Mass spectrometry-based strategies for characterization of histones and their post-translational modifications

Abstract

Due to the intimate interactions between histones and DNA, the characterization of histones has become the focus of great attention. A series of mass spectrometry-based technologies have been dedicated to the characterization and quantitation of different histone forms. This review focuses on the discussion of mass spectrometry-based strategies used for the characterization of histones and their post-translational modifications. Keywordshistone; mass spectrometry; post-translational modification Histones are a group of highly conserved proteins throughout eukaryotic evolution [1]. The core histones (H4, H3, H2A and H2B) form an octamer, in which a H2A-H2B dimer associates on each side of the H3-H4 tetramer through an interaction between the C-terminal halves of H2B and H4 [2]. The negatively charged DNA superhelix wraps around the histone octamer to form repeating nucleosome cores, which further assemble into higher order chromatin fibers stabilized by the linker histones (H1 and H5) and linker DNA [3]. The histone fold regions in core histones are highly conserved α-helices, which are connected by two loops. The third histone structural motif comprises the flexible and irregular histone tails, which are extended and reach outside of the nucleosomal unit to interact with DNA [4]. Challenge of molecular characterization: post-translational modifications & sequence variationsAs a building block of the nucleosome, histones play an important role in chromatin assembly and affect the interactions between DNA and other chromatin-associated proteins. Histones regulate gene transcription through their diverse post-translational modifications (PTMs), which include lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, lysine ubiquitination, lysine sumoylation, and poly-ADP-ribosylation of glutamic acid [5][6][7][8]. Among all the PTMs, histone acetylation and methylation have been most †

Identification of Histone Mutants That Are Defective for Transcription-Coupled Nucleosome Occupancy

“…Interestingly, two of these residues, histone H3 K122 and H4 S47, are highly conserved among eukaryotes and are targets for posttranslational modifications, although the functional significance of these modifications is not known. H3 K122 has been shown to be methylated in mice and humans (74,88) and acetylated in bovine (99); however, similar modifications in yeast have not yet been detected (32,76). The phosphorylation of H4 S47 has been detected in yeast (32,40,99), and a phenotype associated with this residue is dependent on the substitution: S47A and S47E both confer sensitivity to HU, while S47D is not sensitive (40).…”

Comparing and Combining Capillary Electrophoresis Electrospray Ionization Mass Spectrometry and Nano–Liquid Chromatography Electrospray Ionization Mass Spectrometry for the Characterization of Post-translationally Modified Histones

“…Over the past several years, considerable efforts have been expended to develop methods to identify the specific sites of histone modifications. Mass spectrometry (MS) coupled to liquid chromatography (LC) is the dominant technique for their characterization (7)(8)(9)(10)(11)(12)(13)(14). However, because histone proteins contain up to nearly 35% basic amino acids, the analysis of histone peptides is still problematic, as digestion with many commonly used enzymes (e.g.…”

A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies

“…One recent approach used mass spectrometry-based methods. 72 Due to the abundance of histones in normal cells, mass spectrometry can be used to quantify and identify the posttranslational modification patterns. 73,74 This approach might be especially interesting for control of epigenetic therapy whereby global alterations of histone modifications can be analyzed.…”