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PubMed2006

Histone-modifying enzymes: encrypting an enigmatic epigenetic code.

Histone-modifying enzymes catalyze a diverse array of post-translational modifications of core and linker histones within chromatin. These modifications govern a multitude of genomic functions, particularly gene expression, and are believed to constitute an epigenetic code. Histone-modifying enzymes inscribe this code by catalyzing site-selective modifications, which are subsequently interpreted by effector proteins that recognize specific covalent marks. The substrate specificity of these enzymes is of fundamental biological importance because it underpins this epigenetic code. Recently, the structural basis of this specificity has been examined with regards to recently determined structures of GCN5 acetyltransferases and SET domain methyltransferases in complex with their cognate histone substrates.

Animals↗
PubMed1983

Glycosylation, ADP-ribosylation, and methylation of Tetrahymena histones.

We have examined some of the postsynthetic modifications that occur in macronuclear histones from Tetrahymena thermophila. When purified macronuclei are incubated with [32P]NAD+, histones H1, H2A, H2B, and H3 are ADP-ribosylated. Furthermore, histones H1, H2A, H2B, and H3 contain fucose and mannose residues as evidenced by the incorporation of [3H]fucose and by the specific binding to these proteins of gorse seed lectin and concanavalin A. Finally, our studies on incorporation of methyl groups into histones show that histone H2A, together with the related nonhistone protein A24, is methylated in Tetrahymena.

Adenosine Diphosphate Ribose↗
PubMed2004

Distinct dynamics and distribution of histone methyl-lysine derivatives in mouse development.

Histone methylation acts as an epigenetic regulator of chromatin activity through the modification of arginine and lysine residues on histones H3 and H4. In the case of lysine, this includes the formation of mono-, di-, or trimethyl groups, each of which is presumed to represent a distinct functional state at the cellular level. To examine the potential developmental roles of these modifications, we determined the global patterns of lysine methylation involving K9 on histone H3 and K20 on histone H4 in midgestation mouse embryos. For each lysine target site, we observed distinct subnuclear distributions of the mono- and trimethyl versions in 10T1/2 cells that were conserved within primary cultures and within the 3D-tissue architecture of the embryo. Interestingly, three of these modifications, histone H3 trimethyl K9, histone H4 monomethyl K20, and histone H4 trimethyl K20 exhibited marked differences in their distribution within the neuroepithelium. Specifically, both histone H3 trimethyl K9 and H4 monomethyl K20 were elevated in proliferating cells of the neural tube, which in the case of the K9 modification was limited to mitotic cells on the luminal surface. In contrast, histone H4 trimethyl K20 was progressively lost from these medial regions and became enriched in differentiating neurons in the ventrolateral neural tube. The inverse relationship of histone H4 K20 methyl derivatives is even more striking during skeletal and cardiac myogenesis where the accumulation of the trimethyl modification in pericentromeric heterochromatin suggests a role in gene silencing in postmitotic muscle cells. Importantly, our results establish that histone lysine methylation occurs in a highly dynamic manner that is consistent with their function in an epigenetic program for cell division and differentiation.

Animals↗
PubMed2006

Insulin-like growth factor-I stimulates histone H3 and H4 acetylation in the brain in vivo.

IGF-I is essential to normal brain growth and exerts actions on neural stem cells and each major neural cell lineage. Whereas many studies show that IGF-I regulates gene expression, mechanisms by which it modulates transcription have not been explored. Chromatin modifications, such as histone phosphorylation, acetylation, and methylation, are known to be important initial steps in gene regulation, and acetylation of histone H3 and H4 is associated with gene activation. In this study, we show that IGF-I modulates the acetylation of H3 and H4 histones in the brain of two transgenic mouse lines and that these effects are associated with activation of the phosphoinositide 3-kinase/Akt signaling pathway. This provides evidence that the chromatin architecture modification contributes to the action of IGF-I on gene expression in the mammalian central nerve system.

Acetylation↗
PubMed2005

Histone deacetylase inhibitors: a review of their clinical status as antineoplastic agents.

