Further evidence of transcriptional and translational control of histone messenger RNA during the HeLa S3 cycle

The expanding role of WEE1

Upon DNA damage, complex transduction cascades are unleashed to locate, recognise and repair affected lesions. The process triggers a pause in the cell cycle until the damage is resolved. Even under physiologic conditions, this deliberate interruption of cell division is essential to ensure orderly DNA replication and chromosomal segregation. WEE1 is an established regulatory protein in this vast fidelity-monitoring machinery. Its involvement in the DNA damage response and cell cycle has been a subject of study for decades. Emerging studies have also implicated WEE1 directly and indirectly in other cellular functions, including chromatin remodelling and immune response. The expanding role of WEE1 in pathophysiology is matched by the keen surge of interest in developing WEE1-targeted therapeutic agents. This review summarises WEE1 involvement in the cell cycle checkpoints, epigenetic modification and immune signalling, as well as the current state of WEE1 inhibitors in cancer therapeutics.

How does chromatin package DNA within nucleus and regulate gene expression?

The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?

Isolation and analysis of linker histones across cellular compartments

Analysis of histones, especially histone H1, is severely limited by immunological reagent availability. This paper describes the application of cellular fractionation with LC-MS for profiling histones in the cytosol and upon chromatin. First, we show that linker histones enriched by cellular fractionation gives less nuclear contamination and higher histone content than when prepared by nuclei isolation. Second, we profiled the soluble linker histones throughout the cell cycle revealing phosphorylation increases as cells reach mitosis. Finally, we monitored histone H1.2-H1.5 translocation to the cytosol in response to the CDK inhibitor flavopiridol in primary CLL cells treated ex vivo. Data shows that all H1 variants translocate in response to drug treatment with no specific order to their cytosolic appearance. The results illustrate the utility of cellular fractionation in conjunction with LC-MS for the analysis of histone H1 throughout the cell.

BIOLOGICAL SIGNIFICANCE

This paper demonstrates the first time application of cellular fractionation to characterize cytosolic histone H1 by liquid chromatography mass spectrometry (LC-MS). Using the Ramos Burkitt's lymphoma cell line, cellular fractionation was shown to give less nuclear contamination and higher histone content than preparations by nuclei isolation. Further application of the cellular fractionation approach was shown by using primary chronic lymphocytic leukemia (CLL) cells to monitor the movement of histone H1 across cellular compartments in response to the cyclin dependent kinase inhibitor flavopiridol. Collectively, these data establish a mass spectrometric method for exploration into the function of cytosolic histone H1.

CENP-A: the key player behind centromere identity, propagation, and kinetochore assembly

Chromosome segregation is the one of the great problems in biology with complexities spanning from biophysics and polymer dynamics to epigenetics. Here, we summarize the current knowledge and highlight gaps in understanding of the mechanisms controlling epigenetic regulation of chromosome segregation.

H2B Tyr37 phosphorylation suppresses expression of replication-dependent core histone genes

Histone gene transcription is actively downregulated after completion of DNA synthesis to avoid overproduction. However, the precise mechanistic details of the cessation of histone mRNA synthesis are not clear. We found that histone H2B phosphorylation at Tyr37 occurs upstream of histone cluster 1, Hist1, during the late S phase. We identified WEE1 as the kinase that phosphorylates H2B at Tyr37. Loss of expression or inhibition of WEE1 kinase abrogated H2B Tyr37 phosphorylation with a concomitant increase in histone transcription in yeast and mammalian cells. H2B Tyr37 phosphorylation excluded binding of the transcriptional coactivator NPAT and RNA polymerase II and recruited the histone chaperone HIRA upstream of the Hist1 cluster. Taken together, our data show a previously unknown and evolutionarily conserved function for WEE1 kinase as an epigenetic modulator that marks chromatin with H2B Tyr37 phosphorylation, thereby inhibiting the transcription of multiple histone genes to lower the burden on the histone mRNA turnover machinery.

Histone dosage regulates DNA damage sensitivity in a checkpoint-independent manner by the homologous recombination pathway

In eukaryotes, multiple genes encode histone proteins that package genomic deoxyribonucleic acid (DNA) and regulate its accessibility. Because of their positive charge, ‘free’ (non-chromatin associated) histones can bind non-specifically to the negatively charged DNA and affect its metabolism, including DNA repair. We have investigated the effect of altering histone dosage on DNA repair in budding yeast. An increase in histone gene dosage resulted in enhanced DNA damage sensitivity, whereas deletion of a H3–H4 gene pair resulted in reduced levels of free H3 and H4 concomitant with resistance to DNA damaging agents, even in mutants defective in the DNA damage checkpoint. Studies involving the repair of a HO endonuclease-mediated DNA double-strand break (DSB) at the MAT locus show enhanced repair efficiency by the homologous recombination (HR) pathway on a reduction in histone dosage. Cells with reduced histone dosage experience greater histone loss around a DSB, whereas the recruitment of HR factors is concomitantly enhanced. Further, free histones compete with the HR machinery for binding to DNA and associate with certain HR factors, potentially interfering with HR-mediated repair. Our findings may have important implications for DNA repair, genomic stability, carcinogenesis and aging in human cells that have dozens of histone genes.

