The metabolism of basic proteins in HeLa cell nuclei

Physiological levels of poly(ADP-ribose) during the cell cycle regulate HeLa cell proliferation

Protein targets of polyADP-ribosylation undergo covalent modification with high-molecular-weight, branched poly(ADP-ribose) (PAR) of lengths up to 200 or more ADP-ribose residues derived from NAD⁺. PAR polymerase 1 (PARP1) is the most abundant and well-characterized enzyme involved in PAR biosynthesis. Extensive studies have been carried out to determine how polyADP-ribosylation (PARylation) regulates cell proliferation during cell cycle, with conflicting conclusions. Since significant activation of PARP1 occurs during cell lysis in vitro, we changed the standard method for cell lysis, and using our sensitive ELISA system, quantified without addition of a PAR glycohydrolase inhibitor and clarified that the PAR level is significantly higher in S phase than that in G1. Under normal condition in the absence of exogenous DNA-damaging agent, PAR turns over with a half-life of <40 s; consistent with significant decrease of NAD⁺ levels in S phase, which is rescued by PARP inhibitors, in line with the observed rapid turnover of PAR. PARP inhibitors delayed cell cycle in S phase and decreased cell proliferation. Our results underscore the importance of a suitable assay system to measure rapid PAR chain dynamics in living cells and aid our understanding of the function of PARylation during the cell cycle.

Kinetics of histone and protamine synthesis during meiosis and spermiogenesis in the mouse

The separation of mouse spermatogenic cell nuclei by sedimentation velocity at unit gravity has been used to determine the timing of histone and "mouse protamine" synthesis, and the turnover of basic nuclear proteins throughout spermatogenesis. Animals were injected with 3H-arginine or 3H-lysine and at various time intervals (2 hours post-label or from 1 to 30 days post-label) germinal cell nuclei preparations were separated on the staput. Labelled histones and mouse protamine were extracted from staput separated nuclei with hydrocholoric acid and fractionated by polyacrylamide gel electrophoresis. Results indicate that histones are synthesized in association with DNA replication in spermatogonia and preleptotene spermatocytes, in pachytene primary spermatocytes and in spermatids stages 11-16, simultaneously with "mouse protamine". Experiments are reported showing that histones synthesized in pachytene primary spermatocytes and in spermatids stages 11-16 are retained in epididymal spermatozoa, while histones synthesized before meiosis are no longer detectable onto chromatin after meiosis.

Presence of a bi-directional S phase-specific transcription regulatory element in the promoter shared by testis-specific TH2A and TH2B histone genes

During mammalian spermatogenesis, somatic histones are replaced by testis-specific variants. The synthesis of the variants occurs primarily in the germ cells undergoing meiosis in the absence of DNA replication. We have cloned the genes encoding rat somatic and testis-specific H2A (TH2A) histones. The two genes share 300 bp of 5' upstream region with respective H2B genes: somatic H2A with somatic H2B and testis-specific TH2A with testis-specific TH2B gene. The deduced amino acid sequences show that H2A and TH2A histones have eight amino acid differences in the first half of the molecules and three consecutive changes in the C-terminal region. TH2A gene is expressed only in testis. Although synthesis of TH2A and TH2B histones is independent of DNA replication and insensitive to inhibitors of DNA synthesis in testis, the regulatory region shared by the two genes contain a bi-directional S phase-specific transcription regulatory element. In addition, TH2A gene, like TH2B gene, contains the consensus sequence element in the 3' non-coding region which is involved in the S phase-specific stabilization of histone mRNA.

Modifications in molecular mechanisms associated with control of cell cycle regulated human histone gene expression during differentiation

Histone proteins are preferentially synthesized during the S-phase of the cell cycle, and the temporal and functional coupling of histone gene expression with DNA replication is mediated at both the transcriptional and posttranscriptional levels. The genes are transcribed throughout the cell cycle, and a 3-5-fold enhancement in the rate of transcription occurs during the first 2 h following initiation of DNA synthesis. Control of histone mRNA stability also accounts for some of the 20-100fold increase in cellular histone mRNA levels during S-phase and for the rapid and selective degradation of the mRNAs at the natural completion of DNA replication or when DNA synthesis is inhibited. Two segments of the proximal promoter, designated Sites I and II, influence the specificity and rate of histone gene transcription. Occupancy of Sites I and II during all periods of the cell cycle by three transacting factors (HiNF-A, HiNF-C, and HiNF-D) suggests that these protein-DNA interactions are responsible for the constitutive transcription of histone genes. Binding of HiNF-D in Site II is selectively lost, whereas occupancy of Site I by HiNF-A and -C persists when histone gene transcription is down regulated when cells terminally differentiate. These results are consistent with a primary role for interactions of HiNF-D with a proximal promoter element in rendering cell growth regulated human histone genes transcribable in proliferating cells.

