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PubMed2006

Multiple independent evolutionary solutions to core histone gene regulation.

BACKGROUND: Core histone genes are periodically expressed along the cell cycle and peak during S phase. Core histone gene expression is deeply evolutionarily conserved from the yeast Saccharomyces cerevisiae to human. RESULTS: We evaluated the evolutionary dynamics of the specific regulatory mechanisms that give rise to the conserved histone regulatory phenotype. In contrast to the conservation of core histone gene expression patterns, the core histone regulatory machinery is highly divergent between species. There has been substantial evolutionary turnover of cis-regulatory sequence motifs along with the transcription factors that bind them. The regulatory mechanisms employed by members of the four core histone families are more similar within species than within gene families. The presence of species-specific histone regulatory mechanisms is opposite to what is seen at the protein sequence level. Core histone proteins are more similar within families, irrespective of their species of origin, than between families, which is consistent with the shared common ancestry of the members of individual histone families. Structure and sequence comparisons between histone families reveal that H2A and H2B form one related group whereas H3 and H4 form a distinct group, which is consistent with the nucleosome assembly dynamics. CONCLUSION: The dissonance between the evolutionary conservation of the core histone gene regulatory phenotypes and the divergence of their regulatory mechanisms indicates a highly dynamic mode of regulatory evolution. This distinct mode of regulatory evolution is probably facilitated by a solution space for promoter sequences, in terms of functionally viable cis-regulatory sites, that is substantially greater than that of protein sequences.

Base Sequence↗

PubMed2006

Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae.

BACKGROUND: Histone acetylation plays important but incompletely understood roles in gene regulation. A comprehensive understanding of the regulatory role of histone acetylation is difficult because many different histone acetylation patterns exist and their effects are confounded by other factors, such as the transcription factor binding sequence motif information and nucleosome occupancy. RESULTS: We analyzed recent genomewide histone acetylation data using a few complementary statistical models and tested the validity of a cumulative model in approximating the global regulatory effect of histone acetylation. Confounding effects due to transcription factor binding sequence information were estimated by using two independent motif-based algorithms followed by a variable selection method. We found that the sequence information has a significant role in regulating transcription, and we also found a clear additional histone acetylation effect. Our model fits well with observed genome-wide data. Strikingly, including more complicated combinatorial effects does not improve the model's performance. Through a statistical analysis of conditional independence, we found that H4 acetylation may not have significant direct impact on global gene expression. CONCLUSION: Decoding the combinatorial complexity of histone modification requires not only new data but also new methods to analyze the data. Our statistical analysis confirms that histone acetylation has a significant effect on gene transcription rates in addition to that attributable to upstream sequence motifs. Our analysis also suggests that a cumulative effect model for global histone acetylation is justified, although a more complex histone code may be important at specific gene loci. We also found that the regulatory roles among different histone acetylation sites have important differences.

Acetylation↗

PubMed1989

Properties of an adenosine triphosphate-stimulated factor that enhances the nuclear binding of activated glucocorticoid-receptor complex: binding to histone-agarose.

Recently we have purified and characterized a factor in rat liver cytosol that enhances nuclear binding of the activated glucocorticoid-receptor complex in the presence of ATP [an ATP-stimulated translocation promoter (ASTP)]. It has a mol wt of 93,000, S value of 6.5, and pI of 4.5. Here we report studies on the binding of ASTP to histones from calf thymus. Higher salt concentrations were required to disrupt the binding of ASTP to histone-agarose than to disrupt its binding to the anion exchanger diethylaminoethyl-cellulose (half-maximal concentration for inhibition: 200 mM vs. 60 mM KCl). ATP decreased the binding of ASTP to histone-agarose in a dose-dependent fashion, but ADP and AMP had no appreciable effect on the binding. Pyridoxal 5'-phosphate (10 mM) inhibited the binding of ASTP to histone-agarose, whereas 10 mM pyridoxal, pyridoxamine 5'-phosphate, pyridoxamine, and pyridoxine were not inhibitory. ASTP did not bind to histone-agarose that had been pretreated with pyridoxal 5'-phosphate and then reduced with sodium borohydride. In contrast, ASTP pretreated in the same way could bind to histone-agarose. Therefore, modification of lysine residues of histones by pyridoxal 5'-phosphate (Schiff base) presumably inhibited the binding of ASTP to the immobilized histone. Competition experiments with various histones (H1, H2A, H2B, H3, and H4) indicated that ASTP bound to the arginine-rich histones H3 and H4, with preference for H4. These observations together suggest that lysine residues in H4 and H3 are essential for the binding of ASTP to histone. The implications of this interaction are discussed.

