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PubMed2006

Role of DNA methylation and histone H3 lysine 27 methylation in tissue-specific imprinting of mouse Grb10.

Mouse Grb10 is a tissue-specific imprinted gene with promoter-specific expression. In most tissues, Grb10 is expressed exclusively from the major-type promoter of the maternal allele, whereas in the brain, it is expressed predominantly from the brain type promoter of the paternal allele. Such reciprocally imprinted expression in the brain and other tissues is thought to be regulated by DNA methylation and the Polycomb group (PcG) protein Eed. To investigate how DNA methylation and chromatin remodeling by PcG proteins coordinate tissue-specific imprinting of Grb10, we analyzed epigenetic modifications associated with Grb10 expression in cultured brain cells. Reverse transcriptase PCR analysis revealed that the imprinted paternal expression of Grb10 in the brain implied neuron-specific and developmental stage-specific expression from the paternal brain type promoter, whereas in glial cells and fibroblasts, Grb10 was reciprocally expressed from the maternal major-type promoter. The cell-specific imprinted expression was not directly related to allele-specific DNA methylation in the promoters because the major-type promoter remained biallelically hypomethylated regardless of its activity, whereas gametic DNA methylation in the brain type promoter was maintained during differentiation. Histone modification analysis showed that allelic methylation of histone H3 lysine 4 and H3 lysine 9 were associated with gametic DNA methylation in the brain type promoter, whereas that of H3 lysine 27 regulated by the Eed PcG complex was detected in the paternal major-type promoter, corresponding to its allele-specific silencing. Here, we propose a molecular model that gametic DNA methylation and chromatin remodeling by PcG proteins during cell differentiation cause tissue-specific imprinting in embryonic tissues.

Animals↗
PubMed2005

Female-specific hyperacetylation of histone H4 in the chicken Z chromosome.

Birds undergo genetic sex determination using a ZW sex chromosome system. Although the avian mechanisms of neither sex determination nor dosage compensation are understood, a female-specific non-coding RNA (MHM) is expressed soon after fertilisation from the single Z chicken chromosome and is likely to have a role in one or both processes. We have now discovered a prominent female-specific modification to the Z chromatin in the region of the MHM locus. We find that chicken chromatin at Zp21, including the MHM locus, is strongly enriched for acetylation of histone H4 at lysine residue 16 in female but not male chromosomes. Interestingly, this specific histone modification is also enriched along the length of the up-regulated Drosophila melanogaster male X chromosome where it plays a vital role in the dosage compensation process.

Acetylation↗
PubMed2004

Expression and purification of recombinant human histones.

Nucleosomes reconstituted from bacterially expressed histones are useful for functional and structural analyses of histone variants, histone mutants, and histone post-translational modifications. In the present study, we developed a new method for the expression and purification of recombinant human histones. The human histone H2A, H2B, and H3 genes were expressed well in Escherichia coli cells, but the human histone H4 gene was poorly expressed. Therefore, we designed a new histone H4 gene with codons optimized for the E. coli expression system and constructed the H4 gene by chemically synthesized oligodeoxyribonucleotides. The recombinant human histones were expressed as hexahistidine-tagged proteins and were purified by one-step chromatography with nickel-nitrilotriacetic acid agarose in the presence of 6 M urea. The H2A/H2B dimer and the H3/H4 tetramer were refolded by dialysis against buffer without urea, and the hexahistidine-tags of the histones in the H2A/H2B dimer and the H3/H4 tetramer were removed by thrombin protease digestion. The H2A/H2B dimer and the H3/H4 tetramer obtained by this method were confirmed to be proficient in nucleosome formation by the salt dialysis method. The human CENP-A gene, the centromere-specific histone H3 variant, contains 28 minor codons for E. coli. A new CENP-A gene optimized for the E. coli expression system was also constructed, and we found that the purified recombinant CENP-A protein formed a nucleosome-like structure with histones H2A, H2B, and H4.

Amino Acid Sequence↗
PubMed2004

Cytoplasmic sequestration of HDAC7 from mitochondrial and nuclear compartments upon initiation of apoptosis.