Altered binding of human histone gene transcription factors during the shutdown of proliferation and onset of differentiation in HL-60 cells

Two sites of protein-DNA interaction have been identified in vivo and in vitro in the proximal promoter regions of an H4 and an H3 human histone gene. In proliferating cells, these genes are transcribed throughout the cell cycle, and both the more distal site I and the proximal site II are occupied by promoter-binding factors. In this report we demonstrate that during the shutdown of proliferation and onset of differentiation of the human promyelocytic leukemia cell line HL-60 into cells that exhibit phenotypic properties of monocytes, histone gene expression is down-regulated at the level of transcription. In vivo occupancy of site I by promoter factors persists in the differentiated HL-60 cells, but protein-DNA interactions at site II are selectively lost. Furthermore, in vitro binding activity of the site II promoter factor HiNF-D is lost in differentiated cells, and nuclear extracts from differentiated cells do not support in vitro transcription of these histone genes. Our results suggest that the interaction of HiNF-D with proximal promoter site II sequences plays a primary role in rendering cell growth-regulated histone genes transcribable in proliferating cells. It appears that while cell-cycle control of histone gene expression is mediated by both transcription and mRNA stability, with the shutdown of proliferation and onset mRNA stability, with the shutdown of proliferation and onset of differentiation, histone gene expression is regulated at the transcriptional level.

Intracellular distribution of histone mRNAs in human fibroblasts studied by in situ hybridization

We have used in situ hybridization to study the intracellular distribution of mRNAs for cell cycle-dependent core and H1 histone proteins in human WI-38 fibroblasts. Because histones are abundant nuclear proteins and histone mRNA expression is tightly coupled to DNA synthesis, it was of interest to determine whether histone mRNAs are localized near the nucleus. Cells were hybridized with tritiated DNA probes specific for either histone H1, histone H4, actin, or poly(A)+ mRNA and were processed for autoradiography. In exponentially growing cultures, the fraction of histone mRNA-positive cells correlated well with the fraction of cells in S phase and was eliminated by hydroxyurea inhibition of DNA synthesis. Within individual cells the label for histone mRNA was widely distributed throughout the cytoplasm and did not appear to be more heavily concentrated near the nucleus. However, histone mRNA appeared to exhibit patchy, nonhomogeneous localization, and a quantitative evaluation confirmed that grain distributions were not as uniform as they were after hybridizations to poly(A)+ mRNA. Actin mRNA in WI-38 cells was also widely distributed throughout the cytoplasm but differed from histone mRNA in that label for actin mRNA was frequently most dense at the outermost region of narrow cell extensions. The localization of actin mRNA was less pronounced but qualitatively very similar to that previously described for chicken embryonic myoblasts and fibroblasts. We conclude that localization of histones in WI-38 cells is not facilitated by localization of histone protein synthesis near the nucleus and that there are subtle but discrete and potentially functional differences in the distributions of histone, actin, and poly(A)+ mRNAs.

Identification of an enhancer-like element upstream from a cell cycle dependent human H4 histone gene

We have identified a segment of DNA in the region 6,500 nucleotides upstream from a cell-cycle-dependent human H4 histone gene (pF0108A) which exhibits properties of an enhancer element. This distal element is not required for cap site initiation from the F0108A H4 histone gene. When the enhancer element is present in the genome as a stable integrated sequence, either in its natural upstream location or in a construct where the element is moved just upstream from the proximal promoter sequences, a 25-fold increase in the level of human H4 histone RNAs is observed. This increased level of mRNA reflects an increase in the rate of transcription. The enhancer effect is also observed when the distal element is inserted in inverse orientation with respect to this gene. In addition, the far upstream element can increase expression of a prokaryotic chloramphenicol acetyl transferase (CAT) gene under control of the simian virus 40 (SV40) early promotor, indicating that the ability to influence transcription is not confined to the gene with which it is normally associated. The ability of the histone gene distal enhancer element to function in both mouse and human cells indicates that transacting regulatory factors encoded by either the human or murine genome are capable of mediating the functional properties of this element, further supporting the cross-species compatibility of regulatory sequences and molecules that influence transcription of human histone genes.

Targeting of a chimeric human histone fusion mRNA to membrane-bound polysomes in HeLa cells

The subcellular location of histone mRNA-containing polysomes may play a key role in the posttranscriptional events that mediate histone mRNA turnover following inhibition of DNA synthesis. Previously, it has been shown that histone mRNA is found primarily on free polysomes that are associated with the cytoskeleton. We report here the construction of an Escherichia coli pBR322 beta-lactamase signal peptide-human H3 histone fusion gene. The fusion transcript is targeted to membrane-bound polysomes and remains stable following interruption of DNA replication. Relocating mRNA within the cell may provide a procedure for studying the posttranscriptional regulation of gene expression.

Histone mRNA degradation in vivo: the first detectable step occurs at or near the 3' terminus

The first detectable step in the degradation of human H4 histone mRNA occurs at the 3' terminus in a cell-free mRNA decay system (J. Ross and G. Kobs, J. Mol. Biol. 188:579-593, 1986). Most or all of the remainder of the mRNA is then degraded in a 3'-to-5' direction. The experiments described here were designed to determine whether a similar degradation pathway is followed in whole cells. Two sets of short-lived histone mRNA decay products were detected in logarithmically growing erythroleukemia (K562) cells. These products, designated the -5 and -12 RNAs, were generated by the loss of approximately 4 to 6 and 11 to 13 nucleotides, respectively, from the 3' terminus of histone mRNA. The same decay products were observed after a brief incubation in vitro. They were in low abundance or absent from cells that were not degrading histone mRNA. In contrast, they were readily detectable in cells that degraded the mRNA at an accelerated rate, i.e., in cells cultured with a DNA synthesis inhibitor, either cytosine arabinoside or hydroxyurea. During the initial stages of the decay process, as the 3' terminus of the mRNA was being degraded, the 5'-terminal region remained intact. These results indicate that the first detectable step in human H4 histone mRNA decay occurs at the 3' terminus and that degradation proceeds 3' to 5', both in cells and in cell-free reactions.