The histone code refers to specific modifications in the biochemical composition of nucleosome-associated histone proteins involved in the regulation of gene transcription. These modifications include, among several, acetylation, methylation, and phosphorylation of several histone amino acid residues and are associated with different states of chromatin configuration and gene expression. In particular, acetylation of specific residues in histones H3 and H4 has been associated with an open chromatin configuration and a permissive gene transcription state. This particular modification is regulated by several enzymatic activities with the capacity to either transfer acetyl groups or to induce histone deacetylation. This last activity is associated with gene silencing. Several agents have been shown to have histone deacetylase inhibitory activity (HDACI). In vitro, experiments in multiple neoplastic cancer cell lines have demonstrated that treatment with HDACIs results in increased global and gene specific histone acetylation, and reactivation of aberrantly silenced genes. This phenomenon has been associated with cell differentiation and induction of apoptosis. Based on these observations, several of these agents are now in clinical development both for solid tumor and hematological malignancies. In this article, we provide a brief introduction to the field of histone deacetylation inhibition in cancer and review the most relevant clinical data so far published.

Acetylation↗
PubMed2006

Chromatin remodeling, cancer and chemotherapy.

DNA in eukaryotic nucleus is highly condensed with histone proteins as nucleosomes. Three dimensional arrangements of nucleosomes give rise to the formation of chromatin. Extensive studies in the recent years have highlighted that the structure of chromatin plays a critical role in gene expression. Post translational modifications (such as acetylation, deacetylation, methylation and phosphorylation etc.) of tails of histones may occur with the help of various histone modifier proteins which may lead to architectural changes of nucleosomes and chromatin remodeling. Chromatin remodeling may finally enhance or repress gene transcriptions. The neoplastic cells selectively take the advantages of histone modifications for the cell proliferation, differentiation and evasion of apoptosis. There are enough experimental and clinical evidences that various histone modifiers are linked with many human malignancies. The thorough knowledge of manipulation of histone modifiers by cancer cells may help us to design newer anti-neoplastic drugs in future. There is considerable interest in histone deactylase inhibitors as antineoplastic agents and various clinical trials are in progress. This article reviews a general overview of chromatin remodeling proteins, their role in carcinogenesis and the future potential of the histone deacetylase inhibitors in cancer chemotherapy.

Acetylation↗
PubMed1983

Selective isolation of polypeptide chains bearing multiple types of postsynthetic modifications. Recovery of simultaneously acetylated and phosphorylated forms of histone H2A and high mobility group proteins 14 and 17.

In order to study coordinate or simultaneous modifications of chromosomal proteins by phosphorylation and acetylation, duck erythrocytes were incubated with [32P]orthophosphate and the thiol-containing acetate analogue, 2-mercaptoacetate. Enzymatic transfer of the analogue to the epsilon-amino groups of lysine residues permits the selective recovery of the newly thio-derivatized polypeptide chains by Hg-affinity chromatography, and this acetylated subpopulation can then be analyzed for [32P]phosphate uptake. The histones and high mobility group proteins were extracted from cell nuclei, purified, and finally analyzed for incorporation of [32P]phosphate and 2-mercaptoacetate. Several of the nuclear proteins, in particular histone H2A and the high mobility group proteins HMG-14 and HMG-17, were subjected to organomercurial-agarose chromatography. Significant amounts of these cysteine-free proteins were retained on the affinity column, and by this criterion were shown to have incorporated mercaptoacetate. The mercaptoacetylated proteins were further analyzed and found to contain the 32P label as well. These observations provide incontrovertible evidence that individual molecules of chromosomal proteins can carry postsynthetic modifications in the form of phosphorylation and acetylation at the same time, and also establish that both types of modification must have occurred during the short period in which the cells were exposed to the two precursors.

Acetylation↗
PubMed2005

Small interfering RNAs that trigger posttranscriptional gene silencing are not required for the histone H3 Lys9 methylation necessary for transgenic tandem repeat stabilization in Neurospora crassa.

