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Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants

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Plant Transcription Factors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1830))

Abstract

The precise positioning of nucleosomes along the underlying DNA is critical for a variety of biological processes, especially in regulating transcription. The interplay between nucleosomes and transcription factors for accessing the underlying DNA sequences is one of the key determinants that affect transcriptional regulation. Moreover, nucleosomes with various packing statuses confer distinct functions in regulating gene expressions in response to various internal or external signals. Therefore, global mapping of nucleosome positions is one informative way to elucidate the relationship between patterns of nucleosome positioning/occupancy and transcriptional regulations. MNase digestion coupled with high-throughput sequencing (MNase-seq) has been utilized widely for global mapping of nucleosome positioning in eukaryotes that have a sequenced genome. We have developed a robust MNase-seq procedure in plants. It mainly includes plant nuclei isolation, treatment of purified nuclei with MNase, gel recovery of MNase-trimmed mononucleosomal DNA with an approximate size of 150 bp, MNase-seq library preparation followed by Illumina sequencing, and data analysis. MNase-seq has already been successfully applied to identify genome-wide nucleosome positioning in model plants, rice, and Arabidopsis thaliana.

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Acknowledgments

We thank Kevin Coe for editing the manuscript. This work was supported by grants from the National Natural Science Foundation of China for W.Z. (31571579 and 31371239), an “Innovation and Enterprise Scholar” of Jiangsu Province for WZ, and the National Science Foundation for J.J. (MCB-1412948).

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Authors and Affiliations

  1. State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, China

    Wenli Zhang

  2. Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu, China

    Wenli Zhang

  3. Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA

    Jiming Jiang

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  1. Wenli Zhang
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  2. Jiming Jiang
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Correspondence to Wenli Zhang .

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Editors and Affiliations

  1. Plant Stem Cell Regulation and Floral Patterning Laboratory, Nara Institute of Science and Technology, Ikoma, Nara, Japan

    Nobutoshi Yamaguchi

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Zhang, W., Jiang, J. (2018). Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants. In: Yamaguchi, N. (eds) Plant Transcription Factors. Methods in Molecular Biology, vol 1830. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8657-6_21

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  • DOI: https://doi.org/10.1007/978-1-4939-8657-6_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8656-9

  • Online ISBN: 978-1-4939-8657-6

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