Coupling of histone mRNA levels to radioresistant DNA synthesis in ataxia-telangiectasia cells

Cloned genomic DNA for human histone H1, H3 and H4 genes has been used to determine the effects of gamma-radiation on histone mRNA levels and synthesis in ataxia-telangiectasia cells. Synthesis of histone mRNA was determined in cells synchronized with aphidicolin. Effects of irradiation on DNA synthesis and passage through S phase were also monitored. Irradiation was found to slow the passage of control cells through the cell cycle but had no effect on progression of ataxia-telangiectasia cells. H1 and core histone mRNA synthesis was inhibited by radiation in two control cell lines after release from aphidicolin block. No inhibition was observed in one ataxia-telangiectasia cell line and a small degree of inhibition in a second. An increased level of mRNA was observed in both irradiated control and ataxia-telangiectasia cells at 5-7 h post-irradiation compared to unirradiated cells. Similar results were obtained in log phase cells. These results demonstrate that histone mRNA synthesis is radioresistant in ataxia-telangiectasia cells and is coupled to radioresistant DNA synthesis in these cells.

Histone mRNA degradation in vivo: the first detectable step occurs at or near the 3' terminus

The first detectable step in the degradation of human H4 histone mRNA occurs at the 3' terminus in a cell-free mRNA decay system (J. Ross and G. Kobs, J. Mol. Biol. 188:579-593, 1986). Most or all of the remainder of the mRNA is then degraded in a 3'-to-5' direction. The experiments described here were designed to determine whether a similar degradation pathway is followed in whole cells. Two sets of short-lived histone mRNA decay products were detected in logarithmically growing erythroleukemia (K562) cells. These products, designated the -5 and -12 RNAs, were generated by the loss of approximately 4 to 6 and 11 to 13 nucleotides, respectively, from the 3' terminus of histone mRNA. The same decay products were observed after a brief incubation in vitro. They were in low abundance or absent from cells that were not degrading histone mRNA. In contrast, they were readily detectable in cells that degraded the mRNA at an accelerated rate, i.e., in cells cultured with a DNA synthesis inhibitor, either cytosine arabinoside or hydroxyurea. During the initial stages of the decay process, as the 3' terminus of the mRNA was being degraded, the 5'-terminal region remained intact. These results indicate that the first detectable step in human H4 histone mRNA decay occurs at the 3' terminus and that degradation proceeds 3' to 5', both in cells and in cell-free reactions.

Biosynthesis and posttranslational acetylation of histones during spherulation of Physarum polycephalum

Plasmodia of Physarum polycephalum can be induced to differentiate into dormant spherules: DNA-, RNA- and protein-synthesis cease during this process. Analysis of the histone H4 acetylation during spherulation revealed no significant changes of the relative acetate content and percentage of acetylated H4 subspecies. This result does not support a close correlation of histone acetylation and transcriptional activity. Posttranslational incorporation of 3H-acetate into core histones decreased rapidly after start of spherulation. However, acetate incorporation increased significantly at a late stage of spherulation (30 h). To elucidate the role of this elevated acetate incorporation we followed histone synthesis during spherulation. Histone synthesis decreased upon induction of differentiation and stopped after 12 h. After 38 h of spherulation histone synthesis again occurred in the absence of DNA synthesis. The peak of acetate incorporation into core histones clearly preceded this late histone synthesis, indicating acetylation of preexisting histones. We suggest, that this acetate incorporation is part of the mechanism, by which preexisting histones are replaced by newly synthesized histones. Pulse treatment with actinomycin D or cycloheximide during spherulation suggested, that the observed histone synthesis is essential for the germination of spherules. Obviously, new histones have to be synthesized for the coordinate course of the differentiation program.

Involvement of the 5'-leader sequence in coupling the stability of a human H3 histone mRNA with DNA replication

Two lines of evidence derived from fusion gene constructs indicate that sequences residing in the 5'-nontranslated region of a cell cycle-dependent human H3 histone mRNA are involved in the selective destabilization that occurs when DNA synthesis is terminated. The experimental approach was to construct chimeric genes in which fragments of the mRNA coding regions of the H3 histone gene were fused with fragments of genes not expressed in a cell cycle-dependent manner. After transfection in HeLa S3 cells with the recombinant plasmids, levels of fusion mRNAs were determined by S1 nuclease analysis prior to and following DNA synthesis inhibition. When the first 20 nucleotides of an H3 histone mRNA leader were replaced with 89 nucleotides of the leader from a Drosophila heat-shock (hsp70) mRNA, the fusion transcript remained stable during inhibition of DNA synthesis, in contrast to the rapid destabilization of the endogenous histone mRNA in these cells. In a reciprocal experiment, a histone-globin fusion gene was constructed that produced a transcript with the initial 20 nucleotides of the H3 histone mRNA substituted for the human beta-globin mRNA leader. In HeLa cells treated with inhibitors of DNA synthesis and/or protein synthesis, cellular levels of this histone-globin fusion mRNA appeared to be regulated in a manner similar to endogenous histone mRNA levels. These results suggest that the first 20 nucleotides of the leader are sufficient to couple histone mRNA stability with DNA replication.

