title: Genome-wide analysis of c-MYC-regulated mRNAs and miRNAs, and c-MYC DNA binding by next-generation sequencing.
abstract: The c-MYC oncogene is activated in ~50 % of all tumors, and its product, the c-MYC transcription factor, regulates numerous processes, which contribute to tumor initiation and progression. Therefore, the genome-wide characterization of c-MYC targets and their role in different tumor entities is a recurrent theme in cancer research. Recently, next-generation sequencing (NGS) has become a powerful tool to analyze mRNA and miRNA expression, as well as DNA binding of proteins in a genome-wide manner with an extremely high resolution and coverage. Since the c-MYC transcription factor regulates mRNA and miRNA expression by binding to specific DNA elements in the vicinity of promoters, NGS can be used to generate integrated representations of c-MYC-mediated regulations of gene transcription and chromatin modifications. Here, we provide protocols and examples of NGS-based analyses of c-MYC-regulated mRNA and miRNA expression, as well as of DNA binding by c-MYC. Furthermore, the validation of single c-MYC targets identified by NGS is described. Taken together, these approaches allow an accelerated and comprehensive analysis of c-MYC function in numerous cellular contexts which will further illuminate the role of this important oncogene.
authors.affiliation: Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Rene
authors.initials: R
authors.lastname: Jackstadt
authors.forename: Antje
authors.initials: A
authors.lastname: Menssen
authors.forename: Heiko
authors.initials: H
authors.lastname: Hermeking
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs; D016271:Proto-Oncogene Proteins c-myc; D012333:RNA, Messenger