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Patterns of histone acetylation in the cell cycle of Physarum polycephalum.

Labeling of histones in the naturally synchronous cell cycle of Physarum polycephalum with short pulses of tritiated acetate in vivo clearly showed three distinct patterns of histone acetate turnover. In G2 phase, turnover of acetate was observed only in histones H3 and H4, predominantly on the multiple acetylated forms. No acetate turnover was found in histones H2A and H2B compared with histones H3 and H4. In S phase, intense labeling was seen in all four core histones, in histones H3 and H4 predominantly in the low acetylated forms. In addition, cotranslational acetylation of the amino-terminal serines of histones H4 and H1 was observed during S phase. During mitosis, from condensation at prophase to decondensation after telophase, acetate turnover is almost zero. This suggests that within the mitotically condensed chromosomes all potential histone acetylation sites are masked. In G2 phase, when transcription is occurring, only histones H3 and H4 are available for acetate turnover, but in S phase, when both transcription and replication occur, all four histones are available for acetate turnover.

Acetylation↗

Histones of terminally differentiated cells undergo continuous turnover.

In contrast to the widely accepted idea of the nearly absolute metabolic stability of histones, our experiments support the view that the histones of nonproliferating, terminally differentiated cells undergo continuous replacement. This conclusion is based on the incorporation of labeled amino acids into the histones of mouse kidney and liver cells after their intraperitoneal introduction. We have found that the intranuclear uptake of the histones made in the absence of replicative synthesis and their integration into chromatin proceed with striking delay. The metabolic rates of individual histones measured by calculating their half-lives suggest that each histone turns over at a specific rate. With regard to the basic chromatin structure, the nucleosome, such unequal turnover should mean that the histone core does not participate in this process as a single unit but rather as a protein mosaic in which each partner follows its own rate of removal. Additional experiments suggested that intact nucleosomes take part in the replacement, but the relative proportion of the nucleosomes involved should be limited. The nonnucleosomal H1A and H1 degree histones have been found to undergo faster replacement than the core histones. Moreover, in comparison to each other, these two histone subfractions are also replaced at a different rate. The results of autoradiography of isolated kidney and liver nuclei after continuous labeling with [3H]-thymidine suggest that the histone replacement is not associated with the repair of DNA.

Animals↗

In vivo assembly of newly synthesized histones.

Following a labeling period of 2 min, HeLa histones continue to accumulate in chromatin for 10 min, indicating the presence of a histone pool. During the accumulation period, H2A and H2B enter chromatin immediately, while entry of H3 and H4 is more prolonged. Association of newly synthesized core histones with chromatin does not necessarily indicate assembly. When 2-min [3H]lysine-labeled chromatin is exposed to 0.45 M NaCl, nearly half of the newly synthesized histones are dissociated, while mature core histones are stable. H2A and 70% of H2B are salt stable and remain with newly synthesized polynucleosomes. About 30% of H2B, 50% of H4, and all of H3 are salt labile; thus, both the new nucleosomal core histones and salt-labile new core histones are nonstoichiometric. Pulse-labeled core histones are more trypsin-sensitive than mature histones. When the salt-labile, newly synthesized histones are removed, the remaining proteins have the same trypsin sensitivity as bulk core protein. Examination of the tryptic peptides indicated that the increased trypsin sensitivity was due to complete destruction of the loosely associated core histones which undergo a lag prior to assembly. The altered order of appearance of two peptides in stripped, newly assembled nucleosomes indicates that the conformation in these particles is different from that in mature chromatin.

Carbon Radioisotopes↗

Structure of a covalently cross-linked form of core histones present in the starfish sperm.