Subcellular localization of histone messenger RNAs on cytoskeleton-associated free polysomes in HeLa S3 cells

We have examined the subcellular distribution of histone mRNA-containing polysomes in HeLa S3 cells to assess the possible relationship between localization of histone mRNAs and the regulation of cellular histone mRNA levels. The distribution of histone mRNAs on free and membrane bound polysomes was examined as well as the association of histone mRNA-containing polysomes with the cytoskeleton. The subcellular localization of histone mRNAs was compared with that of HLA-B7 mRNAs which encode a cell surface antigen. Histone mRNAs were localized predominantly on the free polysomes, whereas the HLA-B7 mRNA was found almost exclusively on membrane bound polysomes. However, both species of mRNA were found associated with the cytoskeleton. Interruption of DNA synthesis by hydroxyurea treatment resulted in a rapid and selective destabilization of histone mRNAs in each subcellular fraction; in contrast, the stability of HLA-B7 mRNA appeared unaffected. The results presented confirm that histone mRNAs are predominantly located on non-membrane bound polysomes and suggest that these polysomes are associated with the cytoskeletal framework.

Replacement variant histone genes contain intervening sequences

The nucleotide sequences of two chicken histone genes encoding replacement variant H3.3 polypeptides are described. Unlike the replication variant genes of chickens (and almost all other organisms), these genes contain intervening sequences; introns are present in both genes in the 5' noncoding and coding sequences. Furthermore, the replacement variant histone mRNAs are post-transcriptionally polyadenylated. The locations, but not the sizes, of the two introns within the coding segments of the two genes have been exactly conserved, whereas the intron positions in their respective 5' flanking regions differ. Although both H3.3 genes predict the identical histone polypeptide sequence, they are as different from one another as each of them is from a more common replication variant H3.2 gene in silent base substitutions within the coding sequences. Thus, the H3.3 polypeptide sequence has been precisely maintained over a great evolutionary period, suggesting that this class of histones performs a strongly selected biological function. Although replacement variant histones can account for more than 50% of the total H3 protein in the nuclei of specific chicken tissues, the steady-state level of H3.3 mRNA is nearly the same (and is quite low) in all tissues and ages of animals examined. These properties suggest novel mechanisms for the control of the basal histone biosynthesis which takes place outside of the S phase of the cell cycle.

Faithful cell-cycle regulation of a recombinant mouse histone H4 gene is controlled by sequences in the 3'-terminal part of the gene

We have analyzed the expression of endogenous histone H4 genes and of a newly introduced H4 gene in 21-Tb cells, a mouse mastocytoma cell-cycle mutant. Endogenous H4 mRNAs were less abundant by a factor of 120-180 in G1-arrested than in exponentially multiplying cells. However, H4 transcription rates were only decreased by a factor of 3 under these conditions, as determined by in vitro elongation of nascent transcripts. This indicates that post-transcriptional control of histone mRNA levels is important, in accord with published data. We introduced a mouse H4 gene, modified by a 12-base-pair (bp) insertion in its coding sequence, into 21-Tb cells by DNA-mediated gene transfer. The levels of transcripts from this gene were regulated in parallel with those of the endogenous genes. Moreover, fusion of the simian virus 40 (SV40) early promoter to a 463-bp fragment containing the 3'-terminal half of the mouse H4 gene, including 230 bp of spacer sequences, led to the regulated expression of SV40/H4 fusion RNA. However, a small proportion of SV40-initiated transcripts were not processed to histone-specific 3' ends, but extended farther through the downstream Escherichia coli galactokinase gene to a SV40 polyadenylylation site. In contrast to the short SV40/H4 RNA, the levels of these longer transcripts were not reduced in G1-arrested cells. These results show that sequences in the 3'-terminal part of the H4 gene can regulate gene expression in the cell cycle, presumably at the post-transcriptional level, as long as they are not positioned much more distant from the terminus than normal.

Replacement variant histone genes contain intervening sequences

The nucleotide sequences of two chicken histone genes encoding replacement variant H3.3 polypeptides are described. Unlike the replication variant genes of chickens (and almost all other organisms), these genes contain intervening sequences; introns are present in both genes in the 5' noncoding and coding sequences. Furthermore, the replacement variant histone mRNAs are post-transcriptionally polyadenylated. The locations, but not the sizes, of the two introns within the coding segments of the two genes have been exactly conserved, whereas the intron positions in their respective 5' flanking regions differ. Although both H3.3 genes predict the identical histone polypeptide sequence, they are as different from one another as each of them is from a more common replication variant H3.2 gene in silent base substitutions within the coding sequences. Thus, the H3.3 polypeptide sequence has been precisely maintained over a great evolutionary period, suggesting that this class of histones performs a strongly selected biological function. Although replacement variant histones can account for more than 50% of the total H3 protein in the nuclei of specific chicken tissues, the steady-state level of H3.3 mRNA is nearly the same (and is quite low) in all tissues and ages of animals examined. These properties suggest novel mechanisms for the control of the basal histone biosynthesis which takes place outside of the S phase of the cell cycle.

Immunochemical measurement of histone H3 in non-nucleosomal compartments of cultured mammalian cells

We measured histone H3 in the non-nucleosomal compartment of cultured mammalian cells by enzyme-linked immunoelectrotransfer blot assay of cytosolic proteins using affinity-purified rabbit anti-H3 IgG, and peroxidase-linked second antibodies. The cytosolic H3 level was estimated to be 0.5-1.0% of the nucleosomal H3 content in MH-134SC cells (mean generation time 11 h) and 3-4% in HeLa cells (mean generation time 22 h). It showed characteristic changes under the inhibitions of DNA and/or protein synthesis and during the cell cycle of HeLa cells. These indicate an inverse relationship between the cytosolic H3 level and the replicating activity of nuclear DNA. The possible implication of the non-nucleosomal histones in the regulation of histone gene expression is discussed.

