Revealing histone variant induced changes via quantitative proteomics.

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Critical Reviews in Biochemistry and Molecular Biology (Impact Factor: 5.81). 04/2011; 46(4):284-94. DOI: 10.3109/10409238.2011.577052
Source: PubMed

ABSTRACT Histone variants are isoforms of linker and core histone proteins that differ in their amino acid sequences. These variants have distinct genomic locations and posttranslational modifications, thus increasing the complexity of the chromatin architecture. Biological studies of histone variants indicate that they play a role in many processes including transcription, DNA damage response, and the cell cycle. The small differences in amino acid sequence and the diverse posttranslational modification states that exist between histone variants make traditional analysis using immunoassay methods challenging. In recent years, a number of mass spectrometric techniques have been developed to identify and quantify histones at the whole protein or peptide levels. In this review, we discuss the biology of histone variants and methods to characterize them using mass spectrometry-based proteomics.


Available from: Rosalynn Molden, Jan 15, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In the central nervous system, epigenetic processes are involved in a multitude of brain functions ranging from the development and differentiation of the nervous system through to higher-order cognitive processes such as learning and memory. This review summarises the current state of the art for the proteomic analysis of the epigenetic regulation of gene expression, in particular the PTM of histones, in the brain and cellular model systems. It describes the MS technologies that have helped the identification and analysis of histones, histone variants and PTMs in the brain. Strategies for the isolation of histones that allow the qualitative analysis of PTMs and their combinatorial patterns are introduced, methods for the relative and absolute quantification of histone PTMs are described, and future challenges are discussed.
    PROTEOMICS 01/2012; 12:2404-20. · 3.97 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Epigenetic regulation of gene expression is, at least in part, mediated by histone modifications. PTMs of histones change chromatin structure and regulate gene transcription, DNA damage repair, and DNA replication. Thus, studying histone variants and their modifications not only elucidates their functional mechanisms in chromatin regulation, but also provides insights into phenotypes and diseases. A challenge in this field is to determine the best approach(es) to identify histone variants and their PTMs using a robust high-throughput analysis. The large number of histone variants and the enormous diversity that can be generated through combinatorial modifications, also known as histone code, makes identification of histone PTMs a laborious task. MS has been proven to be a powerful tool in this regard. Here, we focus on bottom-up, middle-down, and top-down MS approaches, including CID and electron-capture dissociation/electron-transfer dissociation based techniques for characterization of histones and their PTMs. In addition, we discuss advances in chromatographic separation that take advantage of the chemical properties of the specific histone modifications. This review is also unique in its discussion of current bioinformatic strategies for comprehensive histone code analysis.
    Proteomics 03/2014; 14(4-5). DOI:10.1002/pmic.201300256 · 3.97 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Histones play important roles in chromatin, in the forms of various post-translational modifications (PTMs) and sequence variants, which are called histone proteoforms. Investigating modifications and variants is an ongoing challenge. Previous methods are based on antibodies, and because they usually detect only one modification at a time, they are not suitable for studying the various combinations of modifications on histones. Fortunately, mass spectrometry (MS) has emerged as a high-throughput technology for histone analysis and does not require prior knowledge about any modifications. From the data generated by mass spectrometers, both identification and quantification of modifications, as well as variants, can be obtained easily. On the basis of this information, the functions of histones in various cellular contexts can be revealed. Therefore, MS continues to play an important role in the study of histone proteoforms. In this review, we discuss the analysis strategies of MS, their applications on histones, and some key remaining challenges. Expected final online publication date for the Annual Review of Analytical Chemistry Volume 7 is June 15, 2014. Please see for revised estimates.
    Annual Review of Analytical Chemistry (2008) 08/2013; DOI:10.1146/annurev-anchem-071213-015959 · 7.81 Impact Factor