Adenosine Triphosphate↗

PubMed1975

Histone proteases of avian erythroid cells.

Protease activity associated with avian erythroid chromatin has been studied by gel electrophoresis of histones. Histone degradation is minimal at neutral pH, but is readily detected when chromatin is incubated at pH 3, and is evident to a lesser extent at pH 9. As a result of the pH 3 activity, the f1 and f2 chistones are preferentially degraded when the histone complement is DNA-bound, but these histones are relatively resistant to attack when present as free histone. The pH 3 activity reported here has properties similar to those of neutral histone proteases from other tissues, except that it is not inhibited by bisulphite. Added exogenous proteins are not degraded. The activity of avian erythroid histone protease decreases as maturation of the cells proceeds. Since we have previously shown that turnover of DNA-bound f2c histone occurs in reticulocytes and histone synthesis is absent in erythrocytes, it is possible that the histone protease described here may be involved in f2c histone turnover.

Animals↗

PubMed1991

Hydrostatic pressure influences histone mRNA.

Exposure of HeLa S3 cells to high hydrostatic pressure (6.89 x 10(3) to 6.89 x 10(4) kPa: 1000 to 10,000 lbfin-2) reduced core and H1 histone mRNA levels as determined by hybridization to specific histone DNA probes. At 4.14 x 10(4) kPa for 10 min core histone and H1 histone mRNA levels were reduced 32-38% and 56%, respectively. At 30 min postdecompression core mRNA levels returned to atmospheric control levels while H1 histone mRNA levels continued to be suppressed. Levels of macromolecular synthesis were monitored under hydrostatic pressure with radioactive precursors of RNA, DNA and protein. Macromolecular synthesis was shown to be suppressed in a dose-dependent manner with increasing magnitude and duration of pressure. To determine the influence of pressure on histone mRNA stability, actinomycin D (10 micrograms ml-1) was used to block RNA synthesis. Relative amounts of H4 and H1 mRNA were determined at atmospheric pressure and following treatment with actinomycin D (10 micrograms ml-1), pressure (4.14 x 10(4) kPa) and a combination of pressure and actinomycin D. This study shows that a synthesis component and a stability component are involved in the pressure-induced reduction of core histone mRNA. At 4.14 x 10(4) kPa for 15 min, there was a 42% reduction in core histone mRNA of which approximately one third was due a suppression of transcription and two thirds to a loss of mRNA stability. The pressure-induced reduction in histone mRNA is attributed to the instability of endogenous histone mRNA and a reduction in transcription/processing of new histone mRNA.

HeLa Cells↗

PubMed2006

Flexible histone tails in a new mesoscopic oligonucleosome model.

We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.

Binding Sites↗

PubMed1989

Possible role of histones in the organization of rat liver thyroid hormone receptors in chromatin.

The effects of histone subfractions on rat liver thyroid hormone receptor-DNA interaction were examined using an in-vitro DNA-cellulose binding assay. H1 histones bound to DNA showed reversible and potent inhibition of receptor-DNA binding without affecting receptor hormone binding. Poly-lysine, bovine serum albumin, ovalbumin and cytochrome c did not alter receptor-DNA binding. H1 histone subfractions (calf thymus lysine-rich histone (CTL)-1, CTL-2 and CTL-3) showed potent inhibition of receptor-DNA binding indistinguishable from each other. The quantity of H1 histone subfractions bound to DNA was the same. Although each subfraction has different functional properties, inhibition of receptor-DNA binding was a common feature of all the H1 histone subfractions, which is important for the non-random distribution of the receptor in chromatin. Binding of the receptor to core histones was investigated; it was found to bind to core histones more potently than to other proteins (H1 histone, ovalbumin and cytochrome c). Among core histone subfractions, H4 histone bound to the receptor most potently and is the candidate to be one of the acceptor sites of the receptor in chromatin.

Animals↗

PubMed1999

Poly(ADP-ribosylation) protects maternally derived histones from proteolysis after fertilization.