Effect of adenovirus infection on expression of human histone genes

The influence of adenovirus type 2 infection of HeLa cells upon expression of human histone genes was examined as a function of the period of infection. Histone RNA synthesis was assayed after run-off transcription in nuclei isolated from mock-infected cells and after various periods of adenovirus infection. Histone protein synthesis was measured by [3H]leucine labeling of intact cells and fluorography of electrophoretically fractionated nuclear and cytoplasmic proteins. The cellular representation of RNA species complementary to more than 13 different human histone genes was determined by RNA blot analysis of total cellular, nuclear or cytoplasmic RNA by using a series of 32P-labeled cloned human histone genes as hybridization probes and also by analysis of 3H-labeled histone mRNA species synthesized in intact cells. By 18 h after infection, HeLa cell DNA synthesis and all parameters of histone gene expression, including transcription and the nuclear and cytoplasmic concentrations of core and H1 mRNA species, were reduced to less than 5 to 10% of the control values. By contrast, transcription and processing of other cellular mRNA sequences have been shown to continue throughout this period of infection. The early period of adenovirus infection was marked by an inhibition of transcription of histone genes that accompanied the reduction in rate of HeLa cell DNA synthesis. These results suggest that the adenovirus-induced inhibition of histone gene expression is mediated in part at the transcriptional level. However, the persistence of histone mRNA species at concentrations comparable to those of mock-infected control cells during the early phase of the infection, despite a reduction in histone gene transcription and histone protein synthesis, implies that histone gene expression is also regulated post-transcriptionally in adenovirus-infected cells. These results suggest that the tight coupling between histone mRNA concentrations and the rate of cellular DNA synthesis, observed when DNA replication is inhibited by a variety of drugs, is not maintained after adenovirus infection.

Differential stability of host mRNAs in Friend erythroleukemia cells infected with herpes simplex virus type 1

The consequences of herpes simplex virus type 1 infection on cellular macromolecules were investigated in Friend erythroleukemia cells. The patterns of protein synthesis, examined by polyacrylamide gel electrophoresis, demonstrated that by 4 h postinfection the synthesis of many host proteins, with the exception of histones, was inhibited. Examination of the steady-state level of histone H3 mRNA by molecular hybridization of total RNA to a cloned mouse histone H3 complementary DNA probe demonstrated that the ratio of histone H3 mRNA to total RNA remained unchanged for the first 4 h postinfection. In contrast, the steady-state levels of globin and actin mRNAs decreased progressively at early intervals postinfection. Studies on RNA synthesis in isolated nuclei demonstrated that the transcription of the histone H3 gene was inhibited to approximately the same extent as that of actin gene. We concluded that the stabilization of preexisting histone H3 mRNA was responsible for the persistence of H3 mRNA and histone protein synthesis in herpes simplex virus type 1-infected Friend erythroleukemia cells. The possible mechanisms influencing the differential stability of host mRNAs during the course of productive infection with herpes simplex virus type 1 are discussed.

Is human histone gene expression autogenously regulated?

It has been well documented that core and H1 histone mRNAs accumulate in a manner which closely parallels the initiation of DNA synthesis and histone protein synthesis, suggesting that the onset of histone gene expression early during S phase is at least in part transcriptionally mediated. In fact, it appears that throughout S phase the synthesis of histone proteins is modulated by the availability of histone mRNAs. On the other hand, the stability of histone mRNAs and the destabilization of histone mRNAs when DNA replication is completed or inhibited are highly selective, tightly coupled and largely post-transcriptionally controlled. We present a model to account for histone mRNA turnover whereby the natural or inhibitor-induced termination of DNA replication results in an immediate loss of high affinity binding sites for newly synthesized histone proteins which in turn brings about a transient accumulation of unbound histones. These unbound histones could modify the histone translation complex, via interactions with polysomal histone mRNAs, in such a manner as to render histone mRNAs accessible to cellular ribonucleases. This type of mechanism would be operative solely at the post-transcriptional level and would be compatible with the rapid, RNA synthesis-independent destabilization of histone mRNAs which occurs following inhibition of DNA replication, as well as with the requirement for protein synthesis for histone mRNA destabilization to be initiated.

