Effect of inhibition of DNA synthesis on histone synthesis and deposition

Assembling chromatin: the long and winding road

It has been over 35 years since the acceptance of the "chromatin subunit" hypothesis, and the recognition that nucleosomes are the fundamental repeating units of chromatin fibers. Major subjects of inquiry in the intervening years have included the steps involved in chromatin assembly, and the chaperones that escort histones to DNA. The following commentary offers an historical perspective on inquiries into the processes by which nucleosomes are assembled on replicating and nonreplicating chromatin. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.

Modifications of H3 and H4 during chromatin replication, nucleosome assembly, and histone exchange

Histone posttranslational modifications that accompany DNA replication, nucleosome assembly, and H2A/H2B exchange were examined in human tissue culture cells. Through microsequencing analysis and chromatin immunoprecipitation, it was found that a subset of newly synthesized H3.2/H3.3 is modified by acetylation and methylation at sites that correlate with transcriptional competence. Immunoprecipitation experiments suggest that cytosolic predeposition complexes purified from cells expressing FLAG-H4 contain H3/H4 dimers, not tetramers. Studies of the deposition of newly synthesized H2A/H2B onto replicating and nonreplicating chromatin demonstrated that H2A/H2B exchange takes place in chromatin regions that contain acetylated H4; however, there is no single pattern of H4 acetylation that accompanies exchange. H2A/H2B exchange is also largely independent of the deposition of replacement histone variant, H3.3. Finally, immunoprecipitation of nucleosomes replicated in the absence of de novo nucleosome assembly showed that histone modifications do not prevent the transfer of parental histones to newly replicated DNA and thus have the potential to serve as means of epigenetic inheritance. Our experiments provide an in-depth analysis of the "histone code" associated with chromatin replication and dynamic histone exchange in human cells.

Analysis of nucleosome assembly and histone exchange using antibodies specific for acetylated H4

Using antibodies that specifically recognize the acetylated forms of histone H4, we show that it is possible to immunoprecipitate newly assembled (acetylated) nucleosomes. Newly replicated HeLa cell chromatin was labeled for 5-30 min with [3H]thymidine in the presence of sodium butyrate (thus inhibiting the deacetylation of newly deposited H4); bulk chromatin DNA was labeled for 24 h with [14C]thymidine. When soluble nucleosomes were incubated with immobilized antibodies, a comparison of the bound and unbound fractions showed up to a 65-fold enrichment for new chromatin DNA in the immunoprecipitate (bound), relative to the supernatant (unbound). No enrichment for new DNA was observed when preimmune control serum was used in a similar fashion. The enrichment for new DNA in the immunopellet was paralleled by a similar enrichment for all four newly synthesized histones. Acetylation was required for antibody recognition: When chromatin was replicated in the absence of butyrate (permitting histone deacetylation and chromatin maturation), equally low levels of new and old chromatin were immunoprecipitated, and no enrichment for new DNA was observed. Competition experiments confirmed these results. Analyses of histone deposition during the inhibition of DNA replication established that acetylated chromatin is the preferential target for H2A/H2B exchange. These experiments provide evidence for the highly selective assembly of newly synthesized H3, H2A, and H2B with acetylated H4, and for the involvement of histone acetylation in dynamic chromatin remodeling. In addition, immunoprecipitations of radiolabeled cytosolic extracts identified a possible somatic chromatin preassembly complex, containing newly synthesized H3 and new (acetylated) H4.

Exchange of histones H1, H2A, and H2B in vivo

We have asked whether histones synthesized in the absence of DNA synthesis can exchange into nucleosomal structures. DNA synthesis was inhibited by incubating hepatoma tissue culture cells in medium containing 5.0 mM hydroxyurea for 40 min. During the final 20 min, the cells were pulsed with [3H]lysine to radiolabel the histones (all five histones are substantially labeled under these conditions). By two electrophoretic techniques, we demonstrate that histones H1, H2A, and H2B synthesized in the presence of hydroxyurea do not merely associate with the surface of the chromatin but instead exchange with preexisting histones so that for the latter two histones there is incorporation into nucleosome structures. On the other hand, H3 and H4 synthesized during this same time period appear to be only weakly bound, if at all, to chromatin. These two histones have been isolated from postnuclear washes and purified. Some possible implications of in vivo exchange are discussed.

