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

Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle

Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.

Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S-phase transition

Fidelity of histone gene regulation, and ultimately of histone protein biosynthesis, is obligatory for packaging of newly replicated DNA into chromatin. Control of histone gene expression within the 3-dimensional context of nuclear organization is reflected by two well documented observations. DNA replication-dependent histone mRNAs are synthesized at specialized subnuclear domains designated histone locus bodies (HLBs), in response to activation of the growth factor dependent Cyclin E/CDK2/HINFP/NPAT pathway at the G1/S transition in mammalian cells. Complete loss of the histone gene regulatory factors HINFP or NPAT disrupts HLB integrity that is necessary for coordinate control of DNA replication and histone gene transcription. Here we review the molecular histone-related requirements for G1/S-phase progression during the cell cycle. Recently developed experimental strategies, now enable us to explore mechanisms involved in dynamic control of histone gene expression in the context of the temporal (cell cycle) and spatial (HLBs) remodeling of the histone gene loci.

Epigenomic reprogramming in inorganic arsenic-mediated gene expression patterns during carcinogenesis

Arsenic is a ubiquitous metalloid that is not mutagenic but is carcinogenic. The mechanism(s) by which arsenic causes cancer remain unknown. To date, several mechanisms have been proposed, including the arsenic-induced generation of reactive oxygen species (ROS). However, it is also becoming evident that inorganic arsenic (iAs) may exert its carcinogenic effects by changing the epigenome, and thereby modifying chromatin structure and dynamics. These epigenetic changes alter the accessibility of gene regulatory factors to DNA, resulting in specific changes in gene expression both at the levels of transcription initiation and gene splicing. In this review, we discuss recent literature reports describing epigenetic changes induced by iAs exposure and the possible epigenetic mechanisms underlying these changes.

The abbreviated pluripotent cell cycle

Human embryonic stem cells (hESCs) and induced pluripotent stem cells proliferate rapidly and divide symmetrically producing equivalent progeny cells. In contrast, lineage committed cells acquire an extended symmetrical cell cycle. Self-renewal of tissue-specific stem cells is sustained by asymmetric cell division where one progeny cell remains a progenitor while the partner progeny cell exits the cell cycle and differentiates. There are three principal contexts for considering the operation and regulation of the pluripotent cell cycle: temporal, regulatory, and structural. The primary temporal context that the pluripotent self-renewal cell cycle of hESCs is a short G1 period without reducing periods of time allocated to S phase, G2, and mitosis. The rules that govern proliferation in hESCs remain to be comprehensively established. However, several lines of evidence suggest a key role for the naïve transcriptome of hESCs, which is competent to stringently regulate the embryonic stem cell (ESC) cell cycle. This supports the requirements of pluripotent cells to self-propagate while suppressing expression of genes that confer lineage commitment and/or tissue specificity. However, for the first time, we consider unique dimensions to the architectural organization and assembly of regulatory machinery for gene expression in nuclear microenviornments that define parameters of pluripotency. From both fundamental biological and clinical perspectives, understanding control of the abbreviated ESC cycle can provide options to coordinate control of proliferation versus differentiation. Wound healing, tissue engineering, and cell-based therapy to mitigate developmental aberrations illustrate applications that benefit from knowledge of the biology of the pluripotent cell cycle.

The architectural organization of human stem cell cycle regulatory machinery

Two striking features of human embryonic stem cells that support biological activity are an abbreviated cell cycle and reduced complexity to nuclear organization. The potential implications for rapid proliferation of human embryonic stem cells within the context of sustaining pluripotency, suppressing phenotypic gene expression and linkage to simplicity in the architectural compartmentalization of regulatory machinery in nuclear microenvironments is explored. Characterization of the molecular and architectural commitment steps that license human embryonic stem cells to initiate histone gene expression is providing understanding of the principal regulatory mechanisms that control the G1/S phase transition in primitive pluripotent cells. From both fundamental regulatory and clinical perspectives, further understanding of the pluripotent cell cycle in relation to compartmentalization of regulatory machinery in nuclear microenvironments is relevant to applications of stem cells for regenerative medicine and new dimensions to therapy where traditional drug discovery strategies have been minimally effective.