Fertilization in sea urchins is followed by the replacement of sperm-specific histones by cleavage-stage histone variants recruited from maternal stores. Such remodelling of zygote chromatin involves a cysteine proteinase that degrades the sperm-specific histones in a selective manner, leaving the maternal cleavage-stage histone variants intact. The mechanism that determines the selectivity of the sperm-histone-selective proteinase (SpH-proteinase) was analysed by focusing on the post-translational modification status of both sets of histones. It has previously been reported that only native cleavage-stage histones are poly(ADP-ribosylated), whereas the sperm-specific histones are not modified. To determine whether the poly(ADP-ribose) moiety afforded protection from degradation, the ADP-ribose polymers were removed from the cleavage-stage histones in vitro; these proteins were then assayed as potential substrates of the SpH-proteinase. Strikingly, the cleavage-stage histone variants were extensively degraded after the enzymic removal of their ADP-ribose moieties. In addition, the SpH cysteine proteinase was not inhibited by isolated poly(ADP-ribose) polymers. Consequently, only poly(ADP-ribosylated) cleavage-stage histone variants are protected from proteolysis. These results demonstrate a novel role for this type of post-translational modification, namely the protection of nuclear proteins against nuclear proteinases after fertilization.

Animals↗

PubMed1975

Sites of in vivo histone methylation in developing trout testis.

Specific lysyl residues of trout testis histones H3 and H4 are methylated partially during rainbow trout spermatogenesis. Histones H1, H2A, H2B, and protamine are not methylated. The single site (lysine 20) in histone H4 and the two major sites (lysines 9 and 27) in histone H3 are homologous to those determined for other organisms, but an additional minor site (lysine 4) occurs in histone H3. As described for calf thymus, both histones H3 and H4 contain epsilon-N-mono- and dimethyllysine, while histone H3 contains in addition, epsilon-N-trimethyllysine. The trout-specific histone H6, which accounts for 0.5 to 1.0% of total histone, contains a sequence for residues 3 to 5,-Arg-Lys-Ser-, which is the same as one methylated in histones H3, at lysines 9 and 27. However, histone H6 yields only trace amounts of [3H]methyl incorporation and no detectable methyllysines on amino acid analysis.

Alanine↗

PubMed1977

[In vitro-phosphorylation of histones in chromatin of various tissues in relation to age (author's transl)].

The influence of age on the structure of chromatin of various mammalian cells with modest or terminated mitotic activity has been examined. For this purpose chromatin from dog skeletal muscle, and human neuronal and glial cells, has been incubated together with an exogenous histone phosphokinase and ATP-gamma32P, and the phosphate incorporated into the histones determined. For comparison, also free histone has been phosphorylated. The amount of phosphate incorporated into total histone is 16-18 nmol Pi per mg histone in the case of free histone, and about equal for all cell types and ages. Into chromatin-bound histones only 5.5-8.2 nmol Pi per mg histone are incorporated. The differences between the various cell types and age groups are not significant. The relative phosphate incorporation into the single histone fractions depends on the histone as being free or chromatin-bound. In addition, relative phosphate incorporation into the single fractions of chromatin-bound histones is also cell type- and age-specific. The results permit the conclusion that the chromatin is subject to structural changes in the course of aging.

Adult↗

PubMed1988

Ubiquitin carrier protein-catalyzed ubiquitin transfer to histones. Mechanism and specificity.

Ubiquitinated derivatives of histones H2A and H2B, in which the carboxyl terminus of ubiquitin is joined to epsilon-amino groups of specific lysine residues of each histone, occur in vivo. Certain ubiquitin carrier proteins (E2s) catalyze ubiquitin transfer to histones (Pickart, C. M., and Rose, I. A. (1985) J. Biol. Chem. 260, 1573-1581). The catalytic activities of these purified ubiquitin carrier proteins have been quantitatively characterized with purified histones, in order to determine if one or more of them exhibits specificity for H2A over other histones (H3,H4) which are not known to be ubiquitinated in vivo. The results show the following. 1) No E2 exhibits strong specificity for H2A over the other histones. 2) For a given histone, kinetics of formation of its monoubiquitinated adduct do not differ strongly among the E2s; sigmoid kinetics (nH = 2) are generally observed, with values of K 0.5 ranging from 2-6 microM. 3) E214K catalyzes primarily monoubiquitination. 4) E220K catalyzes multiple ubiquitination (up to three ubiquitin/histone) by a processive mechanism that involves joining of ubiquitin carboxyl termini to multiple histone lysine residues. 5) E235K also catalyzes processive ubiquitination, with formation of polyubiquitinated products exhibiting a lag phase. Many of the polyubiquitinated adducts produced at low histone concentration are larger than expected for monoubiquitination of every histone-lysine residue, and polyubiquitination is selectively inhibited by substitution of reductively methylated ubiquitin for ubiquitin. These results suggest that E235K uniquely catalyzes ubiquitin transfer to lysine residues of previously conjugated ubiquitin molecule(s). The implications of these results for biological mechanisms of histone ubiquitination are discussed.