Control of global histone acetylation status is largely governed by the opposing enzymatic activities of histone acetyltransferases and deacetylases (HDACs). HDACs were originally identified as modulators of nuclear histone acetylation status and have been linked to chromosomal condensation and subsequent gene repression. Accumulating evidence highlights HDAC modification of non-histone targets. Mitochondria were first characterized as intracellular organelles responsible for energy production through the coupling of oxidative phosphorylation to respiration. More recently, mitochondria have been implicated in programmed cell death whereby release of pro-apoptotic inner membrane space factors facilitates apoptotic progression. Here we describe the novel discovery that the nuclear encoded Class II human histone deacetylase HDAC7 localizes to the mitochondrial inner membrane space of prostate epithelial cells and exhibits cytoplasmic relocalization in response to initiation of the apoptotic cascade. These results highlight a previously unrecognized link between HDACs, mitochondria, and programmed cell death.

Acetylation↗
PubMed1979

The conformation of the chromatin core particle is ionic strength-dependent.

We have examined the susceptibilities of the histones within the HeLa chromatin core particle to covalent modification by a diol-epoxide derivative of the carcinogenic polycyclic aromatic hydrocarbon benzo(a)-pyrene. Core-particle histones exhibit substantial variation in their relative susceptibilities to modification, depending upon the ionic strength of the environment. In contrast, the relative susceptibilities of either purified histones or histones in urea-denatured core particles are insensitive to changes in ionic strength. The variations in the pattern of modification of core particle histones occur primarily at ionic strengths at which the histones remain associated with core-particle DNA (0 to 0.6 M NaCl). Non-histone proteins influence the ionic strength-dependent variations in histone modification. The results imply that the ionic strength of the environment affects the conformation of the core particle and that the nucleoprotein has a flexible structure.

Benzopyrenes↗
PubMed1982

Hyper(ADP-ribosyl)ation of histone H1.

Nucleosomal chains of various repeat unit lengths were generated by a mild micrococcal nuclease digestion of purified pancreatic nuclei. Maximal nucleosome associated poly(ADP-ribose) polymerase activity was recovered in trimeric to tetrameric chromatin fragments, after which the enzyme activity gradually decreased and stabilized towards oligomeric periodicities of 11 to 16 nucleosomes. Electrophoresis of [32P]ADP-ribosylated histones on first-dimension acid-urea or acid-urea-Triton gels and on second-dimension acid--urea--cetyltriammonium bromide gels revealed that, of all histones, only histone H1 could be significantly poly(ADP-ribosyl)ated while only minimal modification could be recovered with histone H1(0). Furthermore, the extent of ADP-ribosylation present on pancreatic histone H1 is shown to proportionally retard this protein's electrophoretic mobility in all gel systems and to consist of a distinct series of at least 12 modification intermediates which can be evidenced, in nuclei or nucleosomes, and fully recovered along with histone H1 upon its selective extraction with 5% perchloric acid. The generation of these increasingly ADP-ribosylated forms of histone H1 is also demonstrated to be time dependent and the more complex ADP-ribosylated forms of this histone are favored at high NAD+ concentrations. Moreover, the electrophoretic mobilities of all intermediates are unaffected by the presence of the nonionic detergent Triton X-100.

Animals↗
PubMed2025

A targeted CRISPR screen identifies ETS1 as a regulator of HIV-1 latency.

Human Immunodeficiency virus (HIV) infection is regulated by a wide array of host cell factors that combine to influence viral transcription and latency. To understand the complex relationship between the host cell and HIV-1 latency, we performed a lentiviral CRISPR screen that targeted a set of host cell genes whose expression or activity correlates with HIV-1 expression. We further investigated one of the identified factors - the transcription factor ETS1, and found that it is required for maintenance of HIV-1 latency in both latently infected cell lines and in a primary CD4 T cell latency model. Interestingly, ETS1 played divergent roles in actively infected and latently infected CD4 T cells, with knockout of ETS1 leading to reduced HIV-1 expression in actively infected cells, but increased HIV-1 expression in latently infected cells, indicating that ETS1 can play both a positive and negative role in HIV-1 expression. CRISPR/Cas9 knockout of ETS1 in CD4 T cells from ART-suppressed people with HIV-1 (PWH) confirmed that ETS1 maintains transcriptional repression of the clinical HIV-1 reservoir. Transcriptomic profiling of ETS1-depleted cells from PWH identified a set of host cell pathways involved in viral transcription that are controlled by ETS1 in resting CD4 T cells. In particular, we observed that ETS1 knockout increased expression of the long non-coding RNA MALAT1 that has been previously identified as a positive regulator of HIV-1 expression. Furthermore, the impact of ETS1 depletion on HIV-1 expression in latently infected cells was partially dependent on MALAT1. Additionally, we demonstrate that ETS1 knockout resulted in enhanced abundance of activating modifications (H3K9Ac, H3K27Ac, H3K4me3) on histones located at the HIV-1 long terminal repeat (LTR), indicating that ETS1 regulates the activity of chromatin-targeting complexes at the HIV-1 LTR. Overall, these data demonstrate that ETS1 is an important regulator of HIV-1 latency that impacts HIV-1 expression through repressing MALAT1 expression and by regulating modification of proviral histones.

