A Modified Epigenetics Toolbox to Study Histone Modifications on the Nucleosome Core

Abstract

In the eukaryotic cell nucleus, the DNA is packaged in a structure called chromatin. The fundamental building block of chromatin is the nucleosome, which is composed of DNA wrapped around an octamer of four distinct histone proteins. Post-translational modifications (PTMs) of histone proteins can affect chromatin structure and function and thereby play critical roles in regulating gene expression. Most histone PTMs are found in unstructured histone tails that protrude from the nucleosome core. As a consequence, (synthetic) peptide truncations of these tails provide convenient substrates for the analysis of histone binding proteins and modifying enzymes. Modifications located on residues that reside in the nucleosome core are more difficult to study because short peptides do not recapitulate this defined structured state well. Methylation of histone H3 on Lys79 (H3K79), mediated by the Dot1 enzyme, is an example of such a core PTM. This modification, which is highly conserved, is linked to human leukemia, and pharmacological modulation of Dot1 activity could be a strategy to treat leukemia. Here we review the available and emerging genetic, biochemical, and chemical methods that together are starting to reveal the function and regulation of this and other histone modifications on the nucleosome core.

Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry

“…Although it has numerous advantages as outlined above, the middle-down strategy still provides only a limited view of the global distribution of modifications in histones. H3K56ac [113], H3K79me [114,115] and H4K59ac [116] are examples of modifications which reside on the nucleosome core. Thus, these specific PTMs will not be detected by applying this strategy to isolated N-terminal tails of histones.…”

A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks

“…The corresponding expressed protein ligation (EPL) version can use a recombinant histone amino-terminal peptide with an a-thioester building block, which can be chemically modified to mimic a particular PTM (e.g., Kme1), ligated to the remainder of the unmodified core histone. This approach, when used with yet to be determined DNA templates that allow more uniform positioning of core histones on the DNA, has the potential for being able to incorporate standard PTMs positioned at multiple sites on histone tails into mononucleosomes in good yields, thereby generating designer chromatin for structural and functional studies (reviewed in Allis and Muir 2011;Frederiks et al 2011;Voigt and Reinberg 2011;Fierz and Muir 2012). The potential exists for extending this EPL technology to PTM probes site-specifically incorporated into dinucleosomes and nucleosomal arrays by ligating the DNA of preformed nucleosomes.…”

Structural and Functional Coordination of DNA and Histone Methylation

“…Histone H3 Lys-79 (H3K79) is methylated by Dot1p (reviewed in Frederiks et al 2011), a protein originally identified as a disruptor of telomeric silencing in Saccharomyces cerevisiae (Singer et al 1998). Methylation of H3K79 in S. cerevisiae is important for the proper localization of the silent information regulator complex and DNA damage signaling (see Grunstein and Gasser 2013).…”