Animals↗

PubMed1987

Relationship of H1(0) histone to differentiation and cancer.

The H1(0) histone was first described by Panyim and Chalkley in 1969 as a new electrophoretic band found with histones of non-replicating tissues. Tissues which are active in DNA replication such as ascites tumor cells or thymus cells were reported to lack this band. In this respect the H1(0) histone differs from the bulk of histones which are generally maintained in a constant ratio with respect to each other and to DNA. An inverse relationship between H1(0) histone levels and growth rate was suggested by the decrease in H1(0) histone concentration during regeneration of the pancreas and liver. The synthesis of H1(0) is unusual but not unique in that, unlike the major histone species, it is not restricted to the S phase of the cell cycle. Although there is a general trend for the levels of H1(0) histone to be lower in neoplastic than normal tissues, exceptions have been observed. Compounds such as sodium butyrate and dimethylsulfoxide, which can induce differentiated properties in neoplastic cells, can bring about the accumulation of increased amounts of H1(0) histones. The relative magnitude of these effects exhibits cell-type specificity. There are two H1(0) histone subtypes (a and b) with ratios which differ according to the tissue examined and whose relative importance is not known. The levels of H1(0) histone appear to be more closely related to the degree of differentiation than to the proliferative activity of cells.

Animals↗

PubMed1987

Binding of linker histones to the core nucleosome.

Binding of chicken erythrocyte linker histones H1/H5 to the core nucleosome has been studied. Histones H1/H5 bind very efficiently to the isolated core nucleosome in vitro. The binding of linker histones to the core nucleosome is associated with aggregation of the particles. Approximately one molecule of linker histone binds per core nucleosome in the aggregates, irrespective of the concentration of the linker histones and the salt used. Histone H5 shows greater binding affinity to the core nucleosome as compared to H1. The carboxyl-terminal fragment of the linker histones binds strongly to the core nucleosome while the binding of the central globular domain is weak. Each core nucleosome is capable of binding two molecules of carboxyl-terminal fragment of linker histone. The core nucleosome containing one molecule of carboxyl-terminal fragment of linker histone requires higher salt concentration for aggregation while the core nucleosome containing two molecules of carboxyl-terminal fragment of linker histone can self-associate even at lower salt concentrations. On the basis of these results we are proposing a novel mechanism for the condensation of chromatin by linker histones and other related phenomena.

Animals↗

PubMedDate not supplied

[The loss of CpG dinucleotides from DNA. III. Methylation and evolution of histone genes].

From nucleotide sequences of more than 70 histones genes in 15 species of eucaryotes the probable frequency was determined for CpG----TpG + CpA substitutions, occurring as a result of deamination of 5-methylcytosine residues in DNA. It was found that histone genes differ in the character of CpG methylation with respect to the species studied and may be divided into three groups differing in the value of CpG suppression. In one of them, M-, CpG dinucleotides must have not been methylated throughout the existence of these genes; in another, M+, nearly every other CpG has undergone transition. In the third group, M +/-, no more than 20% of CpG have steadily undergone methylation (and mutation). The CpG deficiency in M+ and M +/- histone genes is in general proportional to the level of methylation of total DNA in different species. It has been noted that the genes of different core histones in the same organism are characterized, as a rule, by the same type of CpG methylation and belong to the same group. Genes H1 and H5 show a higher level of CpG suppression and thus have a higher degree of methylation than the genes of core histones from the same organism. The most conserved among the histone genes, those for H3 and H4 in particular, must have not been methylated in the majority of the species studied. The distribution of methylated and non-methylated spacers and coding sequences of histone genes of man, mouse, hen and yeast reveals a mosaic pattern. It has been found that 5'-flanked regions in most cases are methylated more than respective genes, while the G + C content in them is significantly lower, compared with the coding gene sequences. The absence of methylation in the 5'-regulatory regions does not appear to be mandatory for histone genes. It has been established that the genes of the same histones may differ in the level of methylation even in more or less closely related species. Group M- comprises genes of core histones of man, hen, sea urchin, Drosophila, Neurospora and wheat; group M +/- includes analogous genes of mouse, Xenopus, trout and sea urchins. The results obtained testify against the possible universal involvement of methylation in the regulation of histone gene expression.

