Histone acetylation is required to maintain the unfolded nucleosome structure associated with transcribing DNA

Expression, purification, and structural characterization of human histone H4

Recombinant human histone H4 (hH4) was produced in milligrams quantities in Escherichia coli, without altering the codons of the original cDNA sequence. The hH4 cDNA was subcloned into the pQE30 expression vector, in frame with a sequence encoding an N-terminal stretch of six histidine residues. Purification to electrophoretic homogeneity was obtained by nickel-chelating chromatography, followed by gel filtration. The final yield of the entire expression and purification process was about 1 mg of pure histone H4 per liter of bacterial culture. SDS-PAGE analysis showed for the recombinant H4 a molecular weight corresponding to the expected one (12,535 Da). Circular dichroism spectroscopy was used to estimate the secondary structural composition of recombinant histone, when it is isolated from the physiological core particle. It was observed that under these conditions histone H4 exhibits an altered secondary conformation. In order to induce the recombinant histone to assume a conformation more similar to the one measured when it is organized inside the nucleosome, we resuspended it in buffers at increasing ionic strengths and in the presence of different concentrations of trifluoroethanol. We tried also to mimic the physiological situation of histone H4 by adding an equimolar amount of a commercial DNA to the protein solution. Finally, an estimation of protein thermal stability was evaluated by spectropolarimetry.

Toward a new paradigm of cell plasticity

The standard paradigm of embryologic development and adult tissue reconstitution posits unidirectional, hierarchical lineages. The presumed mechanisms underlying these differentiative pathways are gene restrictions, such as methylation and heterochromatin formation, which are commonly described as irreversible. However, recent discoveries regarding multi-organ stem cells demonstrate that 'true plasticity' exists, with cells of one organ turning into cells of other organs, including differentiative transformations that cross barriers between tissues derived from different primitive germ layers. These findings, along with earlier experiments into heterokaryon formation and longstanding recognition of reactive and neoplastic lesions in humans and animals, suggest that lineage pathways are not, in fact, unidirectional. Moreover, physiologic mechanisms of reversal of gene restrictions have been recognized. Therefore, in response to these observations, we suggest a new paradigm of cell plasticity, elucidating three guiding principles of 'genomic completeness', 'uncertainty of cell characterization', and 'stochastic nature of cell origins and fates'. These principles imply a change in the way data can be interpreted and could alter subsequent hypothesis formation. This new paradigm will hopefully lead us forward to a more flexible and creative exploration of the potential of adult vertebrate cells.

Isolation of transcriptionally active chromatin from human breast cancer cells using Sulfolink coupling gel chromatography

The process of transcription unfolds the nucleosome. The unfolded nucleosome structure will be maintained as long as the histones are in a highly acetylated state. Typically the cysteine residue at position 110 of histone H3 is buried in the interior of the nucleosome. However, the transcribed unfolded nucleosome has its H3 cysteine exposed, offering a tag to isolate and study transcribed nucleosomes. In this study, we applied Sulfolink Coupling Gel chromatography to isolate unfolded nucleosomes from estrogen dependent human cancer T5 cells. Inhibition of histone deacetylase activity did not enhance the yield of unfolded nucleosomes from these cells. We show that the estrogen receptor and c-myc transcribed DNA sequences are associated with unfolded nucleosomes. In chromatin immunoprecipitation (ChIPs) assays, we found that the coding regions of the estrogen receptor and c-myc genes are bound to highly acetylated H3 and H4 in cultured T5 Cells. We conclude that in cultured T5 breast cancer cells H3 and H4 are in highly acetylated states maintaining the unfolded structure of the transcribed nucleosome and facilitating subsequent rounds of elongation.