The interactome of the histone gene regulatory factor HiNF-P suggests novel cell cycle related roles in transcriptional control and RNA processing

HiNF-P is a recently identified histone H4 subtype specific transcriptional regulator that associates with the conserved cell cycle control element in the proximal promoter regions of histone H4 genes. HiNF-P interacts with the global histone gene regulator and direct cyclin E/CDK2 substrate p220(NPAT) to potently upregulate histone H4 gene transcription at the G1/S phase transition in response to cyclin E/CDK2 signaling. To gain insight into the function of HiNF-P in a broader cellular context, we performed a yeast two-hybrid screen to identify its novel interacting proteins. In this study, we detected 67 candidate HiNF-P interacting proteins of varying cellular functions. We have identified multiple RNA associated proteins, including the splicing co-factor SRm300. HiNF-P and SRm300 interact in yeast two-hybrid, co-immunoprecipitation, and co-immunofluorescence assays. Our screen also identified several gene regulators that associate with HiNF-P including THAP7. HiNF-P and THAP7 interact in mammalian cells and THAP7 abrogates HiNF-P/p220 mediated activation of histone H4 gene transcription, consistent with its known role as a transcriptional repressor. Finally, we identified several proliferation related proteins including Ki-67 and X transactivated protein 2 (XTP2) which may be functioning with HiNF-P in cell cycle regulation. The HiNF-P interactome indicates that HiNF-P is a multifunctional gene regulator with a large functional network and roles beyond cell cycle-dependent histone gene regulation.

Molecular characterization and transcription of the histone H2B gene from the protozoan parasite Trypanosoma cruzi

The structure, genomic organization and transcription of the gene encoding histone H2B in the protozoan parasite Trypanosoma cruzi have been studied. This gene consists of a 746-nucleotide unit, tandemly repeated at least 18 times in each of two clusters. DNA probes corresponding to histones H2B and H3 hybridized to different chromosomes revealing that the genes coding for these two histones are not physically linked in the genome of T. cruzi. The primary transcription product of the H2B gene is processed by trans-splicing and polyadenylation. Inhibition of DNA synthesis with aphidicolin resulted in the reduction of histone H2B mRNA to undetectable levels in about two hours, suggesting that its abundance is regulated throughout the cell cycle as it occurs in other eukaryotes. In addition, a concomitant inhibition of translation by cycloheximide reverted this effect indicating that de novo protein synthesis is required for RNA instability. Histone mRNA abundance was dependent on the life-cycle stage of T. cruzi: abundant in amastigotes and epimastigotes, the dividing forms in the host cell and the insect vector, respectively, while undetected in trypomastigotes, the parasite's non-dividing life stage.

Analysis of hepatocellular proliferation: study of archival liver tissue is facilitated by an endogenous marker of DNA replication

Assessment of liver regeneration with endogenous genes that are expressed during DNA replication is physiological, specific and direct. To determine whether H3 histone messenger RNA expression (which is tightly coupled with DNA synthesis) could be used for this purpose, we initially examined liver regeneration in a mouse model. After partial hepatectomy, RNA transblot studies showed induction of H3 histone messenger RNA expression in regenerating mouse livers. In situ molecular hybridization demonstrated that the overall pattern of H3 histone messenger RNA expression correlated with [3H]thymidine labeling of hepatocytes. After partial hepatectomy, H3 histone messenger RNA expression in hepatocytes peaked at 48 hr (greater than 60 times greater than at 24 hr; p less than 0.001) and then rapidly declined. Although hepatocyte labeling with [3H]thymidine showed similar kinetics of liver regeneration, use of this parameter resulted in overestimation of the proliferative compartment when it was compared with H3 histone messenger RNA expression. Next we determined whether H3 histone messenger RNA expression could be used to study hepatocellular proliferation in archival human material. H3 histone messenger RNA-expressing hepatocytes were identified on in situ hybridization in patients with acute or chronic active hepatitis and active cirrhosis, but not inactive cirrhosis. These studies demonstrate that H3 histone messenger RNA is expressed in a phasic manner during liver regeneration. Use of H3 histone messenger RNA expression to evaluate hepatocellular proliferation should facilitate clinical studies and greatly advance our understanding of the pathophysiology of liver regeneration.