In Neurospora crassa, the introduction of a transgene can lead to small interfering RNA (siRNA)-mediated posttranscriptional gene silencing (PTGS) of homologous genes. siRNAs can also guide locus-specific methylation of Lys9 of histone H3 (Lys9H3) in Schizosaccharomyces pombe. Here we tested the hypothesis that transgenically derived siRNAs may contemporaneously both activate the PTGS mechanism and induce chromatin modifications at the transgene and the homologous endogenous gene. We carried out chromatin immunoprecipitation using a previously characterized albino-1 (al-1) silenced strain but detected no alterations in the pattern of histone modifications at the endogenous al-1 locus, suggesting that siRNAs produced from the transgenic locus do not trigger modifications in trans of those histones tested. Instead, we found that the transgenic locus was hypermethylated at Lys9H3 in our silenced strain and remained hypermethylated in the quelling defective mutants (qde), further demonstrating that the PTGS machinery is dispensable for Lys9H3 methylation. However, we found that a mutant in the histone Lys9H3 methyltransferase dim-5 was unable to maintain PTGS, with transgenic copies being rapidly lost, resulting in reversion of the silenced phenotype. These results indicate that the defect in PTGS of the Deltadim-5 strain is due to the inability to maintain the transgene in tandem, suggesting a role for DIM-5 in stabilizing such repeated sequences. We conclude that in Neurospora, siRNAs produced from the transgenic locus are used in the RNA-induced silencing complex-mediated PTGS pathway and do not communicate with an RNAi-induced initiation of transcriptional gene silencing complex to effect chromatin-based silencing.

Chromatin Immunoprecipitation↗
PubMed2006

A highly specific mechanism of histone H3-K4 recognition by histone demethylase LSD1.

Human lysine-specific demethylase (LSD1) is a chromatin-modifying enzyme that specifically removes methyl groups from mono- and dimethylated Lys4 of histone H3 (H3-K4). We used a combination of in vivo and in vitro experiments to characterize the substrate specificity and recognition by LSD1. Biochemical assays on histone peptides show that essentially all epigenetic modifications on the 21 N-terminal amino acids of histone H3 cause a significant reduction in enzymatic activity. Replacement of Lys4 with Arg greatly enhances binding affinity, and a histone peptide incorporating this mutation has a strong inhibitory power. Conversely, a peptide bearing a trimethylated Lys4 is only a weak inhibitor of the enzyme. Rapid kinetics measurements evidence that the enzyme is efficiently reoxidized by molecular oxygen with a second-order rate constant of 9.6x10(3) M-1 s-1, and that the presence of the reaction product does not greatly influence the rate of flavin reoxidation. In vivo experiments provide a correlation between the in vitro inhibitory properties of the tested peptides and their ability of affecting endogenous LSD1 activity. Our results show that epigenetic modifications on histone H3 need to be removed before Lys4 demethylation can efficiently occur. The complex formed by LSD1 with histone deacetylases 1/2 may function as a "double-blade razor" that first eliminates the acetyl groups from acetylated Lys residues and then removes the methyl group from Lys4. We suggest that after H3-K4 demethylation, LSD1 recruits the forthcoming chromatin remodelers leading to the introduction of gene repression marks.

Cell Line↗
PubMed2002

Histone acetylation is involved in hsp70 gene transcription regulation in Drosophila melanogaster.

The acetylation/deacetylation modifications of N-terminal tails of core histones play critical roles in activation/repression of many eukaryotic genes. However, the role of acetylation in transcription regulation of heat shock protein genes (hsp) is still a disputed issue. In this study, we investigated the influences of histone acetylation modification on changes in structure of polytene chromosomes and in expression of hsp70 gene in Drosophila melanogaster, by using histone deacetylase (HDAC) inhibitors Trichostatin A (TSA) and sodium butyrate (BuA), and the heat shock treatment of larvae of the flies. The results presented in this paper demonstrate that both TSA and BuA were able to affect the chromatin structure at the site where hsp70 gene is located along the polytene chromosome. Furthermore, the HDAC inhibitors significantly promoted the hsp70 gene transcription, at an extent similar to that induced by heat shock. The immunofluorescence in situ localization study further confirmed that the hsp70 gene locus was hyperacetylated after the heat induction. We therefore conclude that histone acetylation can significantly enhance both the basal and the inducible expression of hsp70 gene in D. melanogaster and hence plays important roles in hsp gene regulation. This study has provided a basis and a framework for further investigations aimed at the establishment of the correlation between acetylation modification and hsp gene regulation.

