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Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq

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Transcription Factor Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2594))

Abstract

Functional cis-regulatory elements (CREs) act as precise transcriptional switches for fine-tuning gene transcription. Identification of CREs is critical for understanding regulatory mechanisms of gene expression associated with various biological processes in eukaryotes. It is well known that CREs reside in open chromatin that exhibits hypersensitivity to enzyme cleavage and physical shearing. Currently, high-throughput methodologies, such as DNase-seq, ATAC-seq, and FAIRE-seq, have been widely applied in mapping open chromatin in various eukaryotic genomes. More recently, differential MNase (micrococcal nuclease) treatment has been successfully employed to map open chromatin in addition to profiling nucleosome landscape in both mammalian and plant species. We have developed a MNase hypersensitivity sequencing (MH-seq) technique in plants. The MH-seq procedure includes plant nuclei fixation and purification, differential treatments of purified nuclei with MNase, specific recovery of MNase-trimmed small DNA fragments within 20~100 bp in length, and MH-seq library construction followed by Illumina sequencing and data analysis. MH-seq has been successfully applied for global identification of open chromatin in both Arabidopsis thaliana and maize. It has been proven to be an attractive alternative for profiling open chromatin. Thus, MH-seq is expected to be valuable in probing chromatin accessibility on a genome-wide scale for other plants with sequenced genomes. Moreover, MHS data allow to implement footprinting assays to unveil binding sites of transcription factors.

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Acknowledgments

We thank the Bioinformatics Center in Nanjing Agricultural University for providing facilities to assist sequencing data analysis. This work was supported by grants from the National Natural Science Foundation of China for W.Z. (32070561, 31571579) and the Fundamental Research Funds for the Central Universities (KYYJ201808).

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Authors and Affiliations

  1. State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China

    Aicen Zhang, Xinxu Li & Wenli Zhang

  2. Department of Plant Biology, Michigan State University, East Lansing, MI, USA

    Hainan Zhao & Jiming Jiang

  3. Department of Horticulture, Michigan State University, East Lansing, MI, USA

    Jiming Jiang

Authors
  1. Aicen Zhang
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  2. Xinxu Li
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  3. Hainan Zhao
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  4. Jiming Jiang
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  5. Wenli Zhang
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Corresponding author

Correspondence to Wenli Zhang .

Editor information

Editors and Affiliations

  1. Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA

    Qi Song

  2. Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA

    Zhipeng Tao

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Zhang, A., Li, X., Zhao, H., Jiang, J., Zhang, W. (2023). Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq. In: Song, Q., Tao, Z. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 2594. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2815-7_3

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  • DOI: https://doi.org/10.1007/978-1-0716-2815-7_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2814-0

  • Online ISBN: 978-1-0716-2815-7

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