Abstract
Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a widely used method for mapping the genome-wide locations of chromatin-associated proteins. This protocol has been developed and utilized to perform ChIP on histone covalent modifications in various plant species including cereals. DNA and chromatin-associated proteins are crosslinked with formaldehyde. Chromatin is then isolated from nuclei and sheared via sonication. Antibodies targeting the histone modification of interest are incubated with the sheared chromatin and nonspecific interactions are washed away. DNA is purified via phenol-chloroform extraction, end-repaired, ligated to sequencing adapters, and PCR-amplified.
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References
Ji X, Dadon DB, Abraham BJ et al (2015) Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci U S A 112:3841–3846
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128:707–719
Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6:838–849
Albert I, Mavrich TN, Tomsho LP et al (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446:572–576
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837
Johnson DS, Mortazavi A, Myers RM et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502
Mikkelsen TS, Ku M, Jaffe DB et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560
Acknowledgments
This work was supported by NSF PGRP grant 1546867 to X.Z.
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Ricci, W.A., Levin, L., Zhang, X. (2020). Genome-Wide Profiling of Histone Modifications with ChIP-Seq. In: Vaschetto, L. (eds) Cereal Genomics. Methods in Molecular Biology, vol 2072. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9865-4_9
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DOI: https://doi.org/10.1007/978-1-4939-9865-4_9
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Publisher Name: Humana, New York, NY
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