Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53

Kirschner, K., Samarajiwa, S. A., Cairns, J. M., Menon, S., Perez-Mancera, P. A., Tomimatsu, K., Bermejo-Rodriguez, C., Ito, Y., Chandra, T., Narita, M., Lyons, S. K., Lynch, A. G., Kimura, H., Ohbayashi, T., Tavare, S., Narita, M. (March 2015) Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet, 11 (3). e1005053. ISSN 1553-7390

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URL: http://www.ncbi.nlm.nih.gov/pubmed/25790137
DOI: 10.1371/journal.pgen.1005053

Abstract

The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene regulation

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > genes: types > p53
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > Lyons lab
Depositing User: Matt Covey
Date: March 2015
Date Deposited: 14 Oct 2015 18:51
Last Modified: 14 Oct 2015 18:51
PMCID: PMC4366240
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31921

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