Insights into the Role of Histone H3 and Histone H4 Core Modifiable Residues in Saccharomyces cerevisiae

High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
Molecular and Cellular Biology (Impact Factor: 4.78). 12/2005; 25(22):10060-70. DOI: 10.1128/MCB.25.22.10060-10070.2005
Source: PubMed


The biological significance of recently described modifiable residues in the globular core of the bovine nucleosome remains
elusive. We have mapped these modification sites onto the Saccharomyces cerevisiae histones and used a genetic approach to probe their potential roles both in heterochromatic regions of the genome and in
the DNA repair response. By mutating these residues to mimic their modified and unmodified states, we have generated a total
of 39 alleles affecting 14 residues in histones H3 and H4. Remarkably, despite the apparent evolutionary pressure to conserve
these near-invariant histone amino acid sequences, the vast majority of mutant alleles are viable. However, a subset of these
variant proteins elicit an effect on transcriptional silencing both at the ribosomal DNA locus and at telomeres, suggesting
that posttranslational modification(s) at these sites regulates formation and/or maintenance of heterochromatin. Furthermore,
we provide direct mass spectrometry evidence for the existence of histone H3 K56 acetylation in yeast. We also show that substitutions
at histone H4 K91, K59, S47, and R92 and histone H3 K56 and K115 lead to hypersensitivity to DNA-damaging agents, linking
the significance of the chemical identity of these modifiable residues to DNA metabolism. Finally, we allude to the possible
molecular mechanisms underlying the effects of these modifications.

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Available from: Edel M Hyland, Apr 16, 2014
    • "Strains, plasmids, and growth conditions Plasmids pJP11 (pCEN LYS2 HHT1-HHF1 and pCEN-URA3- HST3) (pRS416-based) were described previously (Park et al. 2002; Celic et al. 2006) . The pEMH-based plasmids encoding HHT2-HHF2 gene mutations (pCEN TRP1 HHT2- HHF2) were described previously (Hyland et al. 2005). Tagging of the CDC45 gene with a C-terminal triple HA epitope was achieved by transformation of NcoI-linearized pRS405- CDC45-HA/C (Aparicio et al. 1997) and selection of Leu + colonies where the epitope tagging vector was integrated at the CDC45 locus. "
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    ABSTRACT: In Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56Ac) is present in newly synthesized histones deposited throughout the genome during DNA replication. The sirtuins Hst3 and Hst4 deacetylate H3K56 after S-phase, and virtually all histone H3 molecules are K56-acetylated throughout the cell cycle in hst3∆ hst4∆ mutants. Failure to deacetylate H3K56 causes thermosensitivity, spontaneous DNA damage, and sensitivity to replicative stress via molecular mechanisms that remain unclear. Here we demonstrate that, unlike wild-type cells, hst3∆ hst4∆ cells are unable to complete genome duplication and accumulate persistent foci containing the homologous recombination protein Rad52 after exposure to genotoxic drugs during S-phase. In response to replicative stress, cells lacking Hst3 and Hst4 also displayed intense foci containing the Rfa1 subunit of the single-stranded DNA binding protein complex RPA, as well as persistent activation of DNA damage-induced kinases. To investigate the basis of these phenotypes, we identified histone point mutations that modulate the temperature and genotoxic drug sensitivity of hst3∆ hst4∆ cells. We found that reducing the levels of histone H4 lysine 16 acetylation or H3 lysine 79 methylation partially suppresses these sensitivities and reduces spontaneous and genotoxin-induced activation of the DNA damage response kinase Rad53 in hst3∆ hst4∆ cells. Our data further suggest that elevated DNA damage-induced signalling significantly contributes to the phenotypes of hst3∆ hst4∆ cells. Overall, these results outline a novel interplay between H3K56Ac, H3K79 methylation and H4K16 acetylation in the cellular response to DNA damage. Copyright © 2015, The Genetics Society of America.
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    • "H3K56ac is a common and relatively well-described histone modification in yeasts. Histones with such a modification are mainly a mark of newly synthesized nucleosomes (Hyland et al., 2005; Masumoto et al., 2005; Han et al., 2007a; Li et al., 2008). H3K56ac is involved in nuclear processes that need to rebuild impaired nucleosomes during DNA replication and reparation , or replenish histones behind processing RNA polymerases (Recht et al., 2006; Han et al., 2007b; Tsubota et al., 2007; Wurtele et al., 2012). "
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    ABSTRACT: Posttranslational modifications of histones belong to epigenetic mechanisms that regulate gene expression by chromatin structure changes. Generally, histone acetylation reduces its positive charge and consequently weakens the stability of the nucleosome. Acetylation of lysine 56 on histone H3 is implicated in the processes associated with loosened chromatin structure. H3K56ac is a mark for histones with high nucleosome turnover in the nuclear processes such as gene transcription, DNA replication and reparation in yeasts. During evolution, the main H3K56ac regulatory pathway was lost and the level of H3K56ac remained very low in mammalian cells. Moreover, the function of this modification still remains unclear. In this minireview, we summarize the recent knowledge of the ambiguous role of H3K56ac in mammalian embryonic stem cells.
    Full-text · Article · Nov 2014 · Folia biologica
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    • "In addition to alterations in H3K79me levels, H3K56 substitutions in yeast, also lead to silencing defects, especially at the telomeric regions (Hyland et al. 2005; Xu et al. 2007). The silencing effects are, however, neither due to altered Sir protein recruitment or spreading nor due to changes in other acetylated residues, such as H4K16 (Xu et al. 2007), although it may facilitate slight loosening of Sir binding (Oppikofer et al. 2011). "
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    ABSTRACT: The identification of an increasing number of posttranslationally modified residues within histone core domains is furthering our understanding of how nucleosome dynamics are regulated. In this review, we first discuss how the targeting of specific histone H3 core residues can directly influence the nucleosome structure and then apply this knowledge to provide functional reasoning for their localization to distinct genomic regions. While we focus mainly on transcriptional implications, the principles discussed in this review can also be applied to their roles in other cellular processes. Finally, we highlight some examples of how aberrant modifications of core histone residues can facilitate the pathogenesis of some diseases.
    Full-text · Article · May 2014 · Chromosoma
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