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Nano-electrospray tandem mass spectrometric analysis of the acetylation state of histones H3 and H4 in stationary phase in Saccharomyces cerevisiae

DOI: 10.1186/1471-2091-12-34

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Abstract:

We made use of nano-spray tandem mass spectrometry to perform a precursor ion scan to detect an m/z 126 immonium ion, diagnostic of an Nε-acetylated lysine residue that allowed unambiguous identification of acetylated as opposed to tri-methylated lysine. The fragmentation spectra of peptides thus identified were searched with Mascot against the Swiss-Prot database, and the y-ion and b-ion fragmentation series subsequently analyzed for mass shifts compatible with acetylated lysine residues. We found that K9, K14 and K36 of histone H3 and K12 and K16 of histone H4 were acetylated in exponential phase (bulk histones), but could not detect these modifications in histones isolated from stationary phase cells at the sensitivity level of the mass spectrometer. The corresponding un-acetylated peptides were, however, observed. A significantly higher level of acetylation of these residues in exponential phase was confirmed by immuno-blotting.H4K16 acetylation was previously shown to disrupt formation of condensed chromatin in vitro. We propose that de-acetylation of H4K16 allowed formation of condensed chromatin in stationary phase, and that acetylation of H3K9, H3K14, H3K36, and H4K12 reflected the active transcriptional state of the yeast genome in exponential phase.In 1963 Allfrey and colleagues showed that the acetylation of histone H3 and H4 alleviated the repressive effect of the histones on in vitro RNA synthesis in calf nuclei [1,2]. This initial report saw the birth of epigenetics and an appreciation that covalent modifications of histones provided a mechanism whereby DNA function could be regulated. The nucleosomal packaging of DNA in chromatin was subsequently shown to be an integral component in the regulatory mechanism of the transcription process [3], involving ATP-dependent remodeling complexes, reversible, chemical modification of core histone as well as histone isotype swapping. Many transcriptional activators and repressors were further shown to be enzymes t

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