SV40T-immortalized lung alveolar epithelial cells display post-transcriptional regulation of proliferation-related genes

To study the regulation of proliferation of lung alveolar epithelial type 2 cells, we have established a cell line derived from neonatal type 2 cells by transfection with the SV40 large T antigen gene. We find that this cell line, designated SV40-T2, displays the same post-transcriptional control of expression of proliferation-related genes, including c-myc, ornithine decarboxylase, thymidine kinase, and histone, that we have previously described in primary isolates of type 2 cells (Clement et al., Proc. Natl. Acad. Sci. USA 87, 318-322, 1990). Both proliferating and nonproliferating SV40-T2 cells express these genes at high levels, but their translation products are only detected in proliferating cells. Using the histone gene as an example, we have found that regulation of expression occurs at the level of transcription and of mRNA turnover, as previously described in other mammalian systems. However, in addition, regulation of expression also occurs at the level of translation of the histone mRNA, because its protein product is not detectable in nonproliferating SV40-T2 cells. We have analyzed the steps which are potentially involved in this translational regulation of histone gene expression in SV40-T2 cells. In both proliferating and nonproliferating cells, histone mRNA was found to be efficiently transported from the nucleus to the cytoplasm and to associate with the translationally active heavy polysomal fractions. These results indicate that control of histone gene expression (and perhaps that of other proliferation-related genes) in lung epithelial cells may involve either rapid and selective degradation of histone protein or binding factor(s) which modulate translational efficiency of histone mRNA.

Coordination of protein-DNA interactions in the promoters of human H4, H3, and H1 histone genes during the cell cycle, tumorigenesis, and development

Coordinate transcriptional control of replication-dependent human H4, H3, and H1 histone genes was studied by comparing levels of H3 and H1 histone promoter binding activities with those of H4 histone promoter factor HiNF-D during the cell cycle of both normal diploid and tumor-derived cells, as well as in fetal and adult mammalian tissues. Both H3 and H1 histone promoters interact with binding activities that, as with HiNF-D, are maximal during S-phase but at low levels in the G1-phase of normal diploid cells. However, these analogous DNA binding activities are constitutively maintained at high levels throughout the cell cycle in four different transformed and tumor-derived cells. Downregulation of the H3 and H1 histone promoter factors in conjunction with HiNF-D is observed in vivo at the onset of quiescence and differentiation during hepatic development. Hence, our results indicate a tight temporal coupling of three separate protein-DNA interactions in different histone promoters during the cell cycle, development, and tumorigenesis. This suggests that a key oscillatory, cell-growth-control mechanism modulates three analogous histone gene promoter protein-DNA interactions in concert. The derangement of this mechanism in four distinct tumor cells implies that concerted deregulation of these histone promoter factors is a common event resulting from heterogeneous aberrations in normal cell growth mechanisms during tumorigenesis. We postulate that this mechanism may be involved in the coordinate regulation of the human H4, H3, and H1 histone multigene families.

Inhibitory effect of quercetin on the synthesis of a possibly cell-cycle-related 17-kDa protein, in human colon cancer cells

Quercetin inhibits growth of COLO320 DM cells, derived from a human colon cancer. The inhibitory effect is partially reversible when quercetin is removed from the culture medium. Flow cytometric analysis has revealed that quercetin causes perturbation of the cell cycle, inducing a frozen cell-cycle pattern and a block at the G1/S boundary. The synthesis of a 17-kDa protein was specifically inhibited by the addition of quercetin, and recovered when the cells at the G1/S boundary progressed into S-phase after the removal of quercetin from the culture medium. Furthermore, using synchronized cells obtained by centrifugal elutriation, we have shown that the rate of synthesis of a 17-kDa protein was low in G1, and high in S-phase of the cell cycle. Thus, this protein appears to be cell-cycle-related.

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.

