mechanisms of p53-mediated tumor suppression.},
	doi = {10.1074/mcp.M115.050237 },
	author = {H{\"u}nten, Sabine and Kaller, Markus and Drepper, Friedel and Oeljeklaus, Silke and Thomas Bonfert and Florian Erhard and Dueck, Anne and Eichner, Norbert and Caroline C. Friedel and Gunter Meister and Ralf Zimmer and Warscheid, Bettina and Hermeking, Heiko}
}