Huntingtin is present in the nucleus, interacts with the transcriptional corepressor C-terminal binding protein, and represses transcription

Huntingtin is a protein of unknown function that contains a polyglutamine tract, which is expanded in patients with Huntington's disease (HD). We investigated the localization and a potential function for huntingtin in the nucleus. In human fibroblasts from normal and HD patients, huntingtin localized diffusely in the nucleus and in subnuclear compartments identified as speckles, promyelocytic leukemia protein bodies, and nucleoli. Huntingtin-positive nuclear bodies redistributed after treatment with sodium butyrate. By Western blot, purified nuclei had low levels of full-length huntingtin compared with the cytoplasm but contained high levels of N- and C-terminal huntingtin fragments, which tightly bound the nuclear matrix. Full-length huntingtin co-immunoprecipitated with the transcriptional corepressor C-terminal binding protein, and polyglutamine expansion in huntingtin reduced this interaction. Full-length wild-type and mutant huntingtin repressed transcription when targeted to DNA. Truncated N-terminal mutant huntingtin repressed transcription, whereas the corresponding wild-type fragment did not repress transcription. We speculate that wild-type huntingtin may function in the nucleus in the assembly of nuclear matrix-bound protein complexes involved with transcriptional repression and RNA processing. Proteolysis of mutant huntingtin may alter nuclear functions by disrupting protein complexes and inappropriately repressing transcription in HD.

The human beta-globin locus control region

The human beta-globin gene locus is the subject of intense study, and over the past two decades a wealth of information has accumulated on how tissue-specific and stage-specific expression of its genes is achieved. The data are extensive and it would be difficult, if not impossible, to formulate a comprehensive model integrating every aspect of what is currently known. In this review, we introduce the fundamental characteristics of globin locus regulation as well as questions on which much of the current research is predicated. We then outline a hypothesis that encompasses more recent results, focusing on the modification of higher-order chromatin structure and recruitment of transcription complexes to the globin locus. The essence of this hypothesis is that the locus control region (LCR) is a genetic entity highly accessible to and capable of recruiting, with great efficiency, chromatin-modifying, coactivator, and transcription complexes. These complexes are used to establish accessible chromatin domains, allowing basal factors to be loaded on to specific globin gene promoters in a developmental stage-specific manner. We conceptually divide this process into four steps: (a) generation of a highly accessible LCR holocomplex; (b) recruitment of transcription and chromatin-modifying complexes to the LCR; (c) establishment of chromatin domains permissive for transcription; (d) transfer of transcription complexes to globin gene promoters.

The effect of the histone deacetylase inhibitor, trichostatin A, on total histone synthesis, H1(0) synthesis and histone H4 acetylation in peripheral blood lymphocytes increases as a function of increasing age: a model study

A pilot study was initiated in order to ascertain whether the age of the donor might affect either the induction of the expression of H1(0) or histone H4 acetylation by the very specific histone deacetylase inhibitor, trichostatin A. This was investigated in a cell system which normally does not express this linker histone variant, i.e. peripheral blood lymphocytes (PBL), which were obtained from donors of different ages (25-95 years). Forty-eight hours after activation by the mitogen phytohemaglutinin (PHA), 250 ng of trichostatin A per 10(6) cells per ml culture medium was added and cultured for an additional 24h. Assays were performed 72 h after initiation of cultures, i.e. during the S phase. It was found that in PBL, trichostatin A induced the expression of the linker histone variant, H1(0) as well as histone H4 acetylation, and, more importantly, that these effects were enhanced with increasing age of the donor. More specifically, under the influence of trichostatin A, PBL showed increasing H1(0) synthesis rates and increasing levels of histone H4 acetylation as a function of increasing age of the donor. Moreover, although trichostatin A induced an increasing expression of H1(0) with increasing age, it also concomitantly partially inhibited S phase total histone synthesis. This inhibition also increased as a function of increasing age of the donor.

Histone variants and histone modifications: A structural perspective

In this review, we briefly analyze the current state of knowledge on histone variants and their posttranslational modifications. We place special emphasis on the description of the structural component(s) defining and determining their functional role. The information available indicates that this histone "variability" may operate at different levels: short-range "local" or long-range "global", with different functional implications. Recent work on this topic emphasizes an earlier notion that suggests that, in many instances, the functional response to histone variability is possibly the result of a synergistic structural effect.Key words: histone variants, posttranslational modifications, chromatin.

