Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

Mary Ann Allen, Zdenek Andrysik, Veronica L. Dengler, Hestia S. Mellert, Anna Guarnieri, Justin A. Freeman, Kelly D. Sullivan, Matthew D. Galbraith, Xin Luo, W. Lee Kraus, Robin D. Dowell, Joaquin M. Espinosa

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Article numbere02200
JournaleLife
Volume2014
Issue number3
DOIs
StatePublished - May 27 2014

Fingerprint

p53 Genes
Transcription
Genes
RNA
Null Lymphocytes
Regulator Genes
Transcription Factors
Apoptosis
Microarrays
Growth
Ports and harbors
Tumors
Neoplasms
Chemical activation
nutlin 3

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Medicine(all)
  • Neuroscience(all)

Cite this

Allen, M. A., Andrysik, Z., Dengler, V. L., Mellert, H. S., Guarnieri, A., Freeman, J. A., ... Espinosa, J. M. (2014). Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. eLife, 2014(3), [e02200]. https://doi.org/10.7554/eLife.02200.001

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. / Allen, Mary Ann; Andrysik, Zdenek; Dengler, Veronica L.; Mellert, Hestia S.; Guarnieri, Anna; Freeman, Justin A.; Sullivan, Kelly D.; Galbraith, Matthew D.; Luo, Xin; Lee Kraus, W.; Dowell, Robin D.; Espinosa, Joaquin M.

In: eLife, Vol. 2014, No. 3, e02200, 27.05.2014.

Research output: Contribution to journalArticle

Allen, MA, Andrysik, Z, Dengler, VL, Mellert, HS, Guarnieri, A, Freeman, JA, Sullivan, KD, Galbraith, MD, Luo, X, Lee Kraus, W, Dowell, RD & Espinosa, JM 2014, 'Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms', eLife, vol. 2014, no. 3, e02200. https://doi.org/10.7554/eLife.02200.001
Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA et al. Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. eLife. 2014 May 27;2014(3). e02200. https://doi.org/10.7554/eLife.02200.001
Allen, Mary Ann ; Andrysik, Zdenek ; Dengler, Veronica L. ; Mellert, Hestia S. ; Guarnieri, Anna ; Freeman, Justin A. ; Sullivan, Kelly D. ; Galbraith, Matthew D. ; Luo, Xin ; Lee Kraus, W. ; Dowell, Robin D. ; Espinosa, Joaquin M. / Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. In: eLife. 2014 ; Vol. 2014, No. 3.
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