The post-translational modification of core histones plays an essential role in chromatin remodeling processes. We recently reported the occurrence of a novel histone modification, involving a epsilon-(gamma-glutamyl)lysine cross-link between a glutamine residue of histone H2B and a lysine residue of histone H4 in the testis of the starfish, Asterina pectinifera[Shimizu, T., Hozumi, K., Horiike, S., Nunomura, K., Ikegami, S., Takao, T., and Shimonishi, Y. (1996) Nature 380, 32]. In order to determine the complete structure of the modified histone heterodimer, p28 from both testis and sperm was purified. p28 was digested with Achromobacter lyticus protease I or Staphylococcus aureus V8 protease to give proteolytic fragments that were separated by HPLC. Amino acid analysis, sequencing, and mass spectrometric analysis of the fragments showed that the amino acid sequences of these fragments are identical to those of both histones H2B and H4, except for two NH2-terminal peptides obtained by digestion with A. lyticus protease I. One of the peptides, K8, was identical to that reported previously, and the other was a here-to-fore unidentified peptide, which was designated K10. Amino acid and positive-ion FAB-MS/MS analyses of K10 showed that it to be a fragment, derived from Gly8-Lys10 of histone H2B and Gly9-Lys16 of histone H4. The yields of K8 and K10 were calculated to be 47 and 42%, respectively, expressed as the percent of the total amount of p28 used in the experiment. Based on these data, the structure of p28 was determined to be a heterodimer, composed of histones H2B and H4, formed through a transglutaminase-catalyzed acyl transfer reaction between Gln9 of histone H2B and Lys5 or Lys12 of histone H4.

Amino Acid Sequence↗

Development of H1e histone linker-specific antibodies by means of synthetic peptides.

A large body of data suggests that the linker histones family (H1) affects gene expression. Investigation of the linker histones role is then of a major interest in cell cycle studies with implications in gene therapy. Indeed, it has been shown that in most tissues a switch of histone subtypes occurs when the cells cease to divide. To investigate linker histone role in gene or transgene expression, an antibody against subtypes of H1 would be useful for immunoprecipitation experiments and further assays measuring H1subtypes-DNA interactions in living cells. In order to produce an antibody against the H1e subtype of linker histones, two synthetic peptides derived from two regions of the H1e mouse histone protein were examined for their potential, [as keyhole limpet hemocyanin (KLH) conjugates] to elicit polyclonal anti-H1e antibodies in New Zealand white rabbits. Selection of the peptide sequences was based on amino acid differences within the different classes of histones and between mice and rabbit histones as well. The evaluation of their potential immunogenic properties was based on examination of peptide hydropathy using predicting algorithms. Immunoglobulins (IgG) obtained from immunized and nonimmunized rabbits were tested using enzyme-linked immunosorbent assay (ELISA) procedures, Western immunoblot, and immunofluorescence experiments. Results showed that the selected synthetic peptides gave rise to a high-titer polyclonal antibody able to recognize the H1e histone under various conditions. This polyclonal antibody did not cross-react with other histones. To our knowledge, this is the first antibody produced against the mouse H1e linker histone.

Amino Acid Sequence↗

Nucleosome assembly protein-1 is a linker histone chaperone in Xenopus eggs.

In eukaryotic cells, genomic DNA is primarily packaged into nucleosomes through sequential ordered binding of the core and linker histone proteins. The acidic proteins termed histone chaperones are known to bind to core histones to neutralize their positive charges, thereby facilitating their proper deposition onto DNA to assemble the core of nucleosomes. For linker histones, however, little has been known about the regulatory mechanism for deposition of linker histones onto the linker DNA. Here we report that, in Xenopus eggs, the linker histone is associated with the Xenopus homologue of nucleosome assembly protein-1 (NAP-1), which is known to be a chaperone for the core histones H2A and H2B in Drosophila and mammalian cells [Ito, T., Bulger, M., Kobayashi, R. & Kadonaga, J. T. (1996) Mol. Cell Biol. 16, 3112-3124; Chang, L., Loranger, S. S., Mizzen, C., Ernst, S. G., Allis, C. D. & Annunziato, A. T. (1997) Biochemistry 36, 469-480]. We show that NAP-1 acts as the chaperone for the linker histone in both sperm chromatin remodeling into nucleosomes and linker histone binding to nucleosome core dimers. In the presence of NAP-1, the linker histone is properly deposited onto linker DNA at physiological ionic strength, without formation of nonspecific aggregates. These results strongly suggest that NAP-1 functions as a chaperone for the linker histone in Xenopus eggs.

Amino Acid Sequence↗

Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF.