Histone deacetylase inhibitors induce apoptosis in peripheral blood lymphocytes along with histone H4 acetylation and the expression of the linker histone variant, H1 degrees

The results of this study show that H1 degrees can be induced by sodium butyrate and trichostatin A in peripheral blood lymphocytes, a cell system which does not normally express this linker histone variant. Moreover, this induced expression was found to be correlated in a dose-dependent manner with the concomitant induction of apoptosis and increased levels of histone H4 acetylation. Sodium butyrate and trichostatin A, both inhibitors of histone deacetylases, are known to induce terminal differentiation and at the same time the induction of the linker histone variant, H1 degrees, in a number of tissue/cell systems. Moreover, aside from induced expression by histone deacetylase inhibitors, H1 degrees gene expression has also been tightly associated with the process of terminal differentiation in many physiological tissue/cell systems. The concomitant induction of H1 degrees expression along with apoptosis and histone acetylation in the same cell system has not been previously reported. Histone acetylation is known to be involved in chromatin remodelling events. Such events also occur during apoptosis. The association of H1 degrees gene expression with apoptosis, and not with differentiation in these cells, leads to more general implications as to a potential functional role of H1 degrees during chromatin remodelling.

Follicle-stimulating hormone stimulates protein kinase A-mediated histone H3 phosphorylation and acetylation leading to select gene activation in ovarian granulosa cells

We examined the phosphorylation and acetylation of histone H3 in ovarian granulosa cells stimulated to differentiate by follicle-stimulating hormone (FSH). We found that protein kinase A (PKA) mediates H3 phosphorylation on serine 10, based on inhibition exclusively by PKA inhibitors. FSH-stimulated H3 phosphorylation in granulosa cells is not downstream of mitogen-activated protein kinase/extracellular signal-regulated kinase, ribosomal S6 kinase-2, mitogen- and stress-activated protein kinase-1, p38 MAPK, phosphatidylinositol-3 kinase, or protein kinase C. Transcriptional activation-associated H3 phosphorylation on serine 10 and acetylation of lysine 14 leads to activation of serum glucocorticoid kinase, inhibin alpha, and c-fos genes. We propose that phosphorylation of histone H3 on serine 10 by PKA in coordination with acetylation of H3 on lysine 14 results in reorganization of the promoters of select FSH responsive genes into a more accessible configuration for activation. The unique role of PKA as the physiological histone H3 kinase is consistent with the central role of PKA in initiating granulosa cell differentiation.

Dynamically acetylated histone association with transcriptionally active and competent genes in the avian adult beta-globin gene domain

In chicken immature erythrocytes, class 1 acetylated histones are rapidly tri- and tetra-acetylated and rapidly deacetylated. Class 2 acetylated H3 and H4 are rapidly acetylated to mono- and di-acetylated isoforms and slowly deacetylated. Our previous studies suggested that class 1 acetylated histones were primarily associated with transcriptionally active DNA (beta(A)-globin) but not competent DNA (epsilon-globin). Chromatin salt solubility (chromatin fiber oligomerization) is directly influenced by hyperacetylation. In this study we investigated the association of class 1 histones with beta(A)- and epsilon-globin DNA by measuring their loss of solubility rates in 150 mm NaCl and 3 mm MgCl(2) as a function of hyperacetylated histone deacetylation. Expressed and competent chromatin was associated with class 1 acetylated histones. As most active chromatin and hyperacetylated histones are associated with the low salt-insoluble residual nuclear material containing the nuclear matrix, we investigated whether hyperacetylated histones are bound to the beta(A)- and epsilon-globin DNA in this fraction. In chromatin immunoprecipitation assays, we found that the beta(A)- and epsilon-globin coding regions are bound to hyperacetylated H3 and H4. Our observations are consistent with a model in which nuclear matrix-associated histone acetyltransferases and deacetylases mediate a dynamic attachment between active and competent chromatin and the nuclear matrix.

