Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the most widely used method for analyzing genome-wide DNA–protein interactions. Because there is considerable variation in the modes and strengths of DNA–protein interactions, chromatin immunoprecipitation (ChIP) protocols have been diversified and optimized for different needs. Here, we describe protocols for detecting histone modifications and modifiers using various crosslinking and immunoprecipitation conditions. We provide a complete ChIP-seq workflow covering sample preparation, immunoprecipitation, next-generation sequencing (NGS) library preparation, and data analyses.
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Acknowledgments
This work was supported by the following funding sources: JSPS KAKENHI Grant Numbers 20H04108 and 21 K19513 (S.H.) and 21H02686 and 20KK0185 (M.N.), Takeda Science Foundation (S.H. and M.N.), and the Japan Agency for Medical Research and Development (21gk0210029h0101 (S.H.) and JP19gm4010003 (M.N.)). We would like to thank Editage (www.editage.com) for English language editing.
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Hino, S., Sato, T., Nakao, M. (2023). Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers. In: Hatada, I., Horii, T. (eds) Epigenomics. Methods in Molecular Biology, vol 2577. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2724-2_4
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DOI: https://doi.org/10.1007/978-1-0716-2724-2_4
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