Symmetrical modification within a nucleosome is not required globally for histone lysine methylation

Life Science College, Beijing Normal University, Beijing 100875, China.
EMBO Reports (Impact Factor: 9.06). 02/2011; 12(3):244-51. DOI: 10.1038/embor.2011.6
Source: PubMed


Two copies of each core histone exist in every nucleosome; however, it is not known whether both histones within a nucleosome are required to be symmetrically methylated at the same lysine residues. We report that for most lysine methylation states, wild-type histones paired with mutant, unmethylatable histones in mononucleosomes have comparable methylation levels to bulk histones. Our results indicate that symmetrical histone methylation is not required on a global scale. However, wild-type H4 histones paired with unmethylatable H4K20R histones showed reduced levels of H4K20me2 and H4K20me3, suggesting that some fractions of these modifications might exist symmetrically, and enzymes mediating these modifications might, to some extent, favour nucleosome substrates with premethylated H4K20.

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Available from: She Chen, Jan 11, 2015
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    • "Identification of histone modifications histone paired with wild type. Results demonstrated that lysine methylation levels were very similar between the two types of pairs, indicating that methylation states of histone copies within the nucleosome do not need to be symmetrical, although exceptions could exist (Chen et al., 2011). A later study employed site-specific antibodies and bottom-up MS to directly demonstrate that both symmetrically and asymmetrically modified nucleosomes exist. "
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    • "Addressing the status of histone PTMs on sister histones has so far been hampered by the absence of adequate techniques. A recent report showed that H3 can be methylated at H3K27 even if the sister histone within a nucleosome carries a K27A mutation, which was interpreted as an indication of nucleosome asymmetry (Chen et al., 2011). We suggest that this observation reflects the capability of the enzyme to methylate such a substrate, but may not allow conclusions regarding the in vivo symmetry state. "
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    ABSTRACT: Mononucleosomes, the basic building blocks of chromatin, contain two copies of each core histone. The associated posttranslational modifications regulate essential chromatin-dependent processes, yet whether each histone copy is identically modified in vivo is unclear. We demonstrate that nucleosomes in embryonic stem cells, fibroblasts, and cancer cells exist in both symmetrically and asymmetrically modified populations for histone H3 lysine 27 di/trimethylation (H3K27me2/3) and H4K20me1. Further, we obtained direct physical evidence for bivalent nucleosomes carrying H3K4me3 or H3K36me3 along with H3K27me3, albeit on opposite H3 tails. Bivalency at target genes was resolved upon differentiation of ES cells. Polycomb repressive complex 2-mediated methylation of H3K27 was inhibited when nucleosomes contain symmetrically, but not asymmetrically, placed H3K4me3 or H3K36me3. These findings uncover a potential mechanism for the incorporation of bivalent features into nucleosomes and demonstrate how asymmetry might set the stage to diversify functional nucleosome states.
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    • "The top six abundant ions were fragmented by collision-induced dissociation, and the fragmented ions were scanned with an ion trap. MS/MS spectra for all distinct methylation states were verified according to our previous reports (Chen et al, 2011; Yuan et al, 2011). Mascot search results were analysed with MSquant, and the ratio of heavy/light peptide pairs was calculated based on the extracted ion chromatogram (Mortensen et al, 2010). "
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    ABSTRACT: Histone lysine methylation has been implicated in epigenetic regulation of transcription. Using stable-isotope labelling and quantitative mass spectrometry, we analysed the dynamics of histone lysine methylation. Here we report that histone methylation levels are transiently reduced during S phase and are gradually re-established during subsequent cell cycle stages. However, despite the recovery of overall methylation levels before the next S phase, the methylation levels of parental and newly incorporated histones differ significantly. In addition, histone methylation levels are maintained at steady states by both restriction of methyltransferase activity and the active turnover of methyl groups in cells undergoing an extended G1/S phase arrest. Finally, we propose a 'buffer model' that unifies the imprecise inheritance of histone methylation and the faithful maintenance of underlying gene silencing.
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