Searching for the magic bullet against cancer: the butyrate saga

n-Butyric acid and its "polymorphic" derivatives have been largely but somehow "blindly" studied in oncology and in red cell diseases with consistent results through decades indicating a strong maturative effect determined by enhancement of gene transcription. Although these effects have been observed mainly in vitro, the relative absence of systemic toxicity of butyrates render these compounds appealing as specific therapeutic agents. More interestingly, their specific mechanism of action, i.e. inhibition of histone deacetylase and de-repression of transcription represents at present an unique tool for diseases such as acute leukemias which are characterised by a disregulation of co-repressors and co-activators of gene transcription. More insight into specificity and modalities of action of different butyrate derivatives may be a guarantee for excellent tailored antileukemic therapy in the future.

Targeted and extended acetylation of histones H4 and H3 at active and inactive genes in chicken embryo erythrocytes

Affinity-purified polyclonal antibodies recognizing the most highly acetylated forms of histones H3 and H4 were used in immunoprecipitation assays with chromatin fragments derived from 15-day chicken embryo erythrocytes by micrococcal nuclease digestion. The distribution of hyperacetylated H4 and H3 was mapped at the housekeeping gene, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and the tissue-specific gene, carbonic anhydrase (CA). H3 and H4 acetylation was found targeted to the CpG island region at the 5' end of both these genes, falling off in the downstream direction. In contrast, at the beta(A)-globin gene, both H3 and H4 are highly acetylated throughout the gene and at the downstream enhancer, with a maximum at the promoter. Low level acetylation was observed at the 5' end of the inactive ovalbumin gene. Run-on assays to measure ongoing transcription showed that the GAPDH and CA genes are transcribed at a much lower rate than the adult beta(A)-globin gene. The extensive high level acetylation at the beta(A)-globin gene correlates most simply with its high rate of transcription. The targeted acetylation of histones H3 and H4 at the GAPDH and CA genes is consistent with a role in transcriptional initiation and implies that transcriptional elongation does not necessarily require hyperacetylation.

Chromatin alteration, transcription and replication: What's the opening line to the story?

Polymerase accessibility to chromatin is a limiting step in both RNA and DNA synthesis. Unwinding DNA and nucleosomes during polymerase complex binding and processing likely requires priming by chromatin restructuring. The initiating step in these processes remains an area of speculation. This review focuses on the physical handling of chromatin during transcription and replication, the fate of nucleosomes assembled on DNA during unwinding and processing the chromatin substrate, and how these alterations in chromatin structure may affect gene expression. Transcription or replication may alter chromatin structure during synthesis, enabling regulatory factor binding and, potentially, future rounds of transcription. As chromatin remodeling and transcription factor binding augment transcription and replication, and are themselves increased by these processes, a temporal model of structural alterations and gene activation is built that may be more circular than linear.

Regulation of metallothionein gene expression

The rapid and robust induction of metallothioneins (MT)-I and II by a variety of inducers that include heavy toxic metals, reactive oxygen species, and different types of stress provide a useful system to study the molecular mechanisms of this unique induction process. The specific expression of MT-III in the brain and of MT-IV in the squamous epithelium of skin and tongue offers a unique opportunity to identify and characterize the tissue-specific factors involved in their expression. Studies using transgenic mice that overexpress MTs or MT null mice have revealed the role of MT in the protection of cells against numerous tissue-damaging agents such as reactive oxygen species. The primary physiological function of these proteins, however, remains an enigma. Considerable advances have been made in the identification of the cis-acting elements that are involved in the constitutive and induced expression of MT-I and MT-II. By contrast, only one key trans-activating factor, namely MTF-1, has been extensively characterized. Studies on the epigenetic silencing of MT-I and MT-II by promoter hypermethylation in some cancer cells have posed interesting questions concerning the functional relevance of MT gene silencing, the molecular mechanisms of MT suppression in these cells, particularly chromatin modifications, and the characteristics of the repressors.