Nucleosome Remodeling Factor (NURF) is an ATP-dependent nucleosome remodeling complex that alters chromatin structure by catalyzing nucleosome sliding, thereby exposing DNA sequences previously associated with nucleosomes. We systematically studied how the unstructured N-terminal residues of core histones (the N-terminal histone tails) influence nucleosome sliding. We used bacterially expressed Drosophila histones to reconstitute hybrid nucleosomes lacking one or more histone N-terminal tails. Unexpectedly, we found that removal of the N-terminal tail of histone H2B promoted uncatalyzed nucleosome sliding during native gel electrophoresis. Uncatalyzed nucleosome mobility was enhanced by additional removal of other histone tails but was not affected by hyperacetylation of core histones by p300. In addition, we found that the N-terminal tail of the histone H4 is specifically required for ATP-dependent catalysis of nucleosome sliding by NURF. Alanine scanning mutagenesis demonstrated that H4 residues 16-KRHR-19 are critical for the induction of nucleosome mobility, revealing a histone tail motif that regulates NURF activity. An exchange of histone tails between H4 and H3 impaired NURF-induced sliding of the mutant nucleosome, indicating that the location of the KRHR motif in relation to global nucleosome structure is functionally important. Our results provide functions for the N-terminal histone tails in regulating the mobility of nucleosomes.

Adenosine Triphosphate↗

Location of histones on simian virus 40 DNA.

The physical location of histone molecules in a simian virus 40 DNA-histone complex isolated from purified virions was examined using site-specific restriction endonucleases. The complex contains four host histone species but lacks histone F1. Histones prevent complete cleavage of SV40 DNA by two restriction enzymes, HindIII and EcoRI. From the pattern of DNA fragments resulting from cleavage of the histone-DNA complex by the HindIII endonuclease, which makes six breaks on purified SV 40 DNA, we have concluded that histones are randomly arranged on SV40 DNA relative to restriction enzyme cleavage sites. The EcoRI endonuclease, which makes one break in SV40 NDA, was used to determine the degree of physical coverage of the SV 40 DNA molecule by histones. We observed that 80% of the EcoRI sites in the complex are accessible to the enzyme while 20% are "closed." This degree of coverage is consistent with the mass ratio of DNA:histone in the complex as revealed by the buoyant density of the formaldehyde-fixed complex. We conclude that the histones in the complex are located randomly on the SV 40 genome and cover approximatley 20% of the DNA. These results suggest that the histone species F2b, F2al, F2a2, and F3 are bound without regard to nucleotide sequence of SV 40 DNA.

Binding Sites↗

Nonrandom distribution of histone mRNAs into polysomes and nonpolysomal ribonucleoprotein particles in sea urchin embryos.

In the early sea urchin embryo, newly synthesized cytoplasmic histone mRNA is found both on polysomes and free of ribosomes as nonpolysomal messenger ribonucleoprotein particles (free RNPs). The distribution of newly synthesized histone mRNAs between translating and nontranslating compartments is nonrandom and dependent on the developmental stage. Gel electrophoresis and autoradiography of polysomal and free RNP RNA from embryos at various stages show that (i) the fraction of total newly synthesized histone mRNA that is in polysomes is greater than the fraction of total newly synthesized poly(A)+mRNA that is in polysomes, at all stages examined, and (ii) among the five histone mRNAs. H1 mRNA and H4 mRNA are relatively more enriched in the free RNPs than are the mRNAs for H2A, H2B, and H3. These data suggest that histone mRNA, as a class, is more efficiently utilized as a template than the average mRNA and, of the cytoplasmic histone mRNAs, the mRNAs for histones H2A, H2B, and possibly H3 are selected more frequently for translation than those for H1 and H4. Cell-free translations of polysomal and free RNP RNAs yield different ratios of in vitro histone products, consistent with the RNA distribution data. To test the possibility that the in vivo distribution of the histone mRNAs is the consequence of different intrinsic initiation capabilities of the individual mRNAs, ribosome-binding assays were carried out and unequal binding abilities of the histone mRNAs in the reticulocyte lysate were shown. A translational level component in the regulation of histone synthesis in the sea urchin embryo is indicated.

Animals↗

Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling.

