title: Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.
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.
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States BioFrontiers Institute, Boulder, United States Computational Biosciences Program, University of Colorado, Denver-Anschutz Medical Campus, Aurora, United States.
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Allen
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Zdenek
authors.initials: Z
authors.lastname: Andrysik
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Veronica L
authors.initials: VL
authors.lastname: Dengler
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Hestia S
authors.initials: HS
authors.lastname: Mellert
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Anna
authors.initials: A
authors.lastname: Guarnieri
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Freeman
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Kelly D
authors.initials: KD
authors.lastname: Sullivan
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Galbraith
authors.affiliation: Signalling and Gene Regulation Laboratory, Cecil H and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Luo
authors.affiliation: Signalling and Gene Regulation Laboratory, Cecil H and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States.
authors.forename: W Lee
authors.initials: WL
authors.lastname: Kraus
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States BioFrontiers Institute, Boulder, United States robin.dowell@colorado.edu.
authors.forename: Robin D
authors.initials: RD
authors.lastname: Dowell
authors.affiliation: Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, United States joaquin.espinosa@colorado.edu.
authors.forename: Joaquin M
authors.initials: JM
authors.lastname: Espinosa
mesh_terms: D017209:Apoptosis / Q000235:genetics; D001665:Binding Sites; D002460:Cell Line; D006801:Humans; D051736:Proto-Oncogene Proteins c-mdm2 / Q000037:antagonists & inhibitors; D012313:RNA / Q000378:metabolism; D014158:Transcription, Genetic / Q000502:physiology*; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism / Q000502:physiology*
chemical_list: C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D012313:RNA; C497206:MDM2 protein, human; D051736:Proto-Oncogene Proteins c-mdm2
keywords: PIG3; PUMA; eRNA; genomics; p21; tumor supressor