Abstract
Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms. Mass spectrometry (MS) has progressively developed as a powerful technology for the study of histone variants and their PTMs. Indeed, MS analyses highlighted exquisitely complex combinations of PTMs, suggesting “crosstalk” between them, and also revealed that PTM patterns are often variant-specific. Even though the sensitivity and acquisition speed of MS instruments have considerably increased alongside the development of computational tools for the study of multiple PTMs, it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids. Here, we provide an inventory of MS-based strategies and of the pitfalls inherent to histone PTM and variant characterization, while stressing the complex interplay between PTMs and histone sequence variations. We will particularly illustrate the roles played by MS-based analyses in identifying and quantifying histone variants and modifications.
Highlights
The nucleosome core particle packaging cellular DNA is composed of two copies of H2A, H2B, H3, and H4 histones surrounded by 142 base pairs of DNA [1]
Even though the sensitivity and acquisition speed of mass spectrometry (MS) instruments have considerably increased alongside the development of computational tools for the study of multiple post-translational modifications (PTMs), it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids
These findings suggest that histone modifications as well as histone variants are “docking sites” and a network for the recruitment of protein factors to facilitate the chromatin remodeling, and the regulation of gene expression
Summary
The nucleosome core particle packaging cellular DNA is composed of two copies of H2A, H2B, H3, and H4 histones surrounded by 142 base pairs of DNA [1]. These PTMs can recruit a variety of specific binders, which can either reinforce transcription activation or promote its repression (reviewed in Reference [8]) Another example is the methylation of H3K27 by Polycomb group proteins which establish a strongly repressed chromatin structure. Th2b KO has no effect on male infertility due to a compensatory mechanism mediated by the addition of methyl groups at H4R35, H4R55, H4R67, and H2BR72 [16] These findings suggest that histone modifications as well as histone variants are “docking sites” and a network for the recruitment of protein factors to facilitate the chromatin remodeling, and the regulation of gene expression.
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