DNA binding and the topology of DNA have been determined in complexes formed by >20 archaeal histone variants and archaeal histone dimer fusions with residue replacements at sites responsible for histone fold dimer:dimer interactions. Almost all of these variants have decreased affinity for DNA. They have also lost the flexibility of the wild type archaeal histones to wrap DNA into a negative or positive supercoil depending on the salt environment; they wrap DNA into positive supercoils under all salt conditions. The histone folds of the archaeal histones, HMfA and HMfB, from Methanothermus fervidus are almost identical, but (HMfA)(2) and (HMfB)(2) homodimers assemble into tetramers with sequence-dependent differences in DNA affinity. By construction and mutagenesis of HMfA+HMfB and HMfB+HMfA histone dimer fusions, the structure formed at the histone dimer:dimer interface within an archaeal histone tetramer has been shown to determine this difference in DNA affinity. Therefore, by regulating the assembly of different archaeal histone dimers into tetramers that have different sequence affinities, the assembly of archaeal histone-DNA complexes could be localized and used to regulate gene expression.

Amino Acid Sequence↗

Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry.

The nucleosome, the fundamental structural unit of chromatin, contains an octamer of core histones H3, H4, H2A, and H2B. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function, analysis of histone variants incorporated into the nucleosome and their covalent modifications is required. Here we report the first global mass spectrometric analysis of histone H2A and H2B variants derived from Jurkat cells. A combination of mass spectrometric techniques, HPLC separations, and enzymatic digestions using endoproteinase Glu-C, endoproteinase Arg-C, and trypsin were used to identify histone H2A and H2B subtypes and their modifications. We identified nine histone H2A and 11 histone H2B subtypes, among them proteins that only had been postulated at the gene level. The two main H2A variants, H2AO and H2AC, as well as H2AL were either acetylated at Lys-5 or phosphorylated at Ser-1. For the replacement histone H2AZ, acetylation at Lys-4 and Lys-7 was found. The main histone H2B variant, H2BA, was acetylated at Lys-12, -15, and -20. The analysis of core histone subtypes with their modifications provides a first step toward an understanding of the functional significance of the diversity of histone structures.

Amino Acid Sequence↗

Comparison of benzo[a]pyrene-diol-epoxide binding to histone H2A with different carboxy-terminal regions.

We have compared (+/-)-7r,8t-dihydroxy-9t,10t-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE-I) binding to three vertebrate histones H2A with different C-terminal regions. HPLC analyses of core histones prepared from nuclei exposed to [3H]BPDE-I showed that rat liver and chicken erythrocyte histones H2A were heavily labeled by [3H]BPDE-I, but Xenopus laevis liver histone H2A was not. This result was confirmed by HPLC analyses of V8-protease digests of BPDE-I bound to histone H2A purified from the three different nuclei. There are significant amino acid sequence differences only in the C-terminal regions of the different histones H2A, where rat liver and chicken erythrocyte histones H2A contain two and one histidine residues, respectively, while the amino acid sequence of Xenopus histone H2A contains no histidine. Pre-treatment of the in situ BPDE-I-modified H2A.2 from rat liver with carboxypeptidase B, which should remove the C-terminal lysine from the protein, resulted in increased retention times on reverse-phase HPLC for the adduct-containing peptides upon subsequent V8-protease digestion. This suggested that the site(s) of BPDE-I modification are located primarily in the C-terminal octapeptide of rat H2A.2. To confirm this, C-terminal V8-peptides of the different histones H2A were isolated and reacted with BPDE-I at physiological pH in vitro. The HPLC analyses of the reaction mixtures indicated that the C-terminal peptide of rat liver and chicken erythrocyte histones H2A was a target site for BPDE-I binding in nuclei. It is suggested that the nucleophilic target amino acid for BPDE-I binding in histone H2A may be a histidine located close to the C terminus.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

The self-association of chicken-erythrocyte histones.

