Identification of Acetylation and Methylation Sites of Histone H3 from Chicken Erythrocytes by High-Accuracy Matrix-Assisted Laser Desorption Ionization–Time-of-Flight, Matrix-Assisted Laser Desorption Ionization–Postsource Decay, and Nanoelectrospray Ionization Tandem Mass Spectrometry

Zhang, Kangling; Tang, Hui; Huang, Lan; Blankenship, J. W.; Jones, Patrick R.; Fan, Xianping; Yau, Peter M.; Burlingame, Alma L.

doi:10.1006/abio.2002.5719

Cited by 138 publications

(116 citation statements)

References 26 publications

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“…Using histones purified from different sources (human tissue culture cells, calf thymus, chicken erythrocytes, and Saccharomyces cerevisiae) four groups used peptide mass fingerprinting to identify methylation on lysine residue 79 of histone H3 Ng et al, 2002;van Leeuwen et al, 2002;Zhang et al, 2002a]. The presence of methylation on histone H3 lysine 79 in this divergent collection of organisms indicates that this is a highly conserved modification.…”

Section: Identification Of Sites Of Histone Modification By Mass Specmentioning

confidence: 99%

Application of mass spectrometry to the identification and quantification of histone post‐translational modifications

Freitas

Sklenar

Parthun

2004

J of Cellular Biochemistry

130

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The core histories are the primary protein component of chromatin, which is responsible for the packaging of eukaryotic DNA. The NH 2 -terminal tail domains of the core histones are the sites of numerous post-translational modifications that have been shown to play an important role in the regulation of chromatin structure. In this study, we discuss the recent application of modern analytical techniques to the study of histone modifications. Through the use of mass spectrometry, a large number of new sites of histone modification have been identified, many of which reside outside of the NH 2 -terminal tail domains. In addition, techniques have been developed that allow mass spectrometry to be effective for the quantitation of histone post-translational modifications. Hence, the use of mass spectrometry promises to dramatically alter our view of histone post-translational modifications.

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Section: Identification Of Sites Of Histone Modification By Mass Specmentioning

confidence: 99%

Application of mass spectrometry to the identification and quantification of histone post‐translational modifications

Freitas

Sklenar

Parthun

2004

J of Cellular Biochemistry

130

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“…However, these techniques are time consuming and have certain limitations that do not enable complete characterization of the myriad of modifications present on histones. Mass spectrometry (MS) has complemented the biological work being conducted on histone PTMs, categorizing novel modifications on histones that were previously not detected by any other means [4][5][6][7][8] . Histone proteins pose a formidable challenge to the mass spectrometrist, as their sequences are decorated with an overwhelming number of arginine and lysine residues, especially on the N-termini where most PTMs are known to reside.…”

Section: Introductionmentioning

confidence: 99%

“…Enzymatic digestion with trypsin results in small peptides that are difficult to retain on RP-HPLC columns and analyzed by MS. On the other hand, proteolysis with enzymes that cleave after acidic residues (e.g., Glu-C) generates larger multiply charged peptides whose MS/MS spectra are difficult if not impossible to interpret. MS-related histone work has benefited from the use of limited trypsin or other enzyme digestion [4][5][6] ; however, these methods typically generate several truncated peptides containing the same modification sites, rendering quantification of histone PTMs cumbersome. More recently, the Arg-C digestion of histones has been performed to produce histone peptides that can be used for relative quantification purposes 8 .…”

Section: Introductionmentioning

confidence: 99%

Chemical derivatization of histones for facilitated analysis by mass spectrometry

et al. 2007

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Histone post-translational modifications have been recently intensely studied owing to their role in regulating gene expression. Here, we describe protocols for the characterization of histone modifications in both qualitative and semiquantitative manners using chemical derivatization and tandem mass spectrometry. In these procedures, extracted histones are first derivatized using propionic anhydride to neutralize charge and block lysine residues, and are subsequently digested using trypsin, which, under these conditions, cleaves only the arginine residues. The generated peptides can be easily analyzed using online LC-electrospray ionization-tandem mass spectrometry to identify the modification site. In addition, a stable isotope-labeling step can be included to modify carboxylic acid groups allowing for relative quantification of histone modifications. This methodology has the advantage of producing a small number of predicted peptides from highly modified proteins. The protocol should take approximately 15-19 h to complete, including all chemical reactions, enzymatic digestion and mass spectrometry experiments.