Signal transduction pathways and the modification of chromatin structure

Mechanical and chemical signaling pathways are involved in transmitting information from the exterior of a cell to its chromatin. The mechanical signaling pathway consists of a tissue matrix system that links together the three-dimensional skeletal networks, the extracellular matrix, cytoskeleton, and karyoskeleton. The tissue matrix system governs cell and nuclear shape and forms a structural and functional connection between the cell periphery and chromatin. Further, this mechanical signaling pathway has a role in controlling cell cycle progression and gene expression. Chemical signaling pathways such as the Ras/mitogen-activated protein kinase (MAPK) pathway can stimulate the activity of kinases that modify transcription factors, nonhistone chromosomal proteins, and histones. Activation of the Ras/MAPK pathway results in the alteration of chromatin structure and gene expression. The tissue matrix and chemical signaling pathways are not independent and one signaling pathway can affect the other. In this chapter, we will review chromatin organization, histone variants and modifications, and the impact that signaling pathways have on chromatin structure and function.

RNA polymerase II elongation through chromatin

The machinery that transcribes protein-coding genes in eukaryotic cells must contend with repressive chromatin structures in order to find its target DNA sequences. Diverse arrays of proteins modify the structure of chromatin at gene promoters to help transcriptional regulatory proteins access their DNA recognition sites. The way in which disruption of chromatin structure at a promoter is transmitted through a whole gene has not been defined. Recent breakthroughs suggest that the passage of an RNA polymerase through a gene is coupled to mechanisms that propagate the breakdown of chromatin.

Growth regulation of human variant histone genes and acetylation of the encoded proteins

The family of human histone genes consists of replication-dependent and independent subtypes. The replication-independent histone genes, also known as variants, give rise to distinct mRNAs, whose expression is regulated depending on the growth state of the cell, tissue type and developmental stage. In turn, the histone variants are differentially synthesized and modified by acetylation. Consequently, chromatin structure is altered resulting in complex changes in gene expression. The high conservation among histone protein subtypes suggests that they are indispensable. In addition, conservation of the positions of acetylation within subtypes suggests that the location of these sites is functionally important for the eukaryotic cell. For example, the structures of transcriptionally active and repressed chromatin are different depending on the acetylation state of histone proteins [1-3]. In addition, transcriptionally active and repressed chromatin contains distinct histone variants [4]. Specialized histone variants are targeted to the centromere of the chromosome, where they are essential for chromosome segregation [5]. Other specialized histones exist that are essential for development [6]. Changes in histone acetylation have been implicated in the down-regulation of a tumour suppressor gene in human breast cancer [7]. Acetylation also plays an important role in X chromosome inactivation as well as hormone-mediated transcriptional regulation [8, 9]. We propose here a novel model for histone variant gene regulation at the post-transcriptional level, which provides the groundwork to define the pathways regulating the synthesis of these variants.

Steady-state levels of histone acetylation in Saccharomyces cerevisiae

The importance of control of the levels of histone acetylation for the control of gene expression in eukaryotic chromatin is being elucidated, and the yeast Saccharomyces cerevisiae has proven to be an important model system. The level of histone acetylation in yeast is the highest known. However, only acetylation of H4 has been quantified, and reports reveal loss of acetylation in histone preparations. A chaotropic guanidine-based method for histone isolation from intact wild-type cells or from a single-step nuclear preparation with butyrate preserves acetylation of all core histones. Histone H4 has an average of more than 2 acetylated lysines per molecule, distributed over 4 sites. Histones H2A, H3, and H2B have 0. 2, approximately 2, and >2 acetylated lysines per molecule, respectively, distributed across 2, 5, and 6 sites. Thus, yeast nucleosomes carry, on average, 13 acetylated lysines per octamer, i. e. just above the threshold of 10-12 deduced for transcriptionally activated chromatin of animals, plants, and algae. Following M(r) 100,000 ultrafiltration in 2.5% acetic acid, yeast histone H3 was purified to homogeneity by reversed-phase high pressure liquid chromatography. Other core histones were obtained at 80-95% purity.

