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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Top-down characterization of mouse core histones.

Bingbing Xue1, Kaijie Xiao1, Zhixin Tian1

  • 1School of Chemical Science and Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.

Journal of Mass Spectrometry : JMS
|January 31, 2019
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Summary

This study comprehensively analyzes histone post-translational modifications (PTMs) in mouse cells using top-down proteomics. It identifies 547 histone protein species and localizes PTMs, providing a foundational reference for chromatin biology research.

Keywords:
ProteinGogglecore histonesmouse NIH/3T3 cellspost-translational modificationstop-down proteomics

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Area of Science:

  • Proteomics
  • Epigenetics
  • Cellular Biology

Background:

  • Histone post-translational modifications (PTMs) are crucial for chromatin regulation.
  • Understanding PTM crosstalk at the intact protein level is vital for elucidating biological functions.

Purpose of the Study:

  • To perform a top-down proteomic characterization of core histones from mouse fibroblasts (NIH/3T3).
  • To identify and localize combinatorial PTMs on intact histone proteins.
  • To establish a comprehensive reference map of mouse core histone PTMs.

Main Methods:

  • Nano-liquid chromatography-tandem mass spectrometry (nanoRPLC-MS/MS) for top-down proteomics.
  • ProteinGoggle database for data analysis and identification.
  • High-resolution MS/MS for unambiguous PTM localization and identification.

Main Results:

  • Identification of 547 core histone protein species with high confidence (spectrum-level FDR ≤ 1%).
  • Unambiguous localization of PTMs in 51 protein species (PTM scores ≥ 1).
  • Distinguished acetylation from trimethylation using high-resolution MS/MS data.

Conclusions:

  • This study provides a detailed overview of combinatorial PTMs on mouse core histones.
  • The findings serve as a critical reference for future epigenetic and chromatin biology studies.
  • Top-down proteomics is effective for comprehensive analysis of histone PTMs.