Commitment to a cellular transition precedes genome-wide transcriptional change

In budding yeast, commitment to cell division corresponds to activating the positive feedback loop of G1 cyclins controlled by the transcription factors SBF and MBF. This pair of transcription factors has over 200 targets, implying that cell-cycle commitment coincides with genome-wide changes in transcription. Here, we find that genes within this regulon have a well-defined distribution of transcriptional activation times. Combinatorial use of SBF and MBF results in a logical OR function for gene expression and partially explains activation timing. Activation of G1 cyclin expression precedes the activation of the bulk of the G1/S regulon, ensuring that commitment to cell division occurs before large-scale changes in transcription. Furthermore, we find similar positive feedback-first regulation in the yeasts S. bayanus and S. cerevisiae, as well as human cells. The widespread use of the feedback-first motif in eukaryotic cell-cycle control, implemented by nonorthologous proteins, suggests its frequent deployment at cellular transitions.

Excess histone levels mediate cytotoxicity via multiple mechanisms

The accumulation of excess histone proteins in cells has deleterious consequences such as genomic instability in the form of excessive chromosome loss, enhanced sensitivity to DNA damaging agents and cytotoxicity. Hence, the synthesis of histone proteins is tightly regulated at multiple steps and transcriptional as well as posttranscriptional regulation of histone proteins is well established. Additionally, we have recently demonstrated that histone protein levels are regulated posttranslationally by the DNA damage checkpoint kinase Rad53 and ubiquitin-proteasome dependent proteolysis in the budding yeast. However, the underlying mechanism/s via which excess histones exert their deleterious effects in vivo are not clear. Here we have investigated the mechanistic basis for the deleterious effects of excess histones in budding yeast. We find that the presence of excess histones saturates certain histone modifying enzymes, potentially interfering with their activities. Additionally, excess histones appear to bind non-specifically to DNA as well as RNA, which can adversely affect their metabolism. Microarray analysis revealed that upon overexpression of histone gene pairs, about 240 genes were either up or downregulated by 2-fold or more. Overall, we present evidence that excess histones are likely to mediate their cytotoxic effects via multiple mechanisms that are primarily dependent on inappropriate electrostatic interactions between the positively charged histones and diverse negatively charged molecules in the cell. Our findings help explain the basis for the existence of multiple distinct mechanisms that contribute to the tight control of histone protein levels in cells and highlight their importance in maintaining genomic stability and cell viability.

Developmental and cell cycle regulation of the Drosophila histone locus body

Cyclin E/Cdk2 is necessary for replication-dependent histone mRNA biosynthesis, but how it controls this process in early development is unknown. We show that in Drosophila embryos the MPM-2 monoclonal antibody, raised against a phosphoepitope from human mitotic cells, detects Cyclin E/Cdk2-dependent nuclear foci that colocalize with nascent histone transcripts. These foci are coincident with the histone locus body (HLB), a Cajal body-like nuclear structure associated with the histone locus and enriched in histone pre-mRNA processing factors such as Lsm11, a core component of the U7 small nuclear ribonucleoprotein. Using MPM-2 and anti-Lsm11 antibodies, we demonstrate that the HLB is absent in the early embryo and occurs when zygotic histone transcription begins during nuclear cycle 11. Whereas the HLB is found in all cells after its formation, MPM-2 labels the HLB only in cells with active Cyclin E/Cdk2. MPM-2 and Lsm11 foci are present in embryos lacking the histone locus, and MPM-2 foci are present in U7 mutants, which cannot correctly process histone pre-mRNA. These data indicate that MPM-2 recognizes a Cdk2-regulated protein that assembles into the HLB independently of histone mRNA biosynthesis. HLB foci are present in histone deletion embryos, although the MPM-2 foci are smaller, and some Lsm11 foci are not associated with MPM-2 foci, suggesting that the histone locus is important for HLB integrity.

