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Genome-Wide Analysis of c-MYC-Regulated mRNAs and miRNAs, and c-MYC DNA Binding by Next-Generation Sequencing

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The Myc Gene

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1012))

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.

HiSeq (1), Illumina (2), MiSeq (3), and TruSeq (4) are registered trademarks of Illumina Inc., San Diego, CA.

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Acknowledgments

Work in the Hermeking lab is supported by the German–Israeli Science Foundation (GIF), the Rudolf-Bartling-Stiftung, the Deutsche Krebshilfe, the German Cancer Consortium (DKTK), and the Deutsche Forschungsgemeinschaft (DFG).

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Authors and Affiliations

  1. Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany

    Rene Jackstadt, Antje Menssen & Heiko Hermeking

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  1. Rene Jackstadt
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  2. Antje Menssen
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  3. Heiko Hermeking
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Editors and Affiliations

  1. Fundació Vall d'Hebron Institute of Onco, Barcelona, Spain

    Laura Soucek

  2. Department of Biochemistry Sanger Building, University of Cambridge, Cambridge, United Kingdom

    Nicole M. Sodir

Note added in proof

Note added in proof

While this chapters was in press the authors published a completed analysis of mRNH expression and ONH building further illustrating the approaders drescribed here [83]

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Jackstadt, R., Menssen, A., Hermeking, H. (2013). Genome-Wide Analysis of c-MYC-Regulated mRNAs and miRNAs, and c-MYC DNA Binding by Next-Generation Sequencing. In: Soucek, L., Sodir, N. (eds) The Myc Gene. Methods in Molecular Biology, vol 1012. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-429-6_11

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  • DOI: https://doi.org/10.1007/978-1-62703-429-6_11

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