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“…The sequence information and the exact sites of methylation are usually determined by tandem mass spectrometry (MS/MS) analysis of these peptides. [117][118][119][120] "Topdown" methods directly measure the masses of full length histones, and the methylation level and their relative stoichiometry can be obtained by MS profiling and protein fragmentation. 121,122 Because a significant number of PTMs are located in the N-terminal region of the core histones, an alternative version of top-down method, "middle-town" approach has been applied to characterize large peptides that usually contain less than 50 Nterminal amino acid residues of histone tails.…”

Section: Analysis Of Histone Methylation By Mass Spectrometrymentioning

confidence: 99%

“…14 Close to one hundred PTMs have been discovered thus far, which are located in both the terminal tails and the fold domain. 117,155,[176][177][178] A great challenge in epigenetics research is to elucidate the biochemical effects of specific histone modifications on cell growth and differentiation. Histones isolated from mammalian cells possess complex and heterogeneous modification patterns, 151,163,179 which makes it technically difficult to investigate the contribution from individual modification sites.…”

Section: Site-specific Methylation Of Histones For Mechanistic and Fumentioning

confidence: 99%

Chemical and biochemical approaches in the study of histone methylation and demethylation

Luo

Wang

et al. 2010

Med. Res. Rev.

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Histone methylation represents one of the most critical epigenetic events in DNA function regulation in eukaryotic organisms. Classic molecular biology and genetics tools provide significant knowledge about mechanisms and physiological roles of histone methyltransferases and demethylases in various cellular processes. In addition to this stream line, development and application of chemistry and chemistry-related techniques are increasingly involved in biological study, and provide information otherwise difficulty to obtain by standard molecular biology methods. Herein, we review recent achievements and progress in developing and applying chemical and biochemical approaches in the study of histone methylation, including chromatin immunoprecipitation (ChIP), chemical ligation, mass spectrometry (MS), biochemical assays, and inhibitor development. These technological advances allow histone methylation to be studied from genome-wide level to molecular and atomic levels. With ChIP technology, information can be obtained about precise mapping of histone methylation patterns at specific promoters, genes or other genomic regions. MS is particularly useful in detecting and analyzing methylation marks in histone and nonhistone protein substrates. Chemical approaches that permit site-specific incorporation of methyl groups into histone proteins greatly facilitate the investigation of the biological impacts of methylation at individual modification sites. Discovery and design of selective organic inhibitors of histone methyltransferases and demethylases provide chemical probes to interrogate methylation-mediated cellular pathways. Overall, these chemistry-related technological advances have greatly improved our understanding of the biological functions of histone methylation in normal physiology and diseased states, and also are of great potential to translate basic epigenetics research into diagnostic and therapeutic application in the clinic.

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Identification of Acetylation and Methylation Sites of Histone H3 from Chicken Erythrocytes by High-Accuracy Matrix-Assisted Laser Desorption Ionization–Time-of-Flight, Matrix-Assisted Laser Desorption Ionization–Postsource Decay, and Nanoelectrospray Ionization Tandem Mass Spectrometry

Cited by 138 publications

References 26 publications

Application of mass spectrometry to the identification and quantification of histone post‐translational modifications

Application of mass spectrometry to the identification and quantification of histone post‐translational modifications

Chemical derivatization of histones for facilitated analysis by mass spectrometry

Chemical and biochemical approaches in the study of histone methylation and demethylation

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