Regulation of gene expression of myeloperoxidase during myeloid differentiation

Myeloperoxidase (MPO) is a major heme enzyme involved in inflammatory responses of polymorphonuclear leukocytes. Using cDNA and intron specific probes for MPO we studied the regulation of MPO expression during myeloid differentiation of the promyelocytic HL-60 leukemia cell line. Mature MPO mRNA species of 3.3, 2.8 and 1.6 kb and heterogeneous nuclear (hn) RNA of greater than 8 and approximately 4 kb were observed in wildtype HL-60 cells. Induction of differentiation of the cells towards either granulocytes or macrophages resulted in a profound decrease (greater than 95%) in the concentration of MPO mRNA levels, showing that gene expression of MPO mRNA is closely linked to the stage of development of myeloid cells. Studies using normal and leukemic hematopoietic cells confirmed these findings and showed that myeloblasts and promyelocytes contain MPO mRNA. Rate of transcription of MPO was measured by a nuclear run-on assay in wild-type and day 3- and day -4 differentiated HL-60 cells and was nearly the same in all three. In contrast, rate of transcription of c-myc in the same nuclei became almost undetectable with induction of differentiation. Overall transcription decreased by 60% and 80% on day 3 and 4 of differentiation, respectively, compared to wild-type cells. Stability of mature MPO mRNA was also measured and found to be the same in wild-type and differentiated HL-60. Half-life of MPO hnRNA was less than or equal to 30 min in wild-type HL-60; nevertheless, this hnRNA was easily detectable 3 days after induction of differentiation of these cells. Taken together, the results show that decreased expression of MPO mRNA with differentiation occurs in part post-transcriptionally, possibly due to a failure in RNA processing. In addition, as overall transcription decreases during differentiation, MPO transcription is concomitantly reduced. This indicates that transcriptional and post-transcriptional mechanisms cooperate in the control of MPO gene expression.

Molecular characterization of the histone gene family of Caenorhabditis elegans

The core histone genes (H2A, H2B, H3 and H4) of Caenorhabditis elegans are arranged in approximately 11 dispersed clusters and are not tandemly arrayed in the genome. Three well-characterized genomic clones, which contain histone genes, have one copy of each core histone gene per cluster. One of the clones (lambda Ceh-1) carries one histone cluster surrounded by several thousand base-pairs of non-histone DNA, and another clone (lambda Ceh-3) contains a histone cluster duplication surrounded by non-histone DNA. A third clone (lambda Ceh-2) carries a cluster of core histone genes flanked on one side (12,000 base-pairs away) by a single H2B gene and on the other by non-histone DNA. A fourth cluster (clone BE9) has one copy each of H3 and H4 and two copies each of H2A and H2B. This cluster is also flanked by non-histone DNA. Analysis of cosmid clones which overlap three of the clusters shows that no other histone clusters are closer than 8000 to 60,000 base-pairs, although unidentified non-histone transcription units are present on the flanking regions. Gene order within the histone clusters varies, and histone mRNAs are transcribed from both DNA strands. No H1 sequences are found on these core histone clones. Restriction fragment length polymorphisms between two related nematode strains (Bristol and Bergerac) were used as phenotypic markers in genetic crosses to map one histone cluster to linkage group V and another to linkage group IV. Hybridization of gene-specific probes from sea urchin to C. elegans RNA identifies C. elegans core histone messenger RNAs of sizes similar to sea urchin early stage histone mRNAs (H2A, H2B, H3 and H4). The organization of histone genes in C. elegans resembles the clustering found in most vertebrate organisms and does not resemble the tandem patterns of the early stage histone gene family of sea urchins or the major histone locus of Drosophila.

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.

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.

Histone synthesis and deposition in the G1 and S phases of hepatoma tissue culture cells

Hepatoma tissue culture cells were synchronized in G1 and in S phase in order to examine the level of synthesis of different histone types and to determine the rate, timing, and location of their deposition onto DNA. We observe a basal level of synthesis in G1 (5% of that seen in S phase) for H2A.1, H2A.2, H3.2, H2B, and H4. The minor histone variants X and Z are synthesized at 30% of the rate observed in S cells. The rate of synthesis of the ubiquinated histones uH2A.1,2 is not as depressed in G1 cells as seen for H2A.1 and H2A.2. Histones synthesized in G1 are not deposited on the DNA of these cells at equivalent rates. Thus, histones H3.2 and H4 are not deposited significantly until S phase begins, at which time deposition occurs selectively on newly synthesized DNA. The deposition of H2A.1, H2A.2, H2B, X, and Z proceeds in G1; however, it occurs to a 2-4-fold lower extent than seen for the deposition of H1, HMG 14, and HMG 17. The deposition of all histones synthesized in S phase occurs rapidly, but there are variations in the sites of deposition. Thus, newly synthesized H3.1, H3.2, and H4 deposit primarily on newly replicated DNA whereas H2A.1, H2A.2, uH2A.1, 2, and H2B deposit only partially on new DNA (30%) and mostly on old. H1, HMG 14, and HMG 17 are deposited in an apparently fully random manner over the chromatin. To interpret these observations, we propose a model which includes a measure of histone exchange on the chromatin fiber. The model emphasizes the dynamics of histone-histone and histone-DNA interactions in regions of active genes and at replication forks.