Effect of adenovirus infection on expression of human histone genes

The influence of adenovirus type 2 infection of HeLa cells upon expression of human histone genes was examined as a function of the period of infection. Histone RNA synthesis was assayed after run-off transcription in nuclei isolated from mock-infected cells and after various periods of adenovirus infection. Histone protein synthesis was measured by [3H]leucine labeling of intact cells and fluorography of electrophoretically fractionated nuclear and cytoplasmic proteins. The cellular representation of RNA species complementary to more than 13 different human histone genes was determined by RNA blot analysis of total cellular, nuclear or cytoplasmic RNA by using a series of 32P-labeled cloned human histone genes as hybridization probes and also by analysis of 3H-labeled histone mRNA species synthesized in intact cells. By 18 h after infection, HeLa cell DNA synthesis and all parameters of histone gene expression, including transcription and the nuclear and cytoplasmic concentrations of core and H1 mRNA species, were reduced to less than 5 to 10% of the control values. By contrast, transcription and processing of other cellular mRNA sequences have been shown to continue throughout this period of infection. The early period of adenovirus infection was marked by an inhibition of transcription of histone genes that accompanied the reduction in rate of HeLa cell DNA synthesis. These results suggest that the adenovirus-induced inhibition of histone gene expression is mediated in part at the transcriptional level. However, the persistence of histone mRNA species at concentrations comparable to those of mock-infected control cells during the early phase of the infection, despite a reduction in histone gene transcription and histone protein synthesis, implies that histone gene expression is also regulated post-transcriptionally in adenovirus-infected cells. These results suggest that the tight coupling between histone mRNA concentrations and the rate of cellular DNA synthesis, observed when DNA replication is inhibited by a variety of drugs, is not maintained after adenovirus infection.

Clustering of human H1 and core histone genes

An H1 histone gene was isolated from a 15-kilobase human DNA genomic sequence. The presence of H2A, H2B, H3, and H4 genes in this same 15-kilobase fragment indicates that mammalian core and H1 histone genes are clustered.

Evidence for a human histone gene cluster containing H2B and H2A pseudogenes

Not all members of the human histone gene family are functional. We have isolated a human H2B pseudogene that contains alterations in the protein-coding sequences as well as in the 3' and 5' flanking sequences that preclude expression of a functional H2B histone protein. There are three modifications in the amino acid-coding region: a single-base deletion producing a frame shift, a single-base substitution resulting in a codon change from serine to tryptophan (an amino acid not present in histones), and the absence of a stop codon. Analysis of nucleotide sequences upstream from the AUG start signal indicates the absence of a "TATA" box and other putative consensus regulatory sequences. In the 3' flanking region, a highly conserved block of 22 nucleotides that exhibits hyphenated dyad symmetry is displaced downstream. Within the same genomic segment, the adjacent H2A histone gene is missing 12 nucleotides, resulting in a deletion of four amino acids in a highly conserved region of the protein.

Requirement of protein synthesis for the coupling of histone mRNA levels and DNA replication

H1 and core histone mRNA levels have been examined in the presence of protein synthesis inhibitors with different mechanisms of action. Total HeLa cell RNAs were analyzed by Northern Blot hybridization using cloned human histone genes as probes. Inhibition of DNA replication resulted in a rapid decline in histone mRNA levels. However, in the presence of cycloheximide or puromycin, H1 and core mRNAs did not decrease in parallel with DNA synthesis, but were stabilized and accumulated. Inhibition of DNA synthesis with hydroxyurea after the inhibition of protein synthesis did not lead to a decline in histone mRNA levels. These results suggest that synthesis of a protein(s)--perhaps a histone protein(s)--is required for the coordination of DNA synthesis and histone mRNA levels.

Histone gene expression in human diploid fibroblasts: analysis of histone mRNA levels using cloned human histone genes

The cellular abundance of H2A, H2B, H3 and H4 histone mRNA sequences was determined prior to and at various times after stimulation of non-dividing human diploid fibroblasts to proliferate. The representation of histone mRNAs was quantitated by electrophoretic fractionation of total cellular RNAs, diffusion transfer to nitrocellulose and hybridization with a series of cloned genomic human histone sequences. The levels of mRNAs for the four core histones were observed to be temporally and quantitatively coupled with both DNA replication and histone protein synthesis. Therefore, a contribution to the regulation of histone gene expression at a transcriptional level is suggested.

Cell cycle regulation of human histone H1 mRNA

A cloned genomic DNA fragment containing a human histone H1 gene has been used to analyze histone H1 gene expression in two human cell lines (HeLa S3 and WI-38). The cellular abundance of histone H1 mRNA was compared with that of core (H2A, H2B, H3, and H4) histone mRNAs as a function of the cell cycle: core and H1 histone mRNA levels are related both to each other and to the apparent rate of DNA synthesis and are rapidly destabilized after DNA synthesis inhibition. The use of three synchronization protocols, and of transformed and normal diploid cells in culture, suggests that the detected core and H1 histone mRNA levels are regulated by similar mechanisms in continuously dividing human cell lines and nondividing cells stimulated to proliferate.

Influence of DNA synthesis inhibition on the coordinate expression of core human histone genes during S phase

Core histone mRNA metabolism has been examined in S phase HeLa cells recovering from DNA synthesis inhibition by 1 mM hydroxyurea. Using cloned human histone genes as probes for histone mRNA quantitation, the response to and recovery from DNA synthesis inhibition is shown to depend on the position of the cell with respect to the initiation of DNA replication. The incorporation of 3H-uridine into multiple histone mRNAs in recovering cells does not exceed preinhibition levels, and as this incorporation is maximal in early S phase, the synthesis of core histone mRNA is apparently related to the ordered replication of the genome. The total histone mRNA present in interrupted S phase cells after recovery is not significantly different from that present in control cells, and a temporal and functional coupling between histone mRNA levels and the relative rate of DNA synthesis is maintained in perturbed cells.