Effect of inhibition of DNA synthesis on histone synthesis, turnover, and deposition in the rat testis

In testicular seminiferous epithelial cells (SEC) of normal and hypophysectomized rats, 1-beta-D-arabinofuranosylcytosine and hydroxyurea (at concentrations which inhibited DNA synthesis nearly completely) inhibited histone synthesis only partially, and to a different extent for each histone fraction. In the presence of the inhibitors, the extent of synthesis relative to the corresponding control was TH1-x greater than H1 greater than TH2B-x = X2 = H2A greater than H2B = H3 greater than H4, in which synthesis of the H4 fraction was about 50% of control and that of TH1-x was 90-95% of control. The extent of inhibition of synthesis of each histone fraction was similar after hypophysectomy and, therefore, the changing of the relative populations of heterogeneous cells in the SEC did not influence the relative effects of the inhibitors of DNA synthesis on the synthesis of the various histone fractions. After [3H]leucine injection, the molar proportions of labeled histones relative to H4 decreased markedly between 1.5 h and 6-15 days; this finding indicated that there was rapid removal of histones compared to the H4 fraction during this period. When [14C]thymidine was injected 24 h prior to hydroxyurea treatment and [3H]leucine injection, the ratios of specific activities of histone H4 to DNA did not change significantly over an 11-day period. It appears that newly synthesized histone H4 and other somatic histones are associated with existing DNA in the presence of DNA inhibitors.

In vitro exchange of nucleosomal histones H2a and H2b

We have asked whether exogenous, radiolabeled histones can exchange with nucleosomal histones in an in vitro system. Using two different electrophoretic techniques, we were able to separate the histones contained in nucleosomes from those histones which were simply bound to the surface of the chromatin. Fluorography was used to determine which of the exogenous histones exchange with the nucleosomal histones. We observed substantial exchange of histones H1, H2a, and H2b when the chromatin and exogenous histones were incubated under approximately physiological conditions. We have also observed a small amount of exchange of H2a and H2b, as well as a substantial exchange of H1, from one chromatin fragment to another. Other conditions affecting the exchange of histones H2a and H2b are also reported.

Chromatin assembled in the presence of cytosine arabinoside has a short nucleosome repeat

Incubation of MSB cells with cytosine arabinoside (1-beta-D-arabinofuranosylcytosine, ara-C) inhibits 3H-thymidine incorporation into nascent DNA while nucleosome core histone synthesis proceeds in molar stoichiometry at about 20% of control rates. The excess nascent histone is incorporated into chromatin and nucleosome cores are assembled normally on the small amount of DNA which is synthesized at submaximal levels of ara-C. This DNA becomes packaged into a shortened nucleosome repeat, however. These results indicate that the nucleosome core is a strongly conserved unit of chromatin replication and suggest that the stoichiometry of nascent histone to DNA may be one factor influencing the establishment of the nucleosome repeat length. It cannot be the only factor, however, since the closely packed nucleosomes made in the presence of ara-C begin to return to their normal spacing within six hours after reversal.

Histone synthesis by lymphocytes in G0 and G1

Peripheral blood lymphocytes are a naturally occurring population of G0 cells which can be activated in vitro to grow and divide. Upon activation with phytohemagglutinin (PHA), they enter G1 and, after a 24-h lag, begin DNA replication (S phase). Using radioisotope labeling and gel electrophoresis of acid-soluble chromatin proteins, we investigated histone synthesis in G0, G1, and S phase cultures of human and pig lymphocytes. In G0 and G1 cultures, which have less than 0.1% S phase cells, all five histones are synthesized and are incorporated into chromatin in equimolar amounts. In G0 lymphocytes histone synthesis accounts for at least 6% of nuclear protein radioactivity, and the rate of synthesis is about 2-3% of that of S phase lymphocytes. In contrast to histone synthesis by S phase cultures, G0 and G1 histone synthesis was completely resistant to treatment with hydroxyurea.

Histone and DNA synthesis in differentiating and rapidly proliferating cells in vivo and in vitro

The dependence of histone synthesis upon concurrent DNA synthesis has been studied in rat spermatogenic and brain tumor (RT489) cells, both in vivo and in vitro. The uptake of [3H]amino acids into histone was determined with and without inhibiting DNA synthesis with hydroxyurea (HU). HU reduced [14C]thymidine incorporation into DNA to less than 5% of control values in all cases without affecting the levels of total cellular protein synthesis, confirming the specificity of HU for inhibiting DNA synthesis. RT489 cells, grown either in culture or as a solid tumor, show no detectable histone synthesis when the concentrations of HU are sufficiently high. In the testis, no inhibition of synthesis of histones occurring during the meiotic prophase is observed in vivo or in vitro. These results provide further support for the model that a high degree of coupling of histone and DNA synthesis may occur only in proliferating, non-differentiating cell types and that both types of regulation can be observed both in in vivo and in vitro systems.