The self-association of the separate histone fractions isolated from chicken erythrocytes has been studied in solution at a number of different pH values and ionic strengths. The apparent molecular weights of the histones were determined over a range of macromolecular concentrations using the techniques of osmotic pressure and sedimentation equilibrium. Histone F2c (H5) did not associate under any of the conditions investigated whereas the other histone fractions all appeared to undergo self-association forming dimers, dimers of dimers, etc. The degree of association increased with the pH and ionic strength of the medium. The tendency to aggregate increased in the order; histone F2c (H5) (non-aggregating), histone F2b (H2B), histone F2a2 (H2A), histone F3 (H3), histone F2a1 (H4) (highly aggregating). In the case of histone F2a2 (H2A) at pH 3.0 and ionic strength 0.1, the apparent weight-average molecular weight was determined at a number of macromolecular concentrations at five different temperatures. The self-association was analysed according to the method of Adams (published by Beckman Instruments Inc. in 1967) and shown to be a monomer-dimer-tetramer equilibrium. The association constants were evaluated at each of the temperatures studied and from their variation with temperature the values of the enthalpy and entropy of association were calculated. The intermolecular association was characterised by only a small change in enthalpy but a large, positive, change in entropy. This suggests that the association of histones at acid pH is due to hydrophobic interactions between the relatively uncharged segments of like polypeptide chains.

Animals↗

Metabolic activities of histones in rat liver and spleen.

Synthesis and turnover of histone I and II in normal rat liver and spleen were studied by Amberlite CG 50 column chromatography. Histone I was separated into three or four subfractions, each of which showed a different rate of incorporation of [3H]lysine. This was verified by a more shallow gradient chromatography developed by Kinkade and Cole [3] for very lysine-rich histone (F1), which showed tissue specific differences between liver and spleen in both the elution pattern and synthetic rates. These subfractions were distinguished from each other by dodecylsulphate electrophoresis. The turnover, or disassociation of histone I and II in chromatin was measured by double-labelling of normal rat liver with [3H] and [14C]lysine. A good correspondence was found between the synthesis and turnover patterns of individual histone I fractions, while the histone II synthesized was conserved for over a month. From consideration of the turnover in relation to the cell population of normal liver tissue, which consists of a very small fraction of growing cells and a very large fraction of resting ones, it was concluded that turnover of histone I must occur even in resting cells. When DNA synthesis in the spleen was completely inhibited by hydroxyurea, the synthesis of histone II was inhibited but that of histone I was only partially inhibited. The remaining synthesis seemed to occur in cells in the resting state. It was concluded tentatively, the continuous replacement of very lysine-rich histones of chromatin must occur even in resting cells in which DNA synthesis has ceased. The biological significance of disassociation of histones from chromatin was discussed.

Animals↗

Changes in the stability of a human H3 histone mRNA during the HeLa cell cycle.

A major component of the regulation of histone protein synthesis during the cell cycle is the modulation of the half-life of histone mRNA. We have uncoupled transcriptional and posttranscriptional regulation by using a Drosophila hsp70-human H3 histone fusion gene that produces a marked human H3 histone mRNA upon heat induction. Transcription of this gene can be switched on and off by raising and lowering cell culture temperatures, respectively. HeLa cell lines containing stably integrated copies of the fusion gene were synchronized by double thymidine block. Distinct populations of H3 histone mRNA were produced by heat induction in early S-phase, late S-phase, or G2-phase cells, and the stability of the induced H3 histone mRNA was measured. The H3 histone mRNA induced during early S phase decayed with a half-life of 110 min, whereas the same transcript induced during late S phase had a half-life of 10 to 15 min. The H3 histone mRNA induced in non-S-phase cells is more stable than that induced in late S phase, with a half-life of 40 min. Thus, the stability of histone mRNA is actively regulated throughout the cell cycle. Our results are consistent with an autoregulatory model in which the stability of histone mRNA is determined by the level of free histone protein in the cytoplasm.

Cell Cycle↗

Modulation of histone deposition by the karyopherin kap114.

