Abstract
Chromatin immunoprecipitation (ChIP) is a method used to examine the genomic localization of a target of interest (e.g., proteins, protein posttranslational modifications, or DNA elements). As ChIP provides a snapshot of in vivo DNA–protein interactions, it lends insight to the mechanisms of gene expression and genome regulation. This chapter provides a detailed protocol focused on native-ChIP (N-ChIP), a robust approach to profile stable DNA–protein interactions. We also describe best practices for ChIP , including defined controls to ensure specific and efficient target enrichment and methods for data normalization.
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Acknowledgments
This work was supported by the National Institutes of Health under award numbers R44HG008907, R44GM116584 and R43CA232941 to EpiCypher, Inc. The authors would like to thank Rohan N. Shah, Adrian T. Grzybowski, and Alexander J. Ruthenburg (Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL) for sharing protocols and generation of the raw data analyzed in Fig. 2 [23].
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Small, E.C., Maryanski, D.N., Rodriguez, K.L., Harvey, K.J., Keogh, MC., Johnstone, A.L. (2021). Chromatin Immunoprecipitation (ChIP) to Study DNA–Protein Interactions. In: Posch, A. (eds) Proteomic Profiling. Methods in Molecular Biology, vol 2261. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1186-9_20
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DOI: https://doi.org/10.1007/978-1-0716-1186-9_20
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