Proto-Oncogene Protein c-ets-1↗
PubMed2005

A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response.

DNA breaks are extremely harmful lesions that need to be repaired efficiently throughout the genome. However, the packaging of DNA into nucleosomes is a significant barrier to DNA repair, and the mechanisms of repair in the context of chromatin are poorly understood. Here we show that lysine 56 (K56) acetylation is an abundant modification of newly synthesized histone H3 molecules that are incorporated into chromosomes during S phase. Defects in the acetylation of K56 in histone H3 result in sensitivity to genotoxic agents that cause DNA strand breaks during replication. In the absence of DNA damage, the acetylation of histone H3 K56 largely disappears in G2. In contrast, cells with DNA breaks maintain high levels of acetylation, and the persistence of the modification is dependent on DNA damage checkpoint proteins. We suggest that the acetylation of histone H3 K56 creates a favourable chromatin environment for DNA repair and that a key component of the DNA damage response is to preserve this acetylation.

Acetylation↗
PubMed1976

Methylated blocked 5' terminal sequences of sea urchin embryo messenger RNA classes containing and lacking poly(A).

Sea urchin embryo mRNAs of three distinct classes--histone mRNA, nonhistone mRNA containing poly(A), "[+A] mRNA," and nonhistone mRNA lacking poly(A), "[-A]mRNA"--all contain blocked 5' terminal sequences in which 7-methylguanosine is linked 5'-5' via a triphosphate bridge to a 2'-0-methylated nucleotide. Only one general type of 5' terminal structure, 7mGpppXmpYp, is present. Additional 2'-0-methylation in the Y residue has not been found either in early or late stage embryos. A substantial proportion of the polyribosomal mRNAs in all three classes contain this blocked structure. Whereas both classes of nonhistone mRNAs have internal base methylations, histone mRNAs lack such modifications.

Adenosine↗
PubMed2005

The two faces of NFkappaB in cell survival responses.

Activation of NFkappaB is controlled by a diverse range of stimuli including growth factors, and apoptotic inducers, but paradoxically these stimuli seem to activate the same NFkappaB signaling pathways. In particular, growth factors leading to cell survival and DNA damaging agents leading to apoptosis seem to activate the same NFkappaB signaling pathway. Post-translational modifications of NFkappaB and surrounding histones give selective targeting of NFkappaB regulated genes contributing to cell survival or apoptosis. NFkappaB activation induces death receptor 5 (DR5) expression following DNA damaging agent etoposide treatment but not following growth factor EGF treatment. This differential expression is regulated by the recruitment of histone deacytelasse 1 (HDAC1) to the DR5 gene by NFkappaB following EGF treatment but not etoposide treatment. In addition, HDAC inhibitors induce NFkappaB binding to the DR5 gene and DR5 expression, contributing to HDAC inhibitor induced apoptosis. These findings provide a possible model for selective NFkappaB transcriptional regulation based upon the context of post-translational modifications in surrounding histones on NFkappaB regulated target genes.

Animals↗
PubMed1978

Effect of biotin on phosphorylation, acetylation, methylation of rat liver histones.

Biotin deficient rat liver histones showed decreased phosphorylation and methylation, and increased acetylation rates as compared to normal rat liver histones: these alterations may be related to the observed lower stability of the interactions between histones and DNA. The modifications of the metabolic process might be the consequence of an alteration of the synthesis of the enzymes involved in histone phosphorylation, acetylation and methylation mechanisms and are presumably related to a biotin effect upon the synthesis of RNA and proteins.

