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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 2318))

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, we describe the validation of single c-MYC targets identified by NGS . Taken together, these approaches allow an accelerated and comprehensive analysis of c-MYC function in numerous cellular contexts. Ultimately, these analyses will further illuminate the role of this important oncogene.

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Acknowledgments

Work in the Hermeking lab is supported by the German-Israeli-Science-Foundation (GIF), the Wilhelm-Sander-Stiftung, the Else-Kröner-Fresenius-Stiftung, the Rudolf-Bartling-Stiftung, the Deutsche Krebshilfe, the Deutsches Konsortium für translationale Krebsforschung (DKTK), and the Deutsche Forschungsgemeinschaft (DFG).

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

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Authors and Affiliations

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

    Rene Jackstadt, Markus Kaller & Heiko Hermeking

  2. German Cancer Consortium (DKTK), Munich, Germany

    Antje Menssen & Heiko Hermeking

  3. German Cancer Research Center (DKFZ), Heidelberg, Germany

    Antje Menssen & Heiko Hermeking

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  1. Rene Jackstadt
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  2. Markus Kaller
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  3. Antje Menssen
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  4. Heiko Hermeking
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Correspondence to Heiko Hermeking .

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Editors and Affiliations

  1. Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain

    Laura Soucek

  2. Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain

    Jonathan Whitfield

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Jackstadt, R., Kaller, M., Menssen, A., Hermeking, H. (2021). Genome-Wide Analysis of c-MYC-Regulated mRNAs and miRNAs and c-MYC DNA-Binding by Next-Generation Sequencing. In: Soucek, L., Whitfield, J. (eds) The Myc Gene. Methods in Molecular Biology, vol 2318. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1476-1_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1476-1_7

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1475-4

  • Online ISBN: 978-1-0716-1476-1

  • eBook Packages: Springer Protocols

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