Coordinate regulation of multiple histone mRNAs during the cell cycle in HeLa cells

Core histone gene expression in HeLa S3 cells has been examined as a function of the cell cycle using cloned human histone gene probes. Total cellular histone mRNAs were analyzed by Northern blot analysis, and their relative abundance shown to be temporally coupled to DNA synthesis rates in S phase. The in vivo incorporation of 3H-uridine into at least fifteen heterologous histone mRNAs (in one hour pulse intervals at various times in the cell cycle), was monitored by hybrid selection. Hybridized RNAs were eluted and resolved electrophoretically to give both a quantitative and qualitative assay for multiple mRNA species. Maximal incorporation of 3H-uridine into histone mRNAs precedes their maximal accumulation, indicating that transcriptional regulation is predominant in early S phase. The turnover of histone mRNAs in late S occurs in the presence of a reduced apparent transcription rate, indicating that post-transcriptional regulation is predominant in late S. All the detected multiple histone mRNAs are coordinately regulated during the HeLa cell cycle.

Cell cycle stage-specific accumulation of mRNAs encoding tubulin and other polypeptides in Chlamydomonas

The accumulation pattern of a number of mRNAs during the cell cycle of Chlamydomonas was examined by two-dimensional gel analysis of in vitro translation products and by RNA blot hybridization analysis. Two-dimensional gel analysis revealed that 10-15% of the 300 most abundant translation products are differentially synthesized from RNA obtained at various cell cycle stages. RNAs that direct the synthesis of alpha- and beta-tubulins and that hybridize to cloned alpha- and beta-tubulin probes accumulate coordinately during the predivision period of the cell cycle, reaching peak levels before or during division. Other RNAs represented by selected cloned cDNA probes show a number of different cell cycle patterns of accumulation. The accumulation patterns of these RNAs are not directly influenced by ongoing illumination conditions, even though alternating light-dark illumination cycles are used to synchronize Chlamydomonas cells. The results suggest that there may be a complex program of gene expression correlated with cell cycle progression in Chlamydomonas.

Organization of human histone genes

We describe the isolation and initial characterization of seven independent lambda Charon 4A recombinant phages which contain human histone genomic sequences (designated lambda HHG). Restriction maps of these clones and localization of the genes coding for histones H2A, H2B, H3, and H4 are presented. The presence of histone encoding regions in the lambda HHG clones was demonstrated by several independent criteria including hybridization with specific DNA probes, hybrid selection/in vitro translation, and hybridization of lambda HHG DNAs to reserve Southern blots containing cytoplasmic RNAs from G1-, S-, and arabinofuranosylcytosine (cytosine arabinoside)-treated S-phase cells. In addition, the lambda HHG DNAs were shown to protect in vivo labeled H4 mRNAs from S1 nuclease digestion. Based on the analysis of the lambda HHG clones, human histone genes appear to be clustered in the genome. However, gene clusters do not seem to be present in identical tandem repeats. The lambda HHG clones described in this report fall into at least three distinct types of arrangement. One of these arrangements contains two coding regions for each of the histones H3 and H4. The arrangement of histone genes in the human genome, therefore, appears to be different from that in the sea urchin and Drosophila genomes in which each of the five histone-encoding regions (H1, H2A, H2B, H3, and H4) is present only once in each tandemly repeated cluster. At least one clone, lambda HHG 41, contains, in addition to the histone genes, a region that hybridizes with a cytoplasmic RNA approximately 330 nucleotides in length. This RNA is not similar in size to known histone-encoding RNAs and is present in the cytoplasm of HeLa cells predominantly in the G1 phase of the cell cycle.

Histone proteins in HeLa S3 cells are synthesized in a cell cycle stage specific manner

The synthesis of histone proteins in G1 and S phase HeLa S3 cells was examined by two-dimensional electrophoretic fractionation of nuclear and total cellular proteins. Newly synthesized histones were detected only in S phase cells. Histone messenger RNA sequences, as detected by hybridization with cloned human histone genes, were present in the cytoplasm of S phase but not G1 cells.

Analysis of histone gene expression during the cell cycle in HeLa cells by using cloned human histone genes

Although it is generally agreed that histone protein synthesis is restricted to the S phase of the cell cycle--and therefore parallels DNA replication--both transcriptional and posttranscriptional levels of control have been invoked. Using blot hybridization with several cloned genomic human histone sequences representing different histone gene clusters as probes, we have assessed the steady-state level of histone RNAs in the nucleus and cytoplasm of G1 and S phase HeLa S3 cells. The representation of histone mRNA sequences of G1 compared with S phase cells was less than 1% in the cytoplasm and approximately 1% in the nucleus. These data are consistent with transcriptional control, but we cannot completely dismiss the possibility that regulation of histone gene expression is, to some extent, mediated posttranscriptionally. If histone gene transcription does occur in G1, the RNAs must either be rapidly degraded or be transcribed to a limited extent compared with S phase. An unexpected result was obtained when a blot of cytoplasmic RNA from G1 and S phase cells was hybridized with lambda HHG 41 DNA (containing H3 and H4 human genomic histone sequences). Although hybridization with histone mRNAs was observed for RNAs from S phase but not from G1 cells, hybridization with a nonhistone RNA of approximately 330 nucleotides present predominantly in G1 was also observed.

Coupling of histone and DNA synthesis in the somatic cell cycle

The coupling of histone and DNA synthesis was examined in the temperature-sensitive hamster fibroblast cell line K12. By monitoring total cellular histone synthesis at various times after quiescent cells were stimulated to proliferate at permissive and nonpermissive temperatures, a direct correlation was found between the rates of DNA and histone synthesis. Furthermore, when DNA synthesis was blocked by the K12 mutation, histone synthesis was reduced to the basal rate.