Age-related and steroid induced changes in the histones of the quail liver

Histones were extracted from the liver of young, adult and old Japanese quails. Both linker and core histones were found to vary with age. An extra band, H3X, was found between H2A and H4. Its level is higher in young and old birds in comparison to that of the adult. H3X shows interesting changes under steroid induction. Its level is higher in progesterone administered young birds. In adult and old birds, it is higher in progesterone treated (P) and progesterone primed estradiol administered (P+E) birds, and lower in all estradiol (E) and estradiol primed progesterone administered (E+P) birds. The relative levels of H3X in the steroid administered birds also vary with age. Such changes may influence chromatin conformation and gene expression.

Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus

Gene activation requires chromatin remodeling complexes, which hyperacetylate histones and enable factor access; however, the targeting mechanisms leading to the establishment and maintenance of large, hyperacetylated DNase-sensitive chromatin domains are unknown. Recent work has shown that histone acetyltransferases are associated with RNA-pol II complexes, suggesting that transcription of chromatin plays a role in chromatin modification. Here we show the human beta-globin locus is divided into three differentially activated chromatin subdomains. Large transcripts precisely delineate the active domains at key cell cycle points associated with chromatin transitions and remodeling. We identify an element that initiates these transcripts, located in a region required for chromatin activation. The results suggest that intergenic transcription is required for chromatin remodeling of chromosomal domains.

Control of histone modifications

A role for histone modifications in transcription processes and the remodeling of chromatin structure has been established. This review highlights the recent advances made in studies on histone acetyltransferases, histone deacetylases, histone kinases, and protein phosphatases, as well as their roles in transcriptional activation and repression. Coactivators with histone acetyltransferase activity stimulate transcription, whereas corepressors with histone deacetylase activity repress transcription. Families of histone acetyltransferases and deacetylases have been identified. We have learned that their substrates are not limited to histones but also include transcription factors and architectural proteins. Studies on the composition of multiprotein complexes with histone acetyltransferase or histone deacetylase have revealed mechanisms by which these complexes are recruited to specific genomic sites that are transcriptionally active, silenced, or being repaired. A new and exciting development, presented in this review, is the role of signal transduction pathways in the phosphorylation of histone H3 and the expression of immediate-early genes. J. Cell. Biochem. Suppls. 32/33:141-148, 1999.

Evidence for nonrandom behavior in 208-12 subsaturated nucleosomal array populations analyzed by AFM

Atomic force microscopy was used to determine the population distributions in reconstituted, subsaturated 208-12 nucleosomal arrays. The features found in these distributions vary with the average nucleosome loading per template molecule (n(av)): at n(av) < 4, the distributions show a single peak whose breadth is equal to that expected for a random loading process; at n(av) = 4-8, the distributions are broader than random distributions and are complex; i.e., they contain multiple peaks and/or shoulders. Moreover, the peaks/shoulders typically occur at two nucleosome intervals, i.e., 2, 4, 6 or 3, 5, 7 nucleosomes. This two-nucleosome periodicity is statistically significant. The precise cause for such discrete features within the distributions is unknown, but at least these features would seem to indicate some pairwise preference in nucleosome occupation at these loading levels. In these intermediate-level (n(av) = 4-8) distributions, the major peak contains a larger fraction of the total templates than a random nucleosome loading process would produce. This feature indicates that at these intermediate population levels there is some tendency for correlated nucleosome loading among the templates. Hyperacetylated nucleosomal arrays show only subtle differences in their population distributions compared to nonacetylated arrays and demonstrate the above features. AFM allows one to study unfixed chromatin arrays; we find that nucleosomes on the 208-12 template demonstrate significant lability when they are not glutaraldehyde-fixed.