Chromatin replication, reconstitution and assembly

Many previously held concepts about the replication of chromatin have recently been revised, or seriously challenged. For instance, within the last two years, evidence has accumulated to indicate that newly synthesized DNA is not the sole site of deposition of newly synthesized histones, and that histones are not only made, but are assembled into chromatin in the absence of DNA synthesis. Furthermore, segregation of parental histones to daughter DNA duplexes may be bidirectional, rather than the previously accepted unidirectional mechanism. The storage of histones prior to assembly apparently involves histone pairs rather than octamers, and similarly, histones associate with DNA in (apparent) pairs, rather than as pre-assembled octameric units. It is currently questioned whether or not nucleoplasmin is involved in either histone storage or nucleosome assembly. The onset of histone synthesis has recently been found to occur in late G1 rather than in S, and thus is independent of DNA synthesis; however, the cessation of histone synthesis is linked to that of DNA. Thus, there emerges from this newly accumulated data the conclusion that chromatin biosynthesis is not as straightforward as was believed just a few years ago. As we review the evidence on each of these subjects, we attempt to point out directions for future experimentation.

Human lymphocyte proliferation. II. Formation of activated (G1) cells

The kinetics of phytohemagglutinin (PHA)-stimulated human peripheral blood lymphocytes in the early phases (G0, G1a, G1b) of the first cell cycle have been analyzed in vitro by cytofluorometry and [3H]thymidine incorporation. Cells were detected in the G1a, G1b and S phases 12-14, 20-22 and 24-26 h after stimulation, respectively. The total number of PHA-induced G1 cells reached a plateau after 32 h of incubation, upon which a second increase followed, 10 h later. The latter increase was considered to be a result of cells initiating their second cell cycle, since it could be abolished by hydroxyurea. By examination of supernatants, interleukin 2 (IL 2) activities could be recovered 6-10 h after PHA stimulation. In contrast, the monokine IL 1 was already detected after 2 h. Both interleukins were present in the culture medium before the major G1a cell formation took place. The titer of free IL 2 increased to a maximum after 18-22 h, whereafter a decline was observed. This decline was less pronounced if cultures were treated with hydroxyurea. Finally, among individual donors, the total number of lymphocytes entering the G1 phase and the time at which the G1a-G1b transition took place varied. Lower numbers of G1 cells and delayed G1a-G1b transition coincided with lower IL 2 titers and delayed occurrence of maximal titers in the supernatants.

Inhibition of DNA synthesis does not influence the H1 histone synthesis in Tetrahymena pyriformis

In the protozoan Tetrahymena pyriformis the DNA synthesis is stopped immediately and completely after addition of one of the two DNA synthesis inhibitors methotrexate + uridine and hydroxyurea to a cell suspension. However, the present experiments show, that the accumulation of labeled H1 histone in the inhibited cells is almost totally unaffected for more than two-thirds of a cell cycle after addition of either inhibitor.

Assembly of new histones into nucleosomes and their distribution in replicating chromatin

We studied the assembly of new histones into nucleosomes and their distribution in replicating chromatin in growing P815 mouse cells. New histones and new DNA were density-labeled with 13C, 15N, 2H-substituted amino acids together with [3H]arginine or with 5-iododeoxyuridine and [3H]thymidine, respectively, for 1 hr (approximately 20% of S phase). Mono- di-, tri-, tetra- and larger oligonucleosomes were isolated by sucrose gradient centrifugation of micrococcal nuclease-digested chromatin, and their density distribution was analyzed, without fixation, in metrizamide/triethanolamine density gradients [Russev, G. and Tsanev, R. (1976) Nucleic Acids Res. 3, 697-707] in which mono- and oligonucleosomes containing dense amino acids or 5-iododeoxyuridine separate from the corresponding normal nucleosomes. Under these conditions, approximately 74% of the new histones are found in nucleosomes on newly replicated DNA, and the remainder are on unreplicated DNA. The majority of new histones form entirely new nucleosomes; a minor fraction may form hybrid nucleosomes that also contain preexisting histones. New nucleosomes are distributed to both new daughter DNA molecules with approximately equal probability, and our evidence suggests, but does not prove, that they are distributed in a random manner along new DNA.

