title: Identification of new p53 target microRNAs by bioinformatics and functional analysis.
abstract: BACKGROUND
  The tumor suppressor p53 is a sequence-specific transcription factor that regulates an extensive network of coding genes, long non-coding RNAs and microRNAs, that establish intricate gene regulatory circuits influencing many cellular responses beyond the prototypical control of cell cycle, apoptosis and DNA repair.
  
  
  METHODS
  Using bioinformatic approaches, we identified an additional group of candidate microRNAs (miRs) under direct p53 transcriptional control. To validate p53 family-mediated responsiveness of the newly predicted target miRs we first evaluated the potential for wild type p53, p63β and p73β to transactivate from p53 response elements (REs) mapped in the miR promoters, using an established yeast-based assay.
  
  
  RESULTS
  The REs found in miR-10b, -23b, -106a, -151a, -191, -198, -202, -221, -320, -1204, -1206 promoters were responsive to p53 and 8 of them were also responsive to p63β or p73β. The potential for germline p53 mutations to drive transactivation at selected miR-associated REs was also examined. Chromatin Immuno-Precipitation (ChIP) assays conducted in doxorubicin-treated MCF7 cells and HCT116 p53+/+ revealed moderate induction of p53 occupancy at the miR-202, -1204, -1206, -10b RE-containing sites, while weak occupancy was observed for the miR-23b-associated RE only in MCF7 cells. RT-qPCR analyses cells showed modest doxorubicin- and/or Nutlin-dependent induction of the levels of mature miR-10b, -23b, -151a in HCT116 p53+/+ and MCF7 cells. The long noncoding RNA PVT1 comprising miR-1204 and -1206 was weakly induced only in HCT116 p53+/+ cells, but the mature miRs were not detected. miR-202 expression was not influenced by p53-activating stimuli in our cell systems.
  
  
  CONCLUSIONS
  Our study reveals additional miRs, particularly miR-10b and miR-151a, that could be directly regulated by the p53-family of transcription factors and contribute to the tuning of p53-induced responses.
authors.affiliation: Laboratory of Transcriptional Networks, Center for Integrative Biology, CIBIO, University of Trento, Trento, Italy. ciribilli@science.unitn.it.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Bisio
authors.forename: Veronica
authors.initials: V
authors.lastname: De Sanctis
authors.forename: Valerio
authors.initials: V
authors.lastname: Del Vescovo
authors.forename: Michela A
authors.initials: MA
authors.lastname: Denti
authors.forename: Anil G
authors.initials: AG
authors.lastname: Jegga
authors.forename: Alberto
authors.initials: A
authors.lastname: Inga
authors.forename: Yari
authors.initials: Y
authors.lastname: Ciribilli
mesh_terms: D000903:Antibiotics, Antineoplastic / Q000494:pharmacology; D001665:Binding Sites; D002843:Chromatin; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000502:physiology; D004317:Doxorubicin / Q000494:pharmacology; D015972:Gene Expression Regulation, Neoplastic; D017930:Genes, Reporter; D045325:HCT116 Cells; D006801:Humans; D049409:Luciferases, Firefly / Q000096:biosynthesis / Q000235:genetics; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009687:Nuclear Proteins / Q000502:physiology; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D020218:Response Elements; D012441:Saccharomyces cerevisiae; D014157:Transcription Factors / Q000502:physiology; D015533:Transcriptional Activation; D000072160:Tumor Protein p73; D016159:Tumor Suppressor Protein p53 / Q000502:physiology*; D025521:Tumor Suppressor Proteins / Q000502:physiology
chemical_list: D000903:Antibiotics, Antineoplastic; D002843:Chromatin; D004268:DNA-Binding Proteins; D035683:MicroRNAs; D009687:Nuclear Proteins; D062085:RNA, Long Noncoding; C495901:TP53 protein, human; C115051:TP63 protein, human; D014157:Transcription Factors; D000072160:Tumor Protein p73; D016159:Tumor Suppressor Protein p53; D025521:Tumor Suppressor Proteins; D004317:Doxorubicin; D049409:Luciferases, Firefly