Periodic transcription: a cycle within a cycle

Studies in model organisms indicate that one in every five genes may be subject to cell cycle regulated transcription. Moreover, a high proportion of periodically expressed genes have discrete roles in the cell division process, and their peaks of expression coincide with the interval during which they function. This periodic transcription is commonly regulated by transcription factors that are also periodically transcribed, and there is a growing number of examples where the transcription factors and their targets are conserved in yeast and mammalian cells. As such, it is worth considering why these regulatory circuits persist in such great number, how they are achieved and what role they may play in the cell cycle.

Characterization of the histone H1-binding protein, NASP, as a cell cycle-regulated somatic protein

Nuclear autoantigenic sperm protein (NASP), initially described as a highly autoimmunogenic testis and sperm-specific protein, is a histone-binding protein that is a homologue of the N1/N2 gene expressed in oocytes of Xenopus laevis. Here, we report a somatic form of NASP (sNASP) present in all mitotic cells examined, including mouse embryonic cells and several mouse and human tissue culture cell lines. Affinity chromatography and histone isolation demonstrate that NASP from myeloma cells is complexed only with H1, linker histones. Somatic NASP is a shorter version of testicular NASP (tNASP) with two deletions in the coding region arising from alternative splicing and differs from tNASP in its 5' untranslated regions. We examined the relationship between NASP mRNA expression and the cell cycle and report that in cultures of synchronized mouse 3T3 cells and HeLa cells sNASP mRNA levels increase during S-phase and decline in G(2), concomitant with histone mRNA levels. NASP protein levels remain stable in these cells but become undetectable in confluent cultures of nondividing CV-1 cells and in nonmitotic cells in various body tissues. Expression of sNASP mRNA is regulated during the cell cycle and, consistent with a role as a histone transport protein, NASP mRNA expression parallels histone mRNA expression.

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.

Autogenous regulation of histone mRNA decay by histone proteins in a cell-free system

We tested the hypothesis that histone mRNA turnover is accelerated in the presence of free histone proteins. In an in vitro mRNA decay system, histone mRNA was degraded four- to sixfold faster in reaction mixtures containing core histones and a cytoplasmic S130 fraction than in reaction mixtures lacking these components. The decay rate did not change significantly when histones or S130 was added separately, suggesting either that the histones were modified and thereby activated by S130 or that additional factors besides histones were required. RecA, SSB (single-stranded binding), and histone proteins all formed complexes with histone mRNA, but only histones induced accelerated histone mRNA turnover. Therefore, the effect was not the result of random RNA-protein interactions. Moreover, histone proteins did not induce increased degradation of gamma globin mRNA, c-myc mRNA, or total poly(A)- or poly(A)+ polysomal mRNAs. This autoregulatory mechanism is consistent with the observed accumulation of cytoplasmic histone proteins in cells after DNA synthesis stops, and it can account, in part, for the rapid disappearance of histone mRNA at the end of S phase.

Regulation of histone and beta A-globin gene expression during differentiation of chicken erythroid cells

The expression of the genes for several histones and beta A-globin was examined in the chicken erythroid cells lineage. During the transition from CFU-(E) to the mature erythrocyte, histone H5 gradually increased fourfold in nuclei with little concomitant displacement of the H1 histones. This resulted in a 70% net increase in linker histone (H1 plus H5) content. The differential accumulation of H5 reflected (i) an increase in the transcriptional activity of the H5 gene occurring at the erythroblast stage, (ii) an apparent longer half-life of H5 mRNA, and (iii) a higher stability of the protein. Although the transcriptional activity of the histone genes (except H5) decreased with cell age, it was not tightly coupled to the S phase. On the other hand, the mRNA levels for these histones were tightly regulated during the cell cycle. Use of protein and DNA synthesis inhibitors indicated that the content of H5 mRNA was regulated at the posttranscriptional level by a control mechanism(s) differing from those for the other histones. Although the transcription rates of the H5 and beta A-globin genes were comparable, differential accumulation of beta A-globin mRNA led to a 30- to 170-fold-higher copy number of the beta A-globin mRNA as the cell matured.

Autogenous regulation of histone mRNA decay by histone proteins in a cell-free system

We tested the hypothesis that histone mRNA turnover is accelerated in the presence of free histone proteins. In an in vitro mRNA decay system, histone mRNA was degraded four- to sixfold faster in reaction mixtures containing core histones and a cytoplasmic S130 fraction than in reaction mixtures lacking these components. The decay rate did not change significantly when histones or S130 was added separately, suggesting either that the histones were modified and thereby activated by S130 or that additional factors besides histones were required. RecA, SSB (single-stranded binding), and histone proteins all formed complexes with histone mRNA, but only histones induced accelerated histone mRNA turnover. Therefore, the effect was not the result of random RNA-protein interactions. Moreover, histone proteins did not induce increased degradation of gamma globin mRNA, c-myc mRNA, or total poly(A)- or poly(A)+ polysomal mRNAs. This autoregulatory mechanism is consistent with the observed accumulation of cytoplasmic histone proteins in cells after DNA synthesis stops, and it can account, in part, for the rapid disappearance of histone mRNA at the end of S phase.

