Identification of Histone H3 Lysine 36 Acetylation as a Highly Conserved Histone Modification

The Rockefeller University, New York, New York, United States
Journal of Biological Chemistry (Impact Factor: 4.57). 04/2007; 282(10):7632-40. DOI: 10.1074/jbc.M607909200
Source: PubMed

ABSTRACT Histone lysine acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analyses of H3 purified from Tetrahymena thermophila and Saccharomyces cerevisiae (yeast), we find that H3K36 can be acetylated or methylated. Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals. In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern inversely related to that of H3K36 methylation. The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac. Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex that regulates transcription specifically acetylates H3K36 in vitro. Deletion of GCN5 completely abolishes H3K36ac in vivo. These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as an "acetyl/methyl switch" governing chromatin function along transcription units.

Download full-text


Available from: Brian D Strahl, Sep 29, 2015
32 Reads
  • Source
    • "We hypothesized that while H3K14ac may be critical for transcription, secondary acetylation sites may also play a critical role in biology by improving the binding of bromodomains or competing with methylation (e.g. H3K9) which is critical for gene silencing [35]. This hypothesis is supported by the fact that deletions of gcn5 in vivo result in a loss of acetylation in residues acetylated after K14 [17], . "
    [Show abstract] [Hide abstract]
    ABSTRACT: Lysine acetyltransferases (KATs) play a unique role in regulating gene transcription as well as maintaining the epigenetic state of the cell. KATs such as Gcn5 and p300/CBP can modify multiple residues on a single histone; however, order and specificity of acetylation can be altered by factors such as histone chaperones, subunit proteins or external stimulus. While the importance of acetylation is well documented, it has been difficult to quantitatively measure the specificity and selectivity of acetylation at different residues within a histone. In this paper, we demonstrate a label-free quantitative high throughput mass spectrometry-based assay capable of quantitatively monitoring all known acetylation sites of H3 simultaneously. Using this assay, we are able to analyze the steady-state enzyme kinetics of Gcn5, an evolutionarily conserved KAT. In doing so, we measured Gcn5-mediated acetylation at six residues (K14>K9 ≈ K23> K18> K27 ≈ K36) and the catalytic efficiency (k(cat)/K(m)) for K9, K14, K18, and K23 as well as the nonenzymatic acetylation rate. We observed selectivity differences of up to -4 kcal/mol between K14 and K18, the highest and lowest measurable k(cat)/K(m). These data provide a first look at quantitating the specificity and selectivity of multiple lysines on a single substrate (H3) by Gcn5.
    PLoS ONE 02/2013; 8(2):e54896. DOI:10.1371/journal.pone.0054896 · 3.23 Impact Factor
  • Source
    • "Toward this end, we performed chromatin immunoprecipitation coupled with high-resolution tiling arrays (ChIP-chip) and global gene expression studies to identify and characterize BES1 direct target genes in the Arabidopsis genome. ChIP-chip has been used to generate high-resolution maps of genome-wide distributions of histone modifications (Morris et al., 2007; Opel et al., 2007; Zhang et al., 2007; Minsky et al., 2008) and transcription factor binding sites in several species. The latter can be exemplified by studies on transcription factors such as Twist, Biniou and Ladybird in Drosophila (Jakobsen et al., 2007; Sandmann et al., 2007), estrogen receptor and homeobox C6 in human cancer cells (Carroll et al., 2006; McCabe et al., 2008), as well as HY5, AGL15, PIL5 and FLP in Arabidopsis (Lee et al., 2007; Oh et al., 2009a; Zheng et al., 2009; Xie et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling arrays (ChIP-chip) and gene expression studies, we have identified 1609 putative BES1 target genes, 404 of which are regulated by BRs and/or in gain-of-function bes1-D mutant. BES1 targets contribute to BR responses and interactions with other hormonal or light signaling pathways. Computational modeling of gene expression data using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) reveals that BES1-targeted transcriptional factors form a gene regulatory network (GRN). Mutants of many genes in the network displayed defects in BR responses. Moreover, we found that BES1 functions to inhibit chloroplast development by repressing the expression of GLK1 and GLK2 transcription factors, confirming a hypothesis generated from the GRN. Our results thus provide a global view of BR regulated gene expression and a GRN that guides future studies in understanding BR-regulated plant growth.
    The Plant Journal 02/2011; 65(4):634-46. DOI:10.1111/j.1365-313X.2010.04449.x · 5.97 Impact Factor
  • Source
    • "Recent studies demonstrated that H3K36 can be modified by Set2-mediated methylation and Gcn5-dependent acetylation (59). Acetylation at H3K36 is localized predominantly at the promoters of RNA polymerase II-transcribed genes and functions as a prelude to transcriptional initiation (59,60). The set2Δ eliminated only H3K36 methylation, and H3K36A wiped out both methylation and acetylation at the PHR1 promoter. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The dynamics of histone methylation have emerged as an important issue since the identification of histone demethylases. We studied the regulatory function of Rph1/KDM4 (lysine demethylase), a histone H3K36 demethylase, on transcription in Saccharomyces cerevisiae. Overexpression of Rph1 reduced the expression of PHR1 and increased UV sensitivity. The catalytically deficient mutant (H235A) of Rph1 diminished the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression. Chromatin immunoprecipitation analysis demonstrated that Rph1 was associated at the upstream repression sequence of PHR1 through zinc-finger domains and was dissociated after UV irradiation. Notably, overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter. In addition, the crucial checkpoint protein Rad53 acted as an upstream regulator of Rph1 and dominated the phosphorylation of Rph1 that was required for efficient PHR1 expression and the dissociation of Rph1. The release of Rph1 from chromatin also required the phosphorylation at S652. Our study demonstrates that the histone demethylase Rph1 is associated with a specific chromatin locus and modulates histone modifications to repress a DNA damage responsive gene under control of damage checkpoint signaling.
    Nucleic Acids Research 02/2011; 39(10):4151-65. DOI:10.1093/nar/gkr040 · 9.11 Impact Factor
Show more