A series of repetitive DNA sequences are associated with human core and H1 histone genes

Repetitive DNA sequences, derived from the human beta-globin gene cluster, were mapped within a series of human genomic DNA segments containing core (H2A, H2B, H3 and H4) and H1 histone genes. Cloned recombinant lambda CH4A phage with human histone gene inserts were analyzed by Southern blot analysis using the following 32P-labeled (nick translated) repetitive sequences as probes: Alu I, Kpn I and LTR-like. A cloned DNA designated RS002-5'C6 containing (i) a (TG)16 simple repeat, (ii) an (ATTTT)n repeat and (iii) a 52 base pair alternating purine and pyrimidine sequence was also used as a radiolabelled hybridization probe. Analysis of 12 recombinant phage, containing 6 arrangements of core histone genes, indicated the presence of Alu I, Kpn and RS002-5'C6 repetitive sequences. In contrast, analysis of 4 human genomic DNA segments, containing both core and H1 histone genes, indicated the presence of only Alu I family sequences. LTR-like sequences were not detected in association with any of the core or H1 histone genes examined. These results suggest that human histone and beta-globin genes share certain aspects of sequence organization in flanking regions despite marked differences in their overall structure and pattern of expression.

Citrate-synthase mRNA in relation to enzyme synthesis in division-synchronized Euglena cultures

The regulation of citrate-synthase (EC 4.1.3.7) synthesis in division-synchronized cultures of Euglena gracilis Klebs strain z was investigated. Citrate-synthase activity increased approximately two fold at the end of the light phase and in early dark phase in phototrophic cells synchronized by a 14 h light-10 h dark regime. Anti-(citrate synthase) was used to demonstrate that this increase in activity resulted from an increase in citrate-synthase protein. The amount of polyadenylated RNA per aliquot of culture increased midway through the light phase (before DNA replication) and had doubled by the end of this phase. Anti-(citrate synthase) was used to detect precursor citrate synthase in translations of total polyadenylated RNA in rabbit reticulocyte lysates. Citratesynthase mRNA was found to be present in cells at each stage of a division cycle, so that a stagespecific production of this mRNA to coincide with an increase in enzyme protein is unlikely. It is suggested that a post-transcriptional control operates in the regulation of citrate-synthase synthesis.

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.

Inhibition of protein synthesis stabilizes histone mRNA

The inhibition of protein synthesis in exponentially growing S49 cells leads to a specific fivefold increase in histone mRNA in 30 min. The rate of transcription of histone mRNA, measured in intact or digitonin-permeabilized cells, is increased slightly, if at all, by cycloheximide inhibition of protein synthesis. Both approach-to-equilibrium labeling and pulse-chase experiments show that cycloheximide prolongs histone mRNA half-life from approximately 30 min to greater than 2 h. Histone mRNA made before the addition of cycloheximide becomes stable after the inhibition of protein synthesis, whereas removal of the inhibitor is followed by rapid degradation of histone mRNA. This suggests that the increased stability of histone mRNA during inhibition of protein synthesis results not from alteration of the structure of the mRNA, but from the loss of an activity in the cell which regulates histone mRNA turnover.

Inhibition of protein synthesis stabilizes histone mRNA

The inhibition of protein synthesis in exponentially growing S49 cells leads to a specific fivefold increase in histone mRNA in 30 min. The rate of transcription of histone mRNA, measured in intact or digitonin-permeabilized cells, is increased slightly, if at all, by cycloheximide inhibition of protein synthesis. Both approach-to-equilibrium labeling and pulse-chase experiments show that cycloheximide prolongs histone mRNA half-life from approximately 30 min to greater than 2 h. Histone mRNA made before the addition of cycloheximide becomes stable after the inhibition of protein synthesis, whereas removal of the inhibitor is followed by rapid degradation of histone mRNA. This suggests that the increased stability of histone mRNA during inhibition of protein synthesis results not from alteration of the structure of the mRNA, but from the loss of an activity in the cell which regulates histone mRNA turnover.