Acetylation↗
PubMed2002

Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair.

The modification of newly synthesized histones H3 and H4 by type B histone acetyltransferases has been proposed to play a role in the process of chromatin assembly. The type B histone acetyltransferase Hat1p and specific lysine residues in the histone H3 NH(2)-terminal tail (primarily lysine 14) are redundantly required for telomeric silencing. As many gene products, including other factors involved in chromatin assembly, have been found to participate in both telomeric silencing and DNA damage repair, we tested whether mutations in HAT1 and the histone H3 tail were also sensitive to DNA-damaging agents. Indeed, mutations both in specific lysine residues in the histone H3 tail and in HAT1 resulted in sensitivity to methyl methanesulfonate. The DNA damage sensitivity of the histone H3 and HAT1 mutants was specific for DNA double-strand breaks, as these mutants were sensitive to the induction of an exogenous restriction endonuclease, EcoRI, but not to UV irradiation. While histone H3 mutations had minor effects on nonhomologous end joining, the primary defect in the histone H3 and HAT1 mutants was in the recombinational repair of DNA double-strand breaks. Epistasis analysis indicates that the histone H3 and HAT1 mutants may influence DNA double-strand break repair through Asf1p-dependent chromatin assembly.

Acetyltransferases↗
PubMed1999

Imbalance in dosage of the genes for the heterochromatin components Sir3p and histone H4 results in changes in the length and sequence organization of yeast telomeres.

Telomeric heterochromatin plays an essential role in telomere function, including the regulation of telomere length. We observe that in Saccharomyces cerevisiae an imbalance in the dosage of genes for two protein components of heterochromatin (namely Sir3p and histone H4) causes modifications in telomere length and telomere sequence organization. The effects of Sir3p/H4 imbalance were analyzed in yeast strains in which the wild-type SIR3 gene (normally a single-copy gene) was either absent or present in 20-30 copies, and both histone H4 genes (HHF1 and HHF2) were present or HHF1 was deleted, thus covering a wide range of viable gene-dosage combinations. Modifications of telomeres and of subtelomeric regions were identified by analyzing both the overall telomere population and by focusing on two single telomeric regions: the left telomere of chromosome III (LIII) and the right telomere of chromosome XI (RXI). The modifications induced by alteration of the Sir3p/H4 ratio consist of a reduction in the length and an increase in the instability of the terminal block of (C(1-3)A)n repeats and in susceptibility to insertion of Y' elements into this repeat element. Restoration of the wild-type gene ratio (by removal of the extra copies of SIR3 or by complementation with the missing second copy of HHF) restored the original telomere organization, both with respect to the length of the (C(1-3)A)n repeat stretch and the absence of Y' elements. This behavior shows that the stability of the wild-type sequence organization requires maintenance of the normal structure of telomeric heterochromatin.

Chromosomes, Fungal↗
PubMed2005

Influence of N-methylation on a cation-pi interaction produces a remarkably stable beta-hairpin peptide.

The methylation of lysine in histone tails is a common posttranslational modification that functions in histone-regulated chromatin condensation, with binding of methylated lysine occurring in aromatic pockets on chromodomain proteins. We have synthesized a highly stable 12-residue beta-hairpin peptide that exploits the histone-related cation-pi interaction between a methylated lysine residue and a tryptophan residue. Thermodynamic analysis reveals significant entropic stabilization of the peptide due to methylation of the lysine residue. Chemical denaturation of the peptide demonstrates two-state behavior. In comparison to other reported, highly stable designed beta-hairpins, this peptide is the most thermally stable beta-hairpin reported to date. This study provides insight into the role of Lys methylation in histone proteins and more generally in mediating protein-protein interactions.