Molecular cloning and differential expression of somatic and testis-specific H2B histone genes during rat spermatogenesis

We have cloned cDNA of a testis-specific histone, TH2B (a variant of H2B), and rat somatic H2B gene to investigate regulation of testis-specific histone genes during rat spermatogenesis. The amino acid sequences deduced from DNA sequences show extensive sequence divergence in the N-terminal third of the two histones. The rest is highly conserved. One cysteine residue was found in TH2B. No cysteine is present in somatic histones except in H3 histone. We investigated the expression of TH2B and H2B genes using the regions of sequence divergence as hybridization probes. The TH2B gene is expressed only in the testis, and the expression of this gene is detected 14 days after birth, reaching a maximum at Day 20. The level of H2B mRNA shows a reciprocal pattern. This contrasting pattern can be explained by the gradually changing proportion of spermatogonia and spermatocytes with testicular maturation. In situ cytohybridization studies show that H2B gene is expressed primarily in proliferating spermatogonia and preleptotene spermatocytes, whereas TH2B gene is expressed exclusively in pachytene spermatocytes which first appear in testis about 14 days after birth. H2B and TH2B genes appear to be ideal markers for the study of proliferation and differentiation events in spermatogenesis and their regulatory mechanisms.

Regulation of histone and beta A-globin gene expression during differentiation of chicken erythroid cells

The expression of the genes for several histones and beta A-globin was examined in the chicken erythroid cells lineage. During the transition from CFU-(E) to the mature erythrocyte, histone H5 gradually increased fourfold in nuclei with little concomitant displacement of the H1 histones. This resulted in a 70% net increase in linker histone (H1 plus H5) content. The differential accumulation of H5 reflected (i) an increase in the transcriptional activity of the H5 gene occurring at the erythroblast stage, (ii) an apparent longer half-life of H5 mRNA, and (iii) a higher stability of the protein. Although the transcriptional activity of the histone genes (except H5) decreased with cell age, it was not tightly coupled to the S phase. On the other hand, the mRNA levels for these histones were tightly regulated during the cell cycle. Use of protein and DNA synthesis inhibitors indicated that the content of H5 mRNA was regulated at the posttranscriptional level by a control mechanism(s) differing from those for the other histones. Although the transcription rates of the H5 and beta A-globin genes were comparable, differential accumulation of beta A-globin mRNA led to a 30- to 170-fold-higher copy number of the beta A-globin mRNA as the cell matured.

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.

Cytoskeleton involvement in the distribution of mRNP complexes and small cytoplasmic RNAs

These studies were designed to determine whether small cytoplasmic RNAs and two different mRNAs (actin mRNA and histone H4 mRNA) were uniformly distributed among various subcellular compartments. The cytoplasm of HeLa S3 cells was fractionated into four RNA-containing compartments. The RNAs bound to the cytoskeleton were separated from those in the soluble cytoplasmic phase and each RNA fraction was further separated into those bound and those not bound to polyribosomes. The four cytoplasmic RNA fractions were analysed to determine which RNA species were present in each. The 7 S RNAs were found in all cytoplasmic fractions, as were the 5 S and 5.8 S ribosomal RNAs, while transfer RNA was found largely in the soluble fraction devoid of polysomes. On the other hand a group of prominent small cytoplasmic RNAs (scRNAs of 105-348 nucleotides) was isolated from the fraction devoid of polysomes but bound to the cytoskeleton. Actin mRNA was found only in polyribosomes bound to the cytoskeleton. This mRNA was released into the soluble phase by cytochalasin B treatment, suggesting a dependence upon actin filament integrity for cytoskeletal binding. A significant portion of several scRNAs was also released from the cytoskeleton by cytochalasin B treatment. Analysis of the spatial distribution of histone H4 mRNAs, however, revealed a more widely dispersed message. Although most (60%) of the H4 mRNA was associated with polyribosomes in the soluble phase, a significant amount was also recovered in both of the cytoskeleton bound fractions either associated or free of polyribosome interaction. Treatment with cytochalasin B suggested that only cytoskeleton bound, untranslated H4 mRNA was dependent upon the integrity of actin filaments for cytoskeletal binding.

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.

