Huenten, Sabine and Kaller, Markus and Drepper, Friedel and Oeljeklaus, Silke and Bonfert, Thomas and Erhard, Florian and Dueck, Anne and Eichner, Norbert and Friedel, Caroline C. and Meister, Gunter and Zimmer, Ralf and Warscheid, Bettina and Hermeking, Heiko (2015) p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. MOLECULAR & CELLULAR PROTEOMICS, 14 (10). pp. 2609-2629. ISSN 1535-9476, 1535-9484
Full text not available from this repository. (Request a copy)Abstract
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes 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 down-regulated 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 up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits 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 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | EPITHELIAL-MESENCHYMAL TRANSITION; GENOME-WIDE ANALYSIS; LARGE GENE LISTS; TUMOR-SUPPRESSOR; TRANSCRIPTION-FACTOR; C-MYC; GASTRIC-CANCER; BREAST-CANCER; WILD-TYPE; DIFFERENTIAL REGULATION; |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biochemie, Genetik und Mikrobiologie > Lehrstuhl für Biochemie I > Prof. Dr. Gunter Meister |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 06 Jun 2019 12:36 |
| Last Modified: | 06 Jun 2019 12:36 |
| URI: | https://pred.uni-regensburg.de/id/eprint/4766 |
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