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Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila

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Functional Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1654))

Abstract

A thorough study of the genome-wide binding patterns of chromatin proteins is essential for understanding the regulatory mechanisms of genomic processes in eukaryotic nuclei, including DNA replication, transcription, and repair. The DNA adenine methyltransferase identification (DamID) method is a powerful tool to identify genomic binding sites of chromatin proteins. This method does not require fixation of cells and the use of specific antibodies, and has been used to generate genome-wide binding maps of more than a hundred different proteins in Drosophila tissue culture cells. Recent versions of inducible DamID allow performing cell type-specific profiling of chromatin proteins even in small samples of Drosophila tissues that contain heterogeneous cell types. Importantly, with these methods sorting of cells of interest or their nuclei is not necessary as genomic DNA isolated from the whole tissue can be used as an input. Here, I describe in detail an FLP-inducible DamID method, namely generation of suitable transgenic flies, activation of the Dam transgenes by the FLP recombinase, isolation of DNA from small amounts of dissected tissues, and subsequent identification of the DNA binding sites of the chromatin proteins.

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Acknowledgments

I thank the laboratory of Prof. B. van Steensel at the Netherlands Cancer Institute (Amsterdam, the Netherlands) for providing an excellent working environment, the NKI Genomics Core Facility for help with the development of the protocol for preparation of DNA samples for Illumina high-throughput sequencing; Anna A. Ogienko for technical support; Mario Amendola, Maurizio Gatti, and the members of Laboratory of Cell Division for critical reading of the manuscript and helpful suggestions. This work was supported by the grant of Russian Science Foundation no. 16-14-10288.

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Authors and Affiliations

  1. Laboratory of Cell Division, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia

    Alexey V. Pindyurin

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  1. Alexey V. Pindyurin
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Correspondence to Alexey V. Pindyurin .

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Editors and Affiliations

  1. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Michael Kaufmann

  2. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Claudia Klinger

  3. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Andreas Savelsbergh

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Pindyurin, A.V. (2017). Genome-Wide Cell Type-Specific Mapping of In Vivo Chromatin Protein Binding Using an FLP-Inducible DamID System in Drosophila . In: Kaufmann, M., Klinger, C., Savelsbergh, A. (eds) Functional Genomics. Methods in Molecular Biology, vol 1654. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7231-9_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7231-9_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7230-2

  • Online ISBN: 978-1-4939-7231-9

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