Article

Breaking the histone code with quantitative mass spectrometry

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Expert Review of Proteomics (Impact Factor: 3.54). 10/2011; 8(5):631-43. DOI: 10.1586/epr.11.47
Source: PubMed

ABSTRACT Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be 'epigenetic' or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.

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    • "Posttranslational modification (PTM) of histones by acetylation, methylation, ubiquitination or phosphorylation has been shown to modulate the chromatin structure by changing protein–DNA or protein–protein interactions. Mass spectrometry analysis and application of modification-specific antibodies led to the identification of a large number of different PTM sites, located at the N-terminal tails as well as within the globular domains of histone proteins [1] [2] [3] [4]. Some of these modifications such as histone methylation at K9 or K27 are more stable PTMs and are crucial for development, heterochromatic silencing and maintenance of cell identity [5]. "
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    ABSTRACT: Systematic analysis of histone modifications has revealed a plethora of posttranslational modifications that mediate changes in chromatin structure and gene expression. Histone phosphorylation is a transient histone modification that becomes induced by extracellular signals, DNA damage or entry into mitosis. Importantly, phosphorylation of histone proteins does not only lead to the binding of specific reader proteins but also to changes in the affinity for readers or writers of other histone modifications. This induces a cross-talk between different chromatin modifications that allows the spatio-temporal control of chromatin-associated events. In this review we will summarize the progress in our current knowledge of factors sensing reversible histone phosphorylation in different biological scenarios. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 01/2014; · 5.44 Impact Factor
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    • "Readers may contain or recruit effector proteins, forming a signaling scaffold to alter chromatin function and consequently mediate processes such as gene expression, apoptosis, and DNA damage repair (Jenuwein and Allis, 2001). Histone modification analysis has traditionally been conducted using site-specific antibody-based methods such as western blots, chromatin immunoprecipitation, DNA microarrays, and deep sequencing (Britton et al., 2011). While these types of methods are useful in studying histone PTMs, there are several drawbacks. "
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    ABSTRACT: Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs). Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
    Frontiers in Genetics 12/2013; 4:264. DOI:10.3389/fgene.2013.00264
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    ABSTRACT: For the preceding conference see [Zbl 1241.92023].
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