Abstract
The p53 transcription factor is a potent suppressor of tumor growth. We report here an analysis of its direct transcriptional program using Global Run-On sequencing (GRO-seq). Shortly after MDM2 inhibition by Nutlin-3, low levels of p53 rapidly activate ∼200 genes, most of them not previously established as direct targets. This immediate response involves all canonical p53 effector pathways, including apoptosis. Comparative global analysis of RNA synthesis vs steady state levels revealed that microarray profiling fails to identify low abundance transcripts directly activated by p53. Interestingly, p53 represses a subset of its activation targets before MDM2 inhibition. GRO-seq uncovered a plethora of gene-specific regulatory features affecting key survival and apoptotic genes within the p53 network. p53 regulates hundreds of enhancer-derived RNAs. Strikingly, direct p53 targets harbor pre-activated enhancers highly transcribed in p53 null cells. Altogether, these results enable the study of many uncharacterized p53 target genes and unexpected regulatory mechanisms.DOI: http://dx.doi.org/10.7554/eLife.02200.001.
Highlights
The p53 transcription factor is activated by potentially oncogenic stimuli such as ribosomal stress, DNA damage, telomere erosion, nutrient deprivation and oncogene hyperactivation (Vousden and Prives, 2009)
Diverse signaling pathways converge on the p53/MDM2/MDM4 complex to release p53 from its repressors and enable it to regulate transcription of downstream target genes involved in cellular responses such as cell cycle arrest, apoptosis, senescence, autophagy, DNA repair and central metabolism (Vousden and Prives, 2009). p53 is inactivated in virtually all human cancers, either by mutations in its DNA binding domain or MDM2/MDM4 overexpression
Q-RT-PCR shows that the differential effects of p53 on the basal transcription of its targets are generally translated into differences in mRNA steady level (Figure 3D). These results indicate that p53 acts as a repressor at a subset of its targets in a manner that is relieved by Nutlin, suggesting that MDM2 recruitment by basal levels of p53 may repress transcription at specific loci
Summary
The p53 transcription factor is activated by potentially oncogenic stimuli such as ribosomal stress, DNA damage, telomere erosion, nutrient deprivation and oncogene hyperactivation (Vousden and Prives, 2009). A second class of molecules binds to mutant p53 and partially restores its wild type function (Brown et al, 2009) As these compounds enter clinical trials, their efficacy is limited by the fact that p53 activation leads to cancer cell death only in specific scenarios. A recent comprehensive survey of the literature identified ∼120 genes for which direct regulation has been established (Riley et al, 2008), but a comprehensive analysis of p53-regulated RNAs is still missing Up to this point, the global p53 transcriptional response has been investigated with techniques that measure steady state RNA levels, mostly microarray profiling. GRO-seq revealed widespread activation of enhancer-derived RNAs (eRNAs) arising from p53REs. Interestingly, direct p53 target genes harbor ‘pre-activated’ p53REs, as defined by the strong production of eRNAs in the isogenic p53 null cells. These results elucidate novel p53-regulated RNAs as well as gene-specific regulatory events within the p53 network and pave the road for a myriad of future mechanistic studies
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