Changes in the levels of three different classes of histone mRNA during murine erythroleukemia cell differentiation

We used a gene-specific S1 nuclease assay to study the changes in steady-state mRNA levels of several core histone variants during the differentiation of murine erythroleukemia cells. These studies allowed us to distinguish three distinct expression classes of histone genes. The expression of the major replication-dependent class of histone genes was tightly linked to DNA synthesis. The concentrations of these transcripts decreased rapidly as cell division slowed during the process of differentiation. In contrast, the replication-independent H3.3 transcript levels were constitutively maintained throughout differentiation and were unaffected by inhibitors of DNA or protein synthesis. We also identified among the cloned histone genes used as probes a third expression class, the partially replication-dependent variants. Expression of these transcripts became transiently uncoupled from the reduced rate of DNA synthesis accompanying the early stages of differentiation. We show that their synthesis is sensitive to the DNA synthesis inhibitor hydroxyurea but that selective uncoupling from DNA synthesis of these histone mRNAs occurs at a specific stage of differentiation. We present several hypotheses to explain how this might be accomplished. The expression characteristics of the mRNAs studied coincided with those of the proteins for which they code, indicating that changes in the relative levels of the different variants is mediated at least in part by changes in mRNA levels.

Histone messenger RNAs of the mouse testis

A 6-12S RNA fraction has been isolated following sucrose gradient fractionation of mouse testis RNA, and further resolved into poly A+ and poly A- RNA fractions by oligo-(dt)-cellulose chromatography. Polyacrylamide gel electrophoresis of products formed in a reticulocyte lysate-dependent cell-free translation system has enabled identification of histone variants, H1t, H2S, H2A . X, an H4-like protein and a low Mr protein (presumably TP and/or protamine). Cell-free synthesis of a number of these histone variants appears to be directed by poly A+ mRNAs.

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.

H4 histone messenger RNA decay in cell-free extracts initiates at or near the 3' terminus and proceeds 3' to 5'

The relative decay of four human messenger RNAs, gamma globin, delta globin, c-myc and H4 histone, were compared in a cell-free system. Under appropriate conditions, they are degraded in vitro in approximately the same relative order as in vivo: histone faster than c-myc and delta globin faster than gamma globin. Degradation of polysome-associated H4 histone mRNA and of deproteinized histone mRNA begins at or near the 3' terminus. At least a portion of the mRNA then continues to be degraded in a 3' to 5' direction. Discrete 3'-terminal degradation hold-up points are observed, suggesting that 3' to 5' degradation occurs non-uniformly. Cycloheximide and puromycin inhibit protein synthesis but do not affect the rate or directionality of histone mRNA decay in vitro. We conclude that the rate-limiting step in H4 histone mRNA decay occurs at or near the 3' terminus and that at least a portion of the mRNA molecule is subsequently degraded 3' to 5', probably via a processive exonuclease.

Identification of an autonomously replicating sequence near a histone gene of Physarum polycephalum

Fragments of DNA which function as autonomous replication sequences in yeast were cloned from Physarum polycephalum. The ars activity is located in a 1.2 kbp fragment extending 1.5 kbp to 2.7 kbp upstream of the 5' end of a histone H4 gene. Our recent finding that a replication origin is located at a distance less than 3 kbp of this histone gene suggests that the ars element identified coincides with a specialized replication origin and can be used to direct chromosome replication in Physarum polycephalum.

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.

Changes in the levels of three different classes of histone mRNA during murine erythroleukemia cell differentiation

We used a gene-specific S1 nuclease assay to study the changes in steady-state mRNA levels of several core histone variants during the differentiation of murine erythroleukemia cells. These studies allowed us to distinguish three distinct expression classes of histone genes. The expression of the major replication-dependent class of histone genes was tightly linked to DNA synthesis. The concentrations of these transcripts decreased rapidly as cell division slowed during the process of differentiation. In contrast, the replication-independent H3.3 transcript levels were constitutively maintained throughout differentiation and were unaffected by inhibitors of DNA or protein synthesis. We also identified among the cloned histone genes used as probes a third expression class, the partially replication-dependent variants. Expression of these transcripts became transiently uncoupled from the reduced rate of DNA synthesis accompanying the early stages of differentiation. We show that their synthesis is sensitive to the DNA synthesis inhibitor hydroxyurea but that selective uncoupling from DNA synthesis of these histone mRNAs occurs at a specific stage of differentiation. We present several hypotheses to explain how this might be accomplished. The expression characteristics of the mRNAs studied coincided with those of the proteins for which they code, indicating that changes in the relative levels of the different variants is mediated at least in part by changes in mRNA levels.