Amino Acid Sequence↗
PubMed2006

Loss of linker histone H1 in cellular senescence.

Cellular senescence is a tumor-suppressing mechanism that is accompanied by characteristic chromatin condensation called senescence-associated heterochromatic foci (SAHFs). We found that individual SAHFs originate from individual chromosomes. SAHFs do not show alterations of posttranslational modifications of core histones that mark condensed chromatin in mitotic chromosomes, apoptotic chromatin, or transcriptionally inactive heterochromatin. Remarkably, SAHF-positive senescent cells lose linker histone H1 and exhibit increased levels of chromatin-bound high mobility group A2 (HMGA2). The expression of N-terminally enhanced green fluorescent protein (EGFP)-tagged histone H1 induces premature senescence phenotypes, including increased levels of phosphorylated p53, p21, and hypophosphorylated Rb, and a decrease in the chromatin-bound endogenous histone H1 level but not in p16 level accumulation or SAHF formation. However, the simultaneous ectopic expression of hemagglutinin-tagged HMGA2 and N-terminally EGFP-tagged histone H1 leads to significant SAHF formation (P < 0.001). It is known that histone H1 and HMG proteins compete for a common binding site, the linker DNA. These results suggest that SAHFs are a novel type of chromatin condensation involving alterations in linker DNA-binding proteins.

Bromodeoxyuridine↗
PubMed2002

Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects.

Recent results from diverse organisms point to a self-reinforcing network of interactions among the three best-characterized covalent modifications that mark heterochromatin: histone hypoacetylation, histone H3-Lys9 methylation, and cytosine methylation. These modification systems suggest a mechanistic basis for spreading of heterochromatin over large domains and for stable epigenetic inheritance of the silent state. All three modifications used in packaging heterochromatin are also used in stable silencing of euchromatic genes.

Acetylation↗
PubMedDate not supplied

[Levels of chromatin condensation and activity].

The main progresses which occurred last years in the knowledge of chromatin, in its biochemical components, structure and organization levels, are briefly outlined. Inhibition of transcriptional activity is examined at the molecular, cellular and chromosomal levels. The different states of chromatin condensation according to physiopathological conditions are more particularly reviewed together with recent data on transcriptional regulation depending on histone and DNA modifications.

Animals↗
PubMed2006

Histone H4-K16 acetylation controls chromatin structure and protein interactions.

Acetylation of histone H4 on lysine 16 (H4-K16Ac) is a prevalent and reversible posttranslational chromatin modification in eukaryotes. To characterize the structural and functional role of this mark, we used a native chemical ligation strategy to generate histone H4 that was homogeneously acetylated at K16. The incorporation of this modified histone into nucleosomal arrays inhibits the formation of compact 30-nanometer-like fibers and impedes the ability of chromatin to form cross-fiber interactions. H4-K16Ac also inhibits the ability of the adenosine triphosphate-utilizing chromatin assembly and remodeling enzyme ACF to mobilize a mononucleosome, indicating that this single histone modification modulates both higher order chromatin structure and functional interactions between a nonhistone protein and the chromatin fiber.

Acetylation↗
PubMed2005

Epigenetic regulation by histone methylation and histone variants.

Epigenetics is the study of heritable changes in gene expression that are not mediated at the DNA sequence level. Molecular mechanisms that mediate epigenetic regulation include DNA methylation and chromatin/histone modifications. With the identification of key histone-modifying enzymes, the biological functions of many histone posttranslational modifications are now beginning to be elucidated. Histone methylation, in particular, plays critical roles in many epigenetic phenomena. In this review, we provide an overview of recent findings that shape the current paradigms regarding the roles of histone methylation and histone variants in heterochromatin assembly and the maintenance of the boundaries between heterochromatin and euchromatin. We also highlight some of the enzymes that mediate histone methylation and discuss the stability and inheritance of this modification.

Amino Acid Sequence↗