Effect of growth stage on histone H1 metabolism in human diploid fibroblasts

Metabolism of histone H1 at different stages of cell growth was investigated in order to get a better understanding of the role of histone H1 in the cell growth of human diploid fibroblasts. Histone H1 content exhibited some fluctuation during the culture stage of cell growth. When cells entered confluent phase, the ratio of histone H1 to total histones decreased significantly. Histone H1 had a turnover half-life of 80 hours whereas nucleosomal histones did not significantly turn-over regardless of the growth stage. DNA synthesis was drastically diminished with increased cell density whereas histone synthesis was less sensitive to contact-inhibition. The gradual decline of histone H1 content with increased cell density suggests that its degradation is slightly superior to its residual synthesis. When the confluent cells were seeded at low density, cell proliferation resumed and histone H1 was synthesized and deposited to chromatin in a greater amount than nucleosomal histones, thus resulting in an abrupt increase of histone H1 content. The possible role of histone H1 metabolism in normal cells is discussed.

Lack of coupling between DNA and histone synthesis in growth-arrested Friend erythroleukemia cells

Histone synthesis was studied in Friend cells growth-arrested by culturing in isoleucine-deficient medium for 20-24 hours. Such cells are characterized by a very low level of DNA synthesis (5% of the controls). In contrast, the labelling of total nuclear proteins and of total histones continues at an unreduced level for many hours. At the same time there is no accumulation of histones in the cell nucleus, suggesting histone turnover. The behaviour of histone H1 differs from that of the nucleosomal histones, a fact speaking in favour of the existence of independent control mechanisms.

The Role of the poly(A) sequence in mammalian messenger RNA

The poly(A) sequence is added to 3' termini of nuclear RNA segments destined to become part of the mRNA, and may play an essential role in the selection of these segments. It appears to be required for at least some of the splicing events involved in mRNA processing. In the cytoplasm, the poly(A) segment is the target of a degradation process which causes its gradual shortening, and leads to a heterogeneous steady-state poly(A)-size distribution. Complete loss of the poly(A) is probably followed by inactivation of the mRNA, since chains depleted of poly(A) do not accumulate in the cells. A role for this sequence in the promotion of mRNA stability is suggested by the behavior of globin mRNA depleted of poly(A) after injection into frog oocytes. The poly(A) shortening process may be part of the mRNA inactivation mechanism, as indicated by the greater sensitivity to degradation of the poly(A) of some short-lived mRNAs. However, the stochastic mRNA decay implies that new and old mRNA chains, with long and short poly(A) segments, respectively are equally susceptible to inactivation. The poly(A)-lacking histone mRNAs are stable only in cells engaged in DNA replication. Present knowledge favors a role for poly(A) in the control of mRNA stability. Loss of this sequence could be controlled through modulation of poly(A)-protein interactions or through masking of a sequence directly adjacent to the poly(A). In the nucleus, the poly(A) sequence could also serve as stabilizing agent, but, in addition, it might interact with the splicing machinery.

Histone H1o: its location in chromatin

Histone H1o is an H5-like protein found in mammals. Its location in chromatin from animal tissues has been studied by micrococcal nuclease digestion and by quantitation. It was found that H1o occurs in the linker region of chromatin, and replaces H1 there as it does so. As much as a third of the H1 becomes replaced, at least in some tissues. The abundance of H1o was similar in bulk chromatin and in a mononucleosome population which was putatively enriched in transcribed DNA sequences. It was concluded that H1o probably does not suppress transcription.

Histone exchange in chromatin of hydroxyurea-blocked Ehrlich ascites tumour cells

It is well established that DNA and histone synthesis are tightly coupled. Nevertheless, these two processes can be partially uncoupled by drugs specifically inhibiting protein or DNA synthesis, and also during n-butyrate-induced differentiation of Friend cells. The fate of the histones synthesized in the absence of DNA synthesis is unknown; they could be: (1) degraded without joining chromatin; (2) deposited on chromatin as extra histones; or (3) replace original chromatin histones. The only data concerning this problem are a recent report supporting the second possibility. We present evidence here in favour of the third possibility by showing that the histones synthesized in the absence of DNA synthesis enter chromatin and become organized in nucleosomes.