通过二维液相色谱与自上而下质谱联用对人组蛋白H4进行组合修饰定量分析。

Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

作者信息

Pesavento James J, Bullock Courtney R, LeDuc Richard D, Mizzen Craig A, Kelleher Neil L

机构信息

Center for Biophysics and Computational Biology, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

出版信息

J Biol Chem. 2008 May 30;283(22):14927-37. doi: 10.1074/jbc.M709796200. Epub 2008 Apr 1.

Abstract

Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10(4) using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.

摘要

定量蛋白质组学主要致力于通过开发以蛋白质表达为中心的方法(如同位素编码亲和标签、用于相对和绝对定量的等压标签等)来关联蛋白质丰度、比率和动力学。这些方法有效地检测了蛋白质丰度的变化,但未能全面呈现诸如组蛋白等受翻译后修饰调控的蛋白质多样性。在此,我们报告了使用严格的自上而下质谱方法结合二维液相色谱对HeLa细胞组蛋白H4修饰形式的表征,其动态范围>10(4)。这种增强的动态范围使得能够精确表征和定量42种由甲基化和乙酰化组合独特修饰的形式,包括那些具有三甲基化赖氨酸-20、单甲基化精氨酸-3和新型二甲基化精氨酸-3的形式(每种在所有H4形式中均<1%)。定量分析揭示了取决于赖氨酸-20甲基化状态的乙酰化位点占有率的不同趋势。由于这两种修饰在细胞周期中均受到动态调控,我们同时研究了三个细胞周期阶段的乙酰化和甲基化动力学,并利用这些数据对我们定量分析的稳健性进行了统计评估。这项工作代表了迄今为止报道的对人类细胞中存在的组蛋白H4形式的最全面分析。

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