Regulation of specific genes during the cell cycle. Utilization of homologous cDNAs and cloned sequences for studying histone gene expression in human cells

Evidence for differential gene expression during the cell cycle and approaches for studying cell-cycle-stage specific gene expression are summarized. Attention is focused on regulation of histone gene expression during the cell cycle of continuously dividing cells and after stimulation of nondividing cells to proliferate. The level(s) at which control of histone gene expression occurs and the possible involvement of chromosomal proteins in the regulation of histone gene expression are discussed. The preparation of cloned human histone sequences and their use in studying the structural and functional properties of human histone genes are presented. Index Entries: Cell cycle, gene regulation during; gene regulation, during the cell cycle; regulation of specific genes, during the cell cycle; DNAs, homologous, and histone gene expression; cloned DNAs, and histone gene expression; histone gene expression; gene expression, histone; cloned human histone sequences.

A genetic aspect of chromatin proteins of human brain tumors

Electrophoretic analysis of chromatin proteins was performed on rat and human tissues. Species and organ specific patterns were demonstrated in them. Twenty cases of human brain tumours were also analyzed and each tumor had typical phoretic patterns of chromatin. Proteins obtained from histologically similar tumors display similar electrophoretic patterns. As to the ratio of chromatin protein to DNA, no apparent differences between benign and malignant human brain tumors were observed.

Reassessment of histone gene expression during cell cycle in human cells by using homologous H4 histone cDNA

The representation of H4 histone mRNA sequences in RNAs isolated from G1 and S phase HeLa cells was assessed by use of a homologous H4 histone cDNA. S phase cells were obtained by double thymidine block, and G1 cells were obtained by double thymidine block or mitotic selective detachment. Nuclear and cytoplasmic RNAs from S phase cells hybridized with H4 histone cDNA as did nuclear and cytoplasmic RNAs from G1 cells synchronized by double thymidine block. In contrast, significant levels of hybridization were not observed between H4 histone cDNA and nuclear, polysomal, or postpolysomal cytoplasmic RNAs of G1 cells synchronized by mitotic selective detachment. Double thymidine block yields a G1 cell population containing 20-25% S phase cells whereas the G1 population obtained by mitotic detachment contains less than 0.1% S phase cells. The ability of H4 histone cDNA to hybridize with the RNAs from G1 cells obtained after release from double thymidine block can therefore be explained by the presence of S phase cells in such a G1 population--an artifact of the synchronization procedure. We interpret these results to be consistent with the presence of H4 histone mRNA sequences during the S but not G1 phase of the cell cycle in continuously dividing HeLa S3 cells.

Effect of inhibition of DNA synthesis on histone synthesis and deposition

We have reinvestigated the degree of coupling between DNA and histone synthesis in mammalian cells. In at least one cell line (HTC cells), the coupling is not nearly as tight as had previously been inferred from experiments with HeLa cells. The site of deposition of such histones which continue to be made in the presence of sufficient hydroxyurea to depress DNA synthesis almost totally has been studied. Deposition seems to be on material which absorbs at 260 nm. This material is not a part of the bulk chromatin and binds histone in a relatively tight manner. The possible role of such a material in histone synthesis and deposition is discussed.

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells

Nuclei were isolated from synchronized HeLa S3 cells and transcribed utilizing their endogenous RNA polymerases. Our data suggest that S phase nuclei are capable of synthesizing histone mRNA sequences while nuclei from G1 phase cells are not. Transcription of histone mRNA sequences by S phase nuclei can be abolished completely by low levels of alpha-amanitin (1.0 microgram/ml, a concentration which completely inhibits RNA polymerase II). From these results it appears that transcription of the histone mRNA sequences occurs during the S phase but not during the G1 phase of the cell cycle and that RNA polymerase II is responsible for histone gene readout.

Control of DNA synthesis in tissue culture cells

Eukaryotic DNA is functionally divided into thousands of replicons, each of which may be duplicated at a characteristic time within the DNA synthetic (S) period. Our approach toward an understanding of the molecular mechanisms which control orderly eukaryotic DNA synthesis has been: (a) to devise a method of cell synchrony in a suitable tissue culture system wherein all cells in the population enter and traverse the S period with a high degree of synchrony; (b) to determine, utilizing this system, precisely when during the S period critical events and macromolecular syntheses occur; and (c) to examine, by polyacrylamide-gel electrophoresis, the spectrum of proteins which become associated with chromatin during the S period in such a way as to suggest their involvement with DNA synthesis. Possible mechanisms for control are discussed based on the results presented here.

Activation of histone gene transcription by nonhistone chromosomal proteins in WI-38 human diploid fibroblasts

The regulation of histone gene expression was examined after confluent, nondividing WI-38 human diploid fibroblasts were stimulated to proliferate. Histone mRNA sequences were assayed by hybrid formation with an 3H-labeled single-stranded DNA complementary to histone mRNAs. Histone mRNA became associated with polyribosomes concomitant with the activation of DNA synthesis. The ability of chromatin from WI-38 cells to serve as a template for in vitro transcription of histone mRNA sequences parallels the onset of DNA replication. A role for nonhistone chromosomal proteins in the control of histone gene readout is suggested because, when chromatin from confluent WI-38 cells was dissociated and then reconstituted in the presence of S phase nonhistone chromosomal proteins, a 500-fold activation of histone mRNA sequence transcription was observed.