A unique subspecies of histone H4 mRNA from rat myoblasts contains poly(A)

Fractionation of rat L6 myoblast histone H4 mRNA into its three component subspecies revealed that one of the major subspecies (H4-1) contained poly(A). The unique poly(A)+ H4 mRNA makes up about 8% of the total polysomal H4 mRNA population detected. Unlike the poly(A)- histone mRNAs, whose levels are reduced by greater than 95% when myoblasts differentiate into myotubes, the poly(A)+ subspecies is reduced by only 70%. The poly(A)+ H4 mRNA from myotubes incubated with actinomycin D decays with a half-life of 37-42 min, which is similar to that obtained for the poly(A)- H4 mRNAs in myoblasts. Both the poly(A)+ and poly(A)- subspecies decay at an increased rate after inhibition of DNA synthesis. In myoblasts the poly(A)+ H4 mRNA exists almost exclusively in the polysomal compartment (greater than 95%) with little (less than 5%) in the free ribonucleoprotein (mRNA-protein or mRNP) complex compartment of the cell. Poly(A)- histone H4 mRNA subspecies, on the other hand, are distributed with approximately 80% in the polysomal compartment and 20% in the free mRNP complex compartment. The unique poly(A)+ H4 mRNA is unusual, not only in that it contains poly(A) but also in its behavior compared to poly(A)- H4 mRNAs during terminal differentiation.

Replication timing of the H4 histone genes in Physarum polycephalum

The time of replication of the two H4 histone genes (H41 and H42) was determined during the naturally synchronous mitotic cycle of Physarum polycephalum. 5-Bromo-2'-deoxyuridine labeling and density gradient centrifugation was used to isolate newly synthesized DNA from defined periods of S phase. The DNA was analyzed by Southern hybridization with a cloned probe containing one of the H4 histone genes of Physarum. The results indicate that the two H4 histone genes are replicated in the first 30 min of S phase but not exactly at the same time. H41 is replicated during the first 10 min of S phase, when only 15% of the genome is duplicated, whereas H42 replicates between 20 and 30 min after the onset of S phase. The possible relationship between the periodic expression of the genes and the timing of their replication is discussed.

Coordinate regulation of histone mRNAs during growth and differentiation of rat myoblasts

To determine whether histone genes are coordinately regulated, histone mRNA concentrations were measured in exponentially growing L6 myoblasts, S-phase synchronized myoblasts and in differentiating myoblasts. The levels of various histone mRNA subspecies declined rapidly and coordinately once myoblasts were given the signal to differentiate. mRNA levels were reduced on average to 1-5% of the amount observed in exponentially growing cells by 48 h after the signal to differentiate. The reductions occurred in concert with the cessation of DNA synthesis as the cells differentiated. Inhibition of DNA synthesis by treating myoblasts with Ara-C or hydroxyurea resulted in a histone mRNA half-life of 10-13 min for each of the histones examined. One example of non-coordinate regulation was observed however among the H4 mRNA subspecies in S-phase synchronized cells. The levels of two major subspecies of H4 mRNA increased coordinately in S-phase compared to levels observed in cells growing exponentially. A third subspecies of H4 mRNA on the other hand was found to decline by 50%. These studies suggest that the majority of histone mRNA subspecies are under coordinate control, although one exception has been noted among the subspecies of histone H4.

Use of a cell cycle mutant to delineate the critical period for the control of histone mRNA levels in the mammalian cell cycle

Temporal analysis of DNA replication and histone mRNA accumulation in a hamster fibroblast cell cycle mutant (K12) showed that histone mRNA accumulates periodically during the cell cycle and reaches its highest level in the S phase. The direct correlation between the initiation of DNA synthesis and the accumulation of histone mRNA to high levels in S phase demonstrated the strict interdependence of these two events. Moreover, a critical period necessary for histone mRNA accumulation occurred late in G1 phase. If cells were incubated at the nonpermissive temperature during this critical period, the amount of histone mRNA remained at the basal level. Transcription rate measurements indicated that the triggering of histone mRNA synthesis occurred in late G1 and this mRNA was synthesized at its maximal rate 3 to 5 h before its peak of accumulation. However, if cells were prohibited from synthesizing DNA as a consequence of the temperature-sensitive block in G1, the synthesis of histone mRNA was not initiated.

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.