Role of covalent modifications of histones in regulating gene expression

DNA is organized into a hierarchy of structures, resulting in the level of compaction required to pack 2m of DNA into a nucleus with a diameter of 10 micrometer. The orderly packaging of DNA in the nucleus plays an important role in the functional aspects of gene regulation. A small percentage of chromatin is made available to transcription factors and the transcription machinery, while the remainder of the genome is in a state that is essentially invisible to the RNA polymerases. Modification of histones has a key role in altering chromatin higher order structure and function. In this review, we will present the latest developments in the study of histone modifications (ubiquitination, acetylation, methylation, and phosphorylation) and the enzymes involved in these processes.

Increased Ser-10 phosphorylation of histone H3 in mitogen-stimulated and oncogene-transformed mouse fibroblasts

When the Ras mitogen-activated protein kinase (MAPK) signaling pathway of quiescent cells is stimulated with growth factors or phorbol esters, the early response genes c-fos and c-myc are rapidly induced, and concurrently there is a rapid phosphorylation of histone H3. Using an antibody specific for phosphorylated Ser-10 of H3, we show that Ser-10 of H3 is phosphorylated, and we provide direct evidence that phosphorylated H3 is associated with c-fos and c-myc genes in stimulated cells. H3 phosphorylation may contribute to proto-oncogene induction by modulating chromatin structure and releasing blocks in elongation. Previously we reported that persistent stimulation of the Ras-MAPK signaling pathway in oncogene-transformed cells resulted in increased amounts of phosphorylated histone H1. Here we show that phosphorylated H3 is elevated in the oncogene-transformed mouse fibroblasts. Further we show that induction of ras expression results in a rapid increase in H3 phosphorylation. H3 phosphatase, identified as PP1, activities in ras-transformed and parental fibroblast cells were similar, suggesting that elevated H3 kinase activity was responsible for the increased level of phosphorylated H3 in the oncogene-transformed cells. Elevated levels of phosphorylated H1 and H3 may be responsible for the less condensed chromatin structure and aberrant gene expression observed in the oncogene-transformed cells.

A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme

The elongator complex is a major component of the RNA polymerase II (RNAPII) holoenzyme responsible for transcriptional elongation in yeast. Here we identify Elp3, the 60-kilodalton subunit of elongator/RNAPII holoenzyme, as a highly conserved histone acetyltransferase (HAT) capable of acetylating core histones in vitro. In vivo, ELP3 gene deletion confers typical elp phenotypes such as slow growth adaptation, slow gene activation, and temperature sensitivity. These results suggest a role for a novel, tightly RNAPII-associated HAT in transcription of DNA packaged in chromatin.

The site of binding of linker histone to the nucleosome does not depend upon the amino termini of core histones

Using nucleosomes reconstituted on a defined sequence of DNA, we have investigated the question as to whether the N-terminal tails of core histones play a role in determining the site of binding of a linker histone. Reconstitutes used histone cores of three types: intact, lacking the N-terminal H3 tails, or lacking all tails. In each case the same, single defined position for the histone core was observed, using high-resolution mapping. The affinity for binding of linker histone H1(o) was highest for the intact cores, lowest for the tailless cores. However, the location of the linker histone, as judged by micrococcal nuclease protection, was exactly the same in each case, an asymmetric site of about 17 bp to one side of the core particle DNA.

