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Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

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Eukaryotic Transcriptional and Post-Transcriptional Gene Expression Regulation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1507))

Abstract

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

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Acknowledgment

The authors thank Christopher Wilkins, Jung Kap Park, and Sangtae Kim at the Pacific Northwest National Laboratory (PNNL) for developing the bioinformatics software used in this work. We appreciate the help from other PNNL colleagues: Matthew Monroe and Nikola Tolić for data analysis and Rosalie K. Chu, Rui Zhao, Anil K. Shukla, and Ron Moore for running LCMS experiments. We also thank Jonathan Galazka at the Oregon State University for preparing the fungal histone samples. The research was performed in Environmental Molecular Sciences Laboratory (EMSL), a US Department of Energy (DOE) national user facility at the Pacific Northwest National Laboratory (PNNL) in Richland, WA.

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Authors and Affiliations

  1. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA

    Mowei Zhou, Si Wu, David L. Stenoien, Zhaorui Zhang & Ljiljana Paša-Tolić

  2. Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA

    Si Wu

  3. Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA

    Lanelle Connolly & Michael Freitag

Authors
  1. Mowei Zhou
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  2. Si Wu
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  3. David L. Stenoien
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  4. Zhaorui Zhang
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  5. Lanelle Connolly
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  6. Michael Freitag
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  7. Ljiljana Paša-Tolić
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Corresponding author

Correspondence to Ljiljana Paša-Tolić .

Editor information

Editors and Affiliations

  1. Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA

    Narendra Wajapeyee

  2. Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA

    Romi Gupta

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Zhou, M. et al. (2017). Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry. In: Wajapeyee, N., Gupta, R. (eds) Eukaryotic Transcriptional and Post-Transcriptional Gene Expression Regulation. Methods in Molecular Biology, vol 1507. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6518-2_12

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  • DOI: https://doi.org/10.1007/978-1-4939-6518-2_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6516-8

  • Online ISBN: 978-1-4939-6518-2

  • eBook Packages: Springer Protocols

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