Use of a cell cycle mutant to delineate the critical period for the control of histone mRNA levels in the mammalian cell cycle

Temporal analysis of DNA replication and histone mRNA accumulation in a hamster fibroblast cell cycle mutant (K12) showed that histone mRNA accumulates periodically during the cell cycle and reaches its highest level in the S phase. The direct correlation between the initiation of DNA synthesis and the accumulation of histone mRNA to high levels in S phase demonstrated the strict interdependence of these two events. Moreover, a critical period necessary for histone mRNA accumulation occurred late in G1 phase. If cells were incubated at the nonpermissive temperature during this critical period, the amount of histone mRNA remained at the basal level. Transcription rate measurements indicated that the triggering of histone mRNA synthesis occurred in late G1 and this mRNA was synthesized at its maximal rate 3 to 5 h before its peak of accumulation. However, if cells were prohibited from synthesizing DNA as a consequence of the temperature-sensitive block in G1, the synthesis of histone mRNA was not initiated.

Independent regulation by sodium butyrate of gonadotropin alpha gene expression and cell cycle progression in HeLa cells

Sodium butyrate alters the growth and gene expression of a variety of differentiating and neoplastic cell types. For example, addition of 5 mM butyrate to HeLa cells is reported to both induce gonadotropin alpha subunit biosynthesis and block cell cycling in G1. We have studied these two actions of butyrate on HeLa cells and found that they are regulated in distinct ways. The induction of alpha subunit synthesis was due to an increase in the rate of transcription of the alpha gene. Using synchronized populations of HeLa cells, we determined that butyrate stimulates alpha transcription throughout the cell cycle. In contrast, treated cells arrest in G1 only if exposed to butyrate for a discrete period during the previous S phase. We conclude that butyrate inhibits DNA synthesis through a cell cycle-specific action that is independent from its direct action to stimulate transcription of the gonadotropin alpha gene.

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.

Independent regulation by sodium butyrate of gonadotropin alpha gene expression and cell cycle progression in HeLa cells

Sodium butyrate alters the growth and gene expression of a variety of differentiating and neoplastic cell types. For example, addition of 5 mM butyrate to HeLa cells is reported to both induce gonadotropin alpha subunit biosynthesis and block cell cycling in G1. We have studied these two actions of butyrate on HeLa cells and found that they are regulated in distinct ways. The induction of alpha subunit synthesis was due to an increase in the rate of transcription of the alpha gene. Using synchronized populations of HeLa cells, we determined that butyrate stimulates alpha transcription throughout the cell cycle. In contrast, treated cells arrest in G1 only if exposed to butyrate for a discrete period during the previous S phase. We conclude that butyrate inhibits DNA synthesis through a cell cycle-specific action that is independent from its direct action to stimulate transcription of the gonadotropin alpha gene.

Transcription of human histone genes in extracts from synchronized HeLa cells

Nuclear extracts were prepared from synchronized HeLa cells at various times during the cell cycle and assayed for the ability to transcribe several cellular and viral genes. The efficiency of transcription of a human histone H4 gene is 3- to 10-fold greater in nuclear extracts from S phase nuclei than in extracts from non-S phase cells. In contrast, the adenovirus virus type 2 (Ad2) major late promoter is utilized 3- to 20-fold more efficiently in nuclear extracts from non-S phase cells. Transcription of other genes, including a human histone H3 and the simian virus 40 late transcription unit, is equally efficient in S and non-S phase extracts. Mixing experiments demonstrate that the rate-limiting activities for histone H4 and Ad2 major late transcription function independently and that the effects of these activities are additive. Competition studies suggest that the H4-specific transcription activity can be sequestered by preincubation with the H4 template DNA. These data support the concept that cell cycle regulation of human histone gene transcription may depend in part on soluble transcription activities that are modulated during the cell cycle. Further, in addition to the H4-specific transcription activity, there may exist other transcription factors whose activity can fluctuate according to the cell cycle or according to the growth state of the cells.

Rapid reversible changes in the rate of histone gene transcription and histone mRNA levels in mouse myeloma cells

The levels of histone mRNAs are reduced 90 to 95% after treatment of mouse myeloma cells with inhibitors of DNA synthesis which disrupt deoxynucleotide metabolism. In contrast, novobiocin, which inhibits DNA synthesis but does not alter deoxynucleotide metabolism, did not alter histone mRNA levels. Upon reversing the inhibition by fluorodeoxyuridine by feeding with thymidine, histone mRNA levels are restored to control levels within 40 to 60 min. The rate of histone gene transcription is reduced 75 to 80% within 10 min after treatment with fluorodeoxyuridine and increased to control levels within 10 min after refeeding with thymidine. Inhibition of protein synthesis with cycloheximide or puromycin in cells which had been treated with fluorodeoxyuridine resulted in an increase of histone mRNA levels. This was partly due to an increase in the rate of transcription. The data indicate that both transcription and mRNA degradation are linked to deoxynucleotide metabolism. Continued protein synthesis is necessary for maintaining the inhibition of histone gene transcription.