Acetates↗
PubMed2003

Association of anticancer drug mithramycin with H1-depleted chromatin: a comparison with native chromatin.

Depletion of histone H1 after covalent modification from chromatin is a key step in eukaryotic transcription initiation. We have studied the effect of depletion of linker histone H1 upon the association of transcription inhibitor, (mithramycin)(2):Mg(2+) complex, with chromatin. We have compared the binding characteristics of the above complex with native, H1-depleted chromatin and naked DNA. Binding site size (number of bases per ligand molecule) of the above complex to the chromosomal DNA increases upon removal of histone H1. It implies an increase in the accessibility of the ligand for the linker DNA. Spectroscopic data, and associated enthalpy and entropy values of the interaction of the complex with H1-depleted chromatin are similar to naked DNA rather than native chromatin. These results suggest that under in vivo conditions, depletion of histone H1 from transcriptionally inert native chromatin during gene activation would lead to an enhanced accessibility of linker DNA to the small ligands with the potential to inhibit transcription.

Animals↗
PubMed2025

Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation.

Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications; thus, there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTM's site localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system.

Proteomics↗
PubMed1990

Patterns of histone acetylation.

The N-terminal domains of all four core histones are subject to reversible acetylation at certain lysine residues. This modification has been functionally linked to transcription, histone deposition at replication and to histone removal during spermatogenesis. To increase understanding of the significance of this modification we have studied the specificity of site utilisation in the monoacetyl, diacetyl and triacetyl forms of histones H3, H4 and H2B (histone H2A has only a single modification site), using pig thymus and HeLa cells as the source of histones. The HeLa histones were extracted from cells grown both with and without butyrate treatment. It is found that for histone H3 there is a fairly strict order of site occupancy: Lys14, followed by Lys23, followed by Lys18 in both pig and HeLa histones. Since the order and specificity is the same when butyrate is added to the HeLa cell cultures, we conclude that addition of the fatty acid does not scramble the specificity of site utilisation, but merely allows more of the natural forms of modified histone to accumulate. For histone H4, the monoacetyl form is exclusively modified at Lys16, but further addition of acetyl groups is less specific and progresses through sites 12, 8 and 5 in an N-terminal direction. Similar results were obtained for H4 from both pig thymus and butyrate-treated HeLa cells. Histone H2B could be studied in detail only from butyrate-treated HeLa cells and a much lower level of site specificity was found: sites 12 and 15 were preferred to the more N- and C-terminal sites at Lys5 and Lys20. The data reinforces the view that lysine acetylation in core histones is a very specific phenomenon that plays several functionally distinct roles. The high degree of site specificity makes it unlikely that the structural effects of acetylation are mediated merely by a generalised reduction of charge in the histone N-terminal domains.

Acetylation↗
PubMed2005

MYST family histone acetyltransferases in the protozoan parasite Toxoplasma gondii.

The restructuring of chromatin precedes tightly regulated events such as DNA transcription, replication, and repair. One type of chromatin remodeling involves the covalent modification of nucleosomes by histone acetyltransferase (HAT) complexes. The observation that apicidin exerts antiprotozoal activity by targeting a histone deacetyltransferase has prompted our search for more components of the histone modifying machinery in parasitic protozoa. We have previously identified GNAT family HATs in the opportunistic pathogen Toxoplasma gondii and now describe the first MYST (named for members MOZ, Ybf2/Sas3, Sas2, and Tip60) family HATs in apicomplexa (TgMYST-A and -B). The TgMYST-A genomic locus is singular and generates a approximately 3.5-kb transcript that can encode two proteins of 411 or 471 amino acids. TgMYST-B mRNA is approximately 7.0 kb and encodes a second MYST homologue. In addition to the canonical MYST HAT catalytic domain, both TgMYST-A and -B possess an atypical C2HC zinc finger and a chromodomain. Recombinant TgMYST-A exhibits a predilection to acetylate histone H4 in vitro at lysines 5, 8, 12, and 16. Antibody generated to TgMYST-A reveals that both the long and short (predominant) versions are present in the nucleus and are also plentiful in the cytoplasm. Moreover, both TgMYST-A forms are far more abundant in rapidly replicating parasites (tachyzoites) than encysted parasites (bradyzoites). A bioinformatics survey of the Toxoplasma genome reveals numerous homologues known to operate in native MYST complexes. The characterization of TgMYST HATs represents another important step toward understanding the regulation of gene expression in pathogenic protozoa and provides evolutionary insight into how these processes operate in eukaryotic cells in general.