Purification and initial characterization of a protein which facilitates assembly of nucleosome-like structure from mammalian cells

A protein, which facilitates assembly of a nucleosome-like structure in vitro, was previously partially purified from mouse FM3A cells [Ishimi, Y. et al. (1983) J. Biochem. (Tokyo) 94, 735-744]. The protein has been purified to approximately 80% from FM3A cells by using histone-Sepharose column chromatography. It sedimented at 4.6 S and had a molecular mass of 53kDa. A preincubation of core histones with the 53-kDa peptide before DNA addition was necessary for the nucleosome assembly. The 53-kDa peptide bound to core histones and formed a 12-S complex. This complex contained stoichiometrical amounts of the 53-kDa peptide and core histones, and the core histones in this complex were composed of equal amounts of H2A, H2B, H3 and H4 histones. The nucleosomes were assembled by adding pBR322 DNA to the 12-S complex. When mononucleosome DNA and core histones were mixed in the presence of the 53-kDa peptide, formation of a 10.5-S complex was observed. The complex contained DNA and core histones in equal amounts, while no 53-kDa peptide was detected in the complex. From above results it is suggested that the 53-kDa peptide facilitates nucleosome assembly by mediating formation of histone octamer and transferring it to DNA. Rat antibody against the 53-kDa peptide did not bind to nucleoplasmin from Xenopus eggs. The relationship between the 53-kDa peptide and nucleoplasmin is discussed.

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.

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.

Self-transcription: RNA polymerase transcription of its own genes, and its role in cellular differentiation and cell cycling

The concept of RNA polymerase self-transcription, where eukaryotic RNA polymerase II and prokaryotic holoenzyme are responsible for transcription of their own genes, would give these enzymes a unique role in the cellular transcriptional and translational machinery. This self-transcriptional ability would equip a cell with an exquisite mechanism of autogenous regulation for the appearance of these transcriptional units. Such a mechanism could allow layering of other transcriptional control pathways upon the RNA polymerase self-transcriptional pathway, thus forming a complex array of mechanisms to regulate transcription of genes concerned with cellular differentiation and cell cycling. It is proposed that RNA polymerase self-transcription is the central control point of gene expression in cellular differentiation and for cell cycling, thus fulfilling the role of an intrinsic biological clock.

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.

Increased histone mRNA levels during inhibition of protein synthesis

Inhibition of protein synthesis by cycloheximide or puromycin specifically increases the amount of translatable histone mRNA in exponentially growing and in synchronous G1 HeLa cells by 5-fold in 3 hours. In this case histone gene expression is uncoupled from DNA replication. We conclude that the level of histone mRNA is regulated by a labile protein and is only indirectly dependent on DNA synthesis.

Multiple, independently regulated, polyadenylated messages for histone H3 and H4 in Tetrahymena

Heterologous probes for yeast H4 and H3 histone genes have been used to study the corresponding histone mRNAs in growing and starved Tetrahymena. Histone mRNAs in both physiological states are polyadenylated. Two types of H4 protein and two types of H3 protein have previously identified in Tetrahymena. Two size classes of H4 messages and three classes of H3 messages have been detected by northern analyses. Southern blot analysis indicate that the number of different kinds of H3 and H4 genes is the same or slightly greater than the number of different messages, suggesting that each message is derived from a different gene. Growing cells have -30 times more histone mRNA than starved cells, even though their total mRNA content is only 4 times greater. The relative abundance of different H4 and H3 messages in growing and starved cells is different, demonstrating that the different messages for a particular type of histone are regulated non-coordinately. In starved cells the presence of a single size class of H3 messages correlates with the preferential synthesis of a previously described macronuclear-specific H3 variant. The fraction of histone messages loaded in growing and starved cells is the same as for bulk mRNAs, and the relative concentrations of the multiple messages for H4 and H3 are the same in polysomal and total RNAs of each cell type. These observations suggest that histone synthesis in Tetrahymena is controlled largely at the level of message abundance, and that very little, if any, control occurs at the translational level.

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.

Histone synthesis by lymphocytes in G0 and G1

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