The nuclear import of histones is a prerequisite for the downstream deposition of histones to form chromatin. However, the coordinate regulation of these processes remains poorly understood. Here we demonstrate that Kap114p, the primary karyopherin/importin responsible for the nuclear import of histones H2A and H2B, modulates the deposition of histones H2A and H2B by the histone chaperone Nap1p. We show that a complex comprising Kap114p, histones H2A and H2B, and Nap1p is present in the nucleus and that the presence of this complex is specifically promoted by Nap1p. This places Kap114p in a position to modulate Nap1p function, and we demonstrate by the use of two different assay systems that Kap114p inhibits Nap1p-mediated chromatin assembly. The inhibition of H2A and H2B deposition by Kap114p results in the concomitant inhibition of RCC1 loading onto chromatin. Biochemical evidence suggests that the mechanism by which Kap114p modulates histone deposition primarily involves direct histone binding, while the interaction between Kap114p and Nap1p plays a secondary role. Furthermore, we found that the inhibition of histone deposition by Kap114p is partially reversed by RanGTP. Our results indicate a novel mechanism by which cells can regulate histone deposition and establish a coordinate link between histone nuclear import and chromatin assembly.

Animals↗

Regulation of human histone gene expression during the HeLa cell cycle requires protein synthesis.

We have examined the effects of protein synthesis inhibition on histone gene expression during the HeLa cell cycle. Histone mRNAs, which normally are rapidly degraded in the absence of DNA synthesis, persist and increase in concentration when translation is inhibited before DNA replication is halted. This is not a function of polysomal shielding of these mRNAs from active degradation mechanisms since inhibitors of translation initiation alone effect stabilization and induction. The superinduction of histone mRNAs by protein synthesis inhibition is effective at the G1/S border, and in the S-phase and non-S-phase periods of the cell cycle. However, the relative increase in histone mRNA is greater when cells not synthesizing DNA are treated with a protein synthesis inhibitor than when S-phase cells are so treated. Non-histone mRNAs examined are not superinduced by translation inhibition. Transcription rates from both histone and non-histone genes increase after protein synthesis inhibition. Although the decrease in histone gene transcription associated with DNA synthesis inhibition is prevented and reversed by protein synthesis inhibition, we have no evidence that histone gene-specific transcriptional regulation is dependent on protein synthesis. Transcriptional increases may contribute to the superinduction effect but cannot explain its differential extent during the cell cycle, since these increases are similar when replicating or nonreplicating cells are treated with a protein synthesis inhibitor. We believe that changes in histone mRNA stability can account for much of the differential superinduction effect. Our results indicate a requirement for continuing protein synthesis in the cell cycle regulation of histone mRNAs.

Aphidicolin↗

Identification of the linker histone H1 as a protein kinase Cepsilon-binding protein in vascular smooth muscle.

A variety of anchoring proteins target specific protein kinase C (PKC) isoenzymes to particular subcellular locations or multimeric signaling complexes, thereby achieving a high degree of substrate specificity by localizing the kinase in proximity to specific substrates. PKCepsilon is widely expressed in smooth muscle tissues, but little is known about its targeting and substrate specificity. We have used a Far-Western (overlay) approach to identify PKCepsilon-binding proteins in vascular smooth muscle of the rat aorta. Proteins of approximately 32 and 34 kDa in the Triton-insoluble fraction were found to bind PKCepsilon in a phospholipid/diacylglycerol-dependent manner. Although of similar molecular weight to RACK-1, a known PKCepsilon-binding protein, these proteins were separated from RACK-1 by SDS-PAGE and differential NaCl extraction and were not recognized by an antibody to RACK-1. The PKCepsilon-binding proteins were further purified from the Triton-insoluble fraction and identified by de novo sequencing of selected tryptic peptides by tandem mass spectrometry as variants of the linker histone H1. Their identity was confirmed by Western blotting with anti-histone H1 and the demonstration that purified histone H1 binds PKCepsilon in the presence of phospholipid and diacylglycerol but absence of Ca(2+). The interaction of PKCepsilon with histone H1 was specific since no interaction was observed with histones H2A, H2S or H3S. Bound PKCepsilon phosphorylated histone H1 in a phospholipid/diacylglycerol-dependent but Ca(2+)-independent manner. Ca(2+)-dependent PKC was also shown to interact with histone H1 but not other histones. These results suggest that histone H1 is both an anchoring protein and a substrate for activated PKCepsilon and other PKC isoenzymes and likely serves to localize activated PKCs that translocate to the nucleus in the vicinity of specific nuclear substrates including histone H1 itself. Since PKC isoenzymes have been implicated in regulation of gene expression, stable interaction with histone H1 may be an important step in this process.

Amino Acid Sequence↗