5' Untranslated Regions↗
PubMed2026

ChIP-seq profiling identifies diapause-regulated H3K27me3 targets in the fat body of Culex pipiens.

Culex pipiens, a principal vector of significant arboviruses, survives winter through diapause, a hormonally controlled inactive phase that enhances endurance under severe cold circumstances. Recent data suggests that epigenetic processes, namely histone post-translational modifications (hPTMs), play a crucial role in regulating seasonal dormancy. Prior studies from our laboratory indicated a decrease in the methylation of Histone 3 (H3K27me3) in diapausing fat body tissue, associated with elevated expression of the histone demethylase UTX. Nonetheless, the precise genomic areas impacted by these chromatin alterations remained unidentified. We used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) to delineate the genome-wide distribution of H3K27me3 across fat body chromatin in diapausing (D) and non-diapausing (ND) female Cx. pipiens. Notably, the higher signal at transcription start sites (TSSs) reflects localized redistribution rather than a global decrease, as diapausing fat bodies retain less H3K27me3 overall but concentrate it at promoters. To investigate the functional significance of these chromatin alterations, we confirmed a number of target loci via ChIP-qPCR and assessed gene expression with qRT-PCR. We identified many critical genes that were markedly increased in diapausing mosquitoes, exhibiting an inverse relation to H3K27me3 enrichment. Our data demonstrates different H3K27me3 chromatin landscapes between diapausing and non-diapausing Cx. pipiens, corroborating a hypothesis of selective, locus-specific repression in the non-diapause state and its targeted removal during diapause to permit activation of dormancy-associated genes. These results suggest that chromatin remodeling is a core driver of the diapause switch.

Animals↗
PubMed1980

Concentration-dependent effects of sodium butyrate in Chinese hamster cells: cell-cycle progression, inner-histone acetylation, histone H1 dephosphorylation, and induction of an H1-like protein.

This paper presents the first unified quantitative study of the effects of butyrate concentration upon (1) cell-cycle progression, (2) modification of all inner histones, (3) dephosphorylation of histone H1, and (4) enhancement of an H1-like protein (BEP) in CHO cells. Flow cytometric analysis shows that exposure to butyrate enriches CHO cultures in G1 cells and, at sufficient butyrate concentration, leads to G1 arrest. Additionally, butyrate alters the rate of cell-cycle progression through G2/M and through S. Two-dimensional polyacrylamide electrophoresis and radiolabeling in butyrate-treated cultures indicate the presence of at least one site of internal acetylation in histone H2A, four sites of internal acetylation in histone H2B, five sites of internal acetylation in histone H3, and four sites of internal acetylation in histone H4. Histone H2A is also appreciably phosphorylated, so that it is acetylated and phosphorylated at a total of up to three sites. The distribution of modified species for all the inner (core) histones has been quantified from two-dimensional gels by using the three different methods of analysis? (1) direct densitometry of excised portions of the gel, (2) scintillation spectrometry of 3H-labeled histones, and (3) microdensitometry of photographic negatives. At 15 mM butyrate, 26% of H2B is acetylated at three to four sites, 37% of H3 is acetylated at three to five sites, and 50% of H4 is acetylated at three to four sites. Histone H1 is dephosphorylated as a function of butyrate concentration, and the dephosphorylation can be correlated with an increased proportion of G1 cells in culture. There is also a significant increase in the cellular content of two other proteins when cells are exposed to butyrate. The increase in one of these, BEP, has been quantified as a function of butyrate concentration after 24 h of exposure to butyrate. BEP appears to be related to histone H1O [Panyim, S., & Chalkley, R. (1969) Biochem. Biophys. Res. Commun. 37, 1042] and to induced protein IP25 [Keppel, F., Allet, B., & Eisen, H. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 653]. The other protein (UP), which has a molecular weight of approximately 15 000, has not been identified. Butyrate induces a twofold increase in the cellular content of UP and a change in the distribution of UP molecular species.

Acetylation↗