Purification and characterization of chicken erythrocyte histone deacetylase 1

Histone acetylation is involved in nuclear processes requiring chromatin remodeling. In chicken erythrocytes, DNA replication has ceased, and active reversible histone acetylation is restricted to transcriptionally active/competent chromatin domains. In this study, we set out to identify and purify the erythroid histone deacetylase responsible for catalyzing dynamic acetylation of transcriptionally active chromatin. Histone deacetylase purified from chicken erythrocytes had a molecular mass of 66 kDa. Complementary DNA encoding the chicken histone deacetylase was cloned from erythrocytes, and analysis of the derived amino acid sequence showed the chicken histone deacetylase to be the chicken homologue of mammalian HDAC1. Purified chicken erythrocyte HDAC1 deacetylated the four core histones, with a preference for H3. We present evidence that chicken HDAC1 is a metalloenzyme, the activity of which is lost when incubated with zinc chelators. In Western blot analysis with anti-HDAC1 antibodies, we found that most erythrocyte HDAC1 is associated with the low-salt insoluble chromatin fraction and, to a lesser extent, with 150 mM NaCl-soluble oligo- and polynucleosomes. The distribution of HDAC1 in erythrocyte chromatin parallels that of dynamically acetylated class 1 histones. Further, we show that HDAC1 is associated with the erythroid nuclear matrix and that the enzyme is bound to nuclear DNA in situ. We propose that in addition to catalyzing dynamic acetylation of transcribed chromatin, the enzyme has a role in the organization of nuclear DNA.

Follicle-stimulating hormone promotes histone H3 phosphorylation on serine-10

FSH promoted the rapid phosphorylation of the nuclear protein histone H3 in immature rat ovarian granulosa cells under experimental conditions that lead to cellular differentiation and not proliferation. FSH-stimulated histone H3 phosphorylation correlated with cAMP-dependent protein kinase A (PKA) activation and translocation of the PKA catalytic subunit to a nuclear-enriched fraction and was inhibited by the PKA inhibitor H89, and histone H3 phosphorylation was stimulated in cells treated with agents that raise intracellular cAMP levels such as forskolin and 8-bromo-cAMP. FSH-stimulated histone H3 phosphorylation in granulosa cells mapped to ser-10, a site previously identified as the PKA phosphorylation site in various mitotically active cells as the mitosis-specific phosphorylation site. Injection of the FSH analog PMSG to immature rats, which is known to stimulate granulosa cell proliferation as well as differentiation, also promoted histone H3 phosphorylation on ser-10 in granulosa cells. These results establish that FSH-stimulated histone H3 phosphorylation in granulosa cells is linked not only to granulosa cell mitosis but also to granulosa cell differentiation and that FSH-stimulated histone H3 phosphorylation on ser-10 in isolated granulosa cells is mediated by PKA. These results also identify the PKA-dependent histone H3 phosphorylation as an early nuclear protein marker for FSH-stimulated differentiation of granulosa cells. Based on the recently described function of histone H3 as a coactivator of transcription, these results are consistent with the hypothesis that phosphorylated histone H3 may facilitate PKA-dependent gene transcription in granulosa cells leading to the preovulatory phenotype.

Gcn5p, a transcription-related histone acetyltransferase, acetylates nucleosomes and folded nucleosomal arrays in the absence of other protein subunits

Gcn5p is the catalytic subunit of several type A histone acetyltransferases (HATs). Previous studies performed under a limited range of solution conditions have found that nucleosome core particles and nucleosomal arrays can be acetylated by Gcn5p only when it is complexed with other proteins, e.g. Gcn5-Ada, HAT-A2, and SAGA. Here we demonstrate that when assayed in buffer containing optimum concentrations of either NaCl or MgCl2, purified yeast recombinant Gcn5p (rGcn5p) efficiently acetylates both nucleosome core particles and nucleosomal arrays. Furthermore, under conditions where nucleosomal arrays are extensively folded, rGcn5p acetylates folded arrays approximately 40% faster than nucleosome core particles. Finally, rGcn5p polyacetylates the N termini of free histone H3 but only monoacetylates H3 in nucleosomes and nucleosomal arrays. These results demonstrate both that rGcn5p in and of itself is catalytically active when assayed under optimal solution conditions and that this enzyme prefers folded nucleosomal arrays as a substrate. They further suggest that the structure of the histone H3 N terminus, and concomitantly the accessibility of the H3 acetylation sites, changes upon assembly into nucleosomes and nucleosomal arrays.