Animals↗

PubMed1985

[Effect of the supranucleosomal chromatin organization on histone-DNA interrelations].

It has been demonstrated by the method of competitive displacement of own chromatin histone by excess total histone that chromatin dispersity influence the strength of histone-DNA interactions in a medium of physiological ionic strength. Histone NI was removed from chromatin after the quantity of total histone added to chromatin was equivalent to that existing in chromatin. The proportion of histones H2A and H2B removed from chromatin was increased after mechanical of ultrasonic degradation of chromatin at 5-20-fold excess of total extra-histone. In some histone preparations, the removal of histones H2A and H2B was not detectable at even 200-fold excess of total histone. This may be explained by strengthening histone-DNA interactions in superhelical loops of chromatin.

Animals↗

PubMedDate not supplied

[Unfolding of nucleosome cores induced by chemical acetylation of histones].

Relative accessibility of nucleosomal histones to acetic anhydride during acetylation has been studied as a function of concentration, pH and ionic strength of the solution using high-resolution gel-electrophoresis. It was shown that about 80% of lysine residues in nucleosomal histones and 100% of the same residues in histone complexes without DNA in 2 M NaCl are accessible to the modification, which is proved by the localization of the majority of lysine residues in nucleosomes near the surface of the histone octamer, by their participation in ionic interactions with DNA and, probably, in histone-histone contacts. Gel-electrophoretic experiments with nucleosomes and studies of the histone resistance to mild trypsinolysis indicated that neither nucleosomes themselves nor histone octamers are affected even though 50% of lysine residues in histones have been acetylated. The process of acetylation is accompanied by the growing tendency of histones to participate in mild trypsinolysis and by a gradual decline in electrophoretic mobility and in the value of the sedimentation constant. The circular dichroism spectra and the microscopic appearance of nucleosomes are also markedly changed. These results suggest that a gradual unfolding of nucleosomes occurs when 5 or more lysine residues in the nucleosomal histones have been acetylated.

Acetates↗

PubMed1982

Activation of an NAD:arginine ADP-ribosyltransferase by histone.

An ADP-ribosyltransferase from turkey erythrocytes which utilizes proteins and low molecular weight guanidino compounds such as arginine and agmatine as ADP-ribose acceptors was stimulated by histones. The effect was specific in that choleragen, a bacterial mono(ADP-ribosyl)transferase that increased adenylate cyclase activity in animal cells, was not activated by histones. With the erythrocyte enzyme, histones decreased the apparent Km values for arginine methyl ester and agmatine and increased the stability of the transferase to thermal denaturation. Activation of the transferase by histones was rapid, with a minimal delay observed upon addition of histones to a histone-free assay. Activation by histones was reversed upon dilution of a sample containing histones into an assay mix free of histone. In the absence of histone, the transferase existed as a rapidly sedimenting species; in the presence of histone, the transferase sedimented as a protomer.

ADP Ribose Transferases↗

PubMed1980

[Isolation of histones from the nuclei of the flagellatum Astasia longa].

A new procedure for isolation of purified nuclear fraction from the cells of the phytoflagellatum Astasia longa has been developed. The resulting preparations were characterized in terms of their chemical composition. A method of isolation to total histone preparations from the nuclear fractions of A. longa based on the metabolic peculiarities of the phytoflagellatum has been developed. Pure histone fractions were obtained by intensive disruption and thorough washing of the nuclear fraction from the non-histone proteins with weak solutions of salts. The intensive proteolysis of the histones in the course of washing was stopped by an addition of the specific inhibitors of proteinases--phenylmethylsulfanylfluoride and pCMB (pH 7,8--8,0). The use of NaHSO3 or boiling of the nuclear fraction to suppress the histone proteolysis were found to be ineffective. Extraction of the histones by 1 M CaCl2 appeared more productive than the use of mineral acids solutions. The total histone preparation isolated under optimal conditions was found in the chromatin in amounts equivalent to those of DNA; its amino acid composition was typical for histones. During polyacrylamide gel electrophoresis in an acidic system in the presence of urea the histones produced four main bands, whereas in the presence of DS-Na--five bands. In terms of the amino acid composition and electrophoretic properties in different systems the histones of A. longa are similar but not identical to calf thymus histones.

Amino Acids↗