ABSTRACT
The tumor-suppressor p53 can induce various biological responses. Yet, it is not clear whether it is p53 in vivo promoter selectivity that triggers different transcription programs leading to different outcomes. Our analysis of genome-wide chromatin occupancy by p53 using chromatin immunoprecipitation (ChIP)-seq revealed 'p53 default program', that is, the pattern of major p53-bound sites that is similar upon p53 activation by nutlin3a, reactivation of p53 and induction of tumor cell apoptosis (RITA) or 5-fluorouracil in breast cancer cells, despite different biological outcomes. Parallel analysis of gene expression allowed identification of 280 novel p53 target genes, including p53-repressed AURKA. We identified Sp1 as one of the p53 modulators, which confer specificity to p53-mediated transcriptional response upon RITA. Further, we found that STAT3 antagonizes p53-mediated repression of a subset of genes, including AURKA.
Subject(s)
Chromatin/metabolism , Genome, Human , Tumor Suppressor Protein p53/metabolism , Aurora Kinase A , Aurora Kinases , Chromatin Immunoprecipitation , Chromosome Mapping , Furans/pharmacology , Gene Expression Regulation, Neoplastic/drug effects , HCT116 Cells , Humans , Imidazoles/pharmacology , MCF-7 Cells , Piperazines/pharmacology , Promoter Regions, Genetic , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Response Elements , STAT3 Transcription Factor/metabolism , Sp1 Transcription Factor/metabolism , Transcription, Genetic , Tumor Suppressor Protein p53/geneticsABSTRACT
A method is presented that reliably detects spherical viruses from a wide variety of noisy low-contrast electron micrographs. Such detection is one of the first image analysis steps in the computer-aided reconstruction of three-dimensional density distribution models of viruses. Particle detection is based on the comparison of intensity in a circular area and in the surrounding ring followed by a number of tests to validate the potential particles. The only required input from the user in addition to the micrograph is an approximate radius of the particle. The method has been implemented as program ETHAN that has been tested for several different data sets. ETHAN has also successfully been used to detect DNA-less virus particles for an actual reconstruction.