Cell cycle regulation of mouse H3 histone mRNA metabolism

The mechanisms responsible for the periodic accumulation and decay of histone mRNA in the mammalian cell cycle were investigated in mouse erythroleukemia cells, using a cloned mouse H3 histone gene probe that hybridizes with most or all H3 transcripts. Exponentially growing cells were fractionated into cell cycle-specific stages by centrifugal elutriation, a method for purifying cells at each stage of the cycle without the use of treatments that arrest growth. Measurements of H3 histone mRNA content throughout the cell cycle show that the mRNA accumulates gradually during S phase, achieving its highest value in mid-S phase when DNA synthesis is maximal. The mRNA content then decreases as cells approach G2. These results demonstrate that the periodic synthesis of histones during S phase is due to changes in the steady-state level of histone mRNA. They are consistent with the conventional view in which histone synthesis is regulated coordinately with DNA synthesis in the cell cycle. The periodic accumulation and decay of H3 histone mRNA appear to be controlled primarily by changes in the rate of appearance of newly synthesized mRNA in the cytoplasm, determined by pulse-labeling whole cells with [3H]uridine. Measurements of H3 mRNA turnover by pulse-chase experiments with cells in S and G2 did not provide evidence for changes in the cytoplasmic stability of the mRNA during the period of its decay in late S and G2. Furthermore, transcription measurements carried out by brief pulse-labeling in vivo and by in vitro transcription in isolated nuclei indicate that the rate of H3 gene transcription changes to a much smaller extent than the steady-state levels of the mRNA or the appearance of newly synthesized mRNA in the cytoplasm. The results suggest that post-transcriptional processes make an important contribution to the periodic accumulation and decay of histone mRNA and that these processes may operate within the nucleus.

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.

Rapid reversible changes in the rate of histone gene transcription and histone mRNA levels in mouse myeloma cells

The levels of histone mRNAs are reduced 90 to 95% after treatment of mouse myeloma cells with inhibitors of DNA synthesis which disrupt deoxynucleotide metabolism. In contrast, novobiocin, which inhibits DNA synthesis but does not alter deoxynucleotide metabolism, did not alter histone mRNA levels. Upon reversing the inhibition by fluorodeoxyuridine by feeding with thymidine, histone mRNA levels are restored to control levels within 40 to 60 min. The rate of histone gene transcription is reduced 75 to 80% within 10 min after treatment with fluorodeoxyuridine and increased to control levels within 10 min after refeeding with thymidine. Inhibition of protein synthesis with cycloheximide or puromycin in cells which had been treated with fluorodeoxyuridine resulted in an increase of histone mRNA levels. This was partly due to an increase in the rate of transcription. The data indicate that both transcription and mRNA degradation are linked to deoxynucleotide metabolism. Continued protein synthesis is necessary for maintaining the inhibition of histone gene transcription.

Cell cycle regulation of mouse H3 histone mRNA metabolism

The mechanisms responsible for the periodic accumulation and decay of histone mRNA in the mammalian cell cycle were investigated in mouse erythroleukemia cells, using a cloned mouse H3 histone gene probe that hybridizes with most or all H3 transcripts. Exponentially growing cells were fractionated into cell cycle-specific stages by centrifugal elutriation, a method for purifying cells at each stage of the cycle without the use of treatments that arrest growth. Measurements of H3 histone mRNA content throughout the cell cycle show that the mRNA accumulates gradually during S phase, achieving its highest value in mid-S phase when DNA synthesis is maximal. The mRNA content then decreases as cells approach G2. These results demonstrate that the periodic synthesis of histones during S phase is due to changes in the steady-state level of histone mRNA. They are consistent with the conventional view in which histone synthesis is regulated coordinately with DNA synthesis in the cell cycle. The periodic accumulation and decay of H3 histone mRNA appear to be controlled primarily by changes in the rate of appearance of newly synthesized mRNA in the cytoplasm, determined by pulse-labeling whole cells with [3H]uridine. Measurements of H3 mRNA turnover by pulse-chase experiments with cells in S and G2 did not provide evidence for changes in the cytoplasmic stability of the mRNA during the period of its decay in late S and G2. Furthermore, transcription measurements carried out by brief pulse-labeling in vivo and by in vitro transcription in isolated nuclei indicate that the rate of H3 gene transcription changes to a much smaller extent than the steady-state levels of the mRNA or the appearance of newly synthesized mRNA in the cytoplasm. The results suggest that post-transcriptional processes make an important contribution to the periodic accumulation and decay of